Starting phenix.real_space_refine on Sun Jun 15 14:30:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ez0_28725/06_2025/8ez0_28725_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ez0_28725/06_2025/8ez0_28725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ez0_28725/06_2025/8ez0_28725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ez0_28725/06_2025/8ez0_28725.map" model { file = "/net/cci-nas-00/data/ceres_data/8ez0_28725/06_2025/8ez0_28725_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ez0_28725/06_2025/8ez0_28725_neut.cif" } resolution = 3.7 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= 0.004 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 3460 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 122 5.16 5 C 9300 2.51 5 N 2502 2.21 5 O 2716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14640 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6601 Classifications: {'peptide': 816} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 771} Chain breaks: 6 Chain: "B" Number of atoms: 6593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6593 Classifications: {'peptide': 815} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 770} Chain breaks: 7 Chain: "D" 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: "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: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain breaks: 1 Chain: "G" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 347 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain breaks: 1 Time building chain proxies: 9.09, per 1000 atoms: 0.62 Number of scatterers: 14640 At special positions: 0 Unit cell: (132.84, 122.04, 172.8, 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 122 16.00 O 2716 8.00 N 2502 7.00 C 9300 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " 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=2.04 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 435 " - pdb=" SG CYS A 468 " distance=2.02 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=2.04 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 159 " - pdb=" SG CYS B 182 " 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=2.04 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=2.04 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 Simple disulfide: pdb=" SG CYS G 7 " - pdb=" SG CYS G 62 " distance=2.03 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 75 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 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: 3.59 Conformation dependent library (CDL) restraints added in 1.7 seconds 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3418 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 32 sheets defined 18.7% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'A' and resid 16 through 23 removed outlier: 3.914A pdb=" N ARG A 19 " --> pdb=" O ASN A 16 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.639A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 318 Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.601A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (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 640 through 645 removed outlier: 3.778A pdb=" N PHE A 644 " --> pdb=" O ASP A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 716 Processing helix chain 'A' and resid 865 through 872 Processing helix chain 'B' and resid 16 through 23 removed outlier: 4.041A pdb=" N ARG B 19 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU B 22 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 255 through 268 removed outlier: 3.643A pdb=" N CYS B 259 " --> pdb=" O ASN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 318 removed outlier: 3.546A pdb=" N GLU B 318 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 378 through 382 removed outlier: 4.493A pdb=" N PHE B 381 " --> pdb=" O SER B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.738A pdb=" N GLY B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 removed outlier: 3.578A pdb=" N ARG B 451 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLN B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 448 through 452' Processing helix chain 'B' and resid 640 through 645 removed outlier: 3.574A pdb=" N PHE B 644 " --> pdb=" O ASP B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 716 Processing helix chain 'B' and resid 864 through 872 Processing helix chain 'D' and resid 8 through 19 removed outlier: 3.573A pdb=" N VAL D 12 " --> pdb=" O GLY D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 67 through 73 Processing helix chain 'E' and resid 8 through 19 removed outlier: 3.562A pdb=" N VAL E 12 " --> pdb=" O GLY E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 62 Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'F' and resid 8 through 19 removed outlier: 4.207A pdb=" N VAL F 12 " --> pdb=" O GLY F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 74 removed outlier: 3.819A pdb=" N TYR F 74 " --> pdb=" O GLN F 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 19 removed outlier: 4.211A pdb=" N VAL G 12 " --> pdb=" O GLY G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 Processing helix chain 'G' and resid 67 through 74 removed outlier: 3.547A pdb=" N TYR G 74 " --> pdb=" O GLN G 70 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 removed outlier: 6.571A pdb=" N MET A 11 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N LEU A 36 " --> pdb=" O MET A 11 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILE A 13 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N MET A 38 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLN A 34 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU A 63 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU A 36 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG A 65 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N GLU A 120 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE A 95 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ASN A 122 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL A 117 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL A 146 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE A 119 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN A 148 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LYS A 121 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.515A pdb=" N ILE A 29 " --> pdb=" O MET A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 Processing sheet with id=AA4, first strand: chain 'A' and resid 212 through 216 removed outlier: 5.823A pdb=" N LEU A 213 " --> pdb=" O CYS A 228 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N CYS A 228 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASN A 215 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AA6, first strand: chain 'A' and resid 278 through 280 Processing sheet with id=AA7, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 312 Processing sheet with id=AA9, first strand: chain 'A' and resid 319 through 321 removed outlier: 6.562A pdb=" N LYS A 319 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU A 368 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N LEU A 403 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE A 370 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LYS A 425 " --> pdb=" O TYR A 398 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A 400 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=AB2, first strand: chain 'A' and resid 486 through 487 Processing sheet with id=AB3, first strand: chain 'A' and resid 530 through 534 removed outlier: 3.532A pdb=" N GLY A 502 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 508 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 601 through 609 removed outlier: 5.864A pdb=" N ASP A 602 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS A 618 " --> pdb=" O ASP A 602 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLN A 612 " --> pdb=" O ASN A 608 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 761 through 765 removed outlier: 3.948A pdb=" N GLY A 780 " --> pdb=" O GLN A 637 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 817 through 824 removed outlier: 5.115A 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: 3.544A pdb=" N GLU A 848 " --> pdb=" O ARG A 889 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG A 889 " --> pdb=" O GLU A 848 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 882 " --> pdb=" O VAL A 907 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.607A pdb=" N MET B 11 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LEU B 36 " --> pdb=" O MET B 11 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE B 13 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N MET B 38 " --> pdb=" O ILE B 13 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLN B 34 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU B 63 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU B 36 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ARG B 65 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU B 93 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N GLU B 120 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE B 95 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ASN B 122 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B 117 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL B 146 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE B 119 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASN B 148 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LYS B 121 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AC1, first strand: chain 'B' and resid 172 through 173 Processing sheet with id=AC2, first strand: chain 'B' and resid 212 through 216 removed outlier: 5.723A pdb=" N LEU B 213 " --> pdb=" O CYS B 228 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N CYS B 228 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN B 215 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 231 through 233 removed outlier: 3.760A pdb=" N PHE B 231 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 238 " --> pdb=" O PHE B 231 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.728A pdb=" N HIS B 247 " --> pdb=" O CYS B 284 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 292 through 294 Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 312 Processing sheet with id=AC7, first strand: chain 'B' and resid 319 through 321 removed outlier: 6.513A pdb=" N LYS B 319 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 340 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ARG B 371 " --> pdb=" O LEU B 340 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE B 342 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=AC9, first strand: chain 'B' and resid 486 through 487 Processing sheet with id=AD1, first strand: chain 'B' and resid 530 through 534 removed outlier: 3.527A pdb=" N GLY B 502 " --> pdb=" O LEU B 571 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS B 508 " --> pdb=" O ALA B 565 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 601 through 609 removed outlier: 6.344A pdb=" N LYS B 616 " --> pdb=" O PRO B 603 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER B 605 " --> pdb=" O ILE B 614 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE B 614 " --> pdb=" O SER B 605 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N SER B 607 " --> pdb=" O GLN B 612 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N GLN B 612 " --> pdb=" O SER B 607 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 761 through 765 Processing sheet with id=AD4, first strand: chain 'B' and resid 821 through 824 Processing sheet with id=AD5, first strand: chain 'B' and resid 858 through 863 removed outlier: 3.541A pdb=" N ARG B 889 " --> pdb=" O GLU B 848 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B 852 " --> pdb=" O SER B 885 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY B 882 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL B 907 " --> pdb=" O GLY B 882 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 936 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: 5.07 Time building geometry restraints manager: 4.28 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: 4786 1.34 - 1.46: 3542 1.46 - 1.58: 6517 1.58 - 1.70: 0 1.70 - 1.82: 146 Bond restraints: 14991 Sorted by residual: bond pdb=" CA ASP A 142 " pdb=" CB ASP A 142 " ideal model delta sigma weight residual 1.530 1.556 -0.026 1.75e-02 3.27e+03 2.13e+00 bond pdb=" CB CYS B 182 " pdb=" SG CYS B 182 " ideal model delta sigma weight residual 1.808 1.767 0.041 3.30e-02 9.18e+02 1.54e+00 bond pdb=" CB ASP A 142 " pdb=" CG ASP A 142 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.53e+00 bond pdb=" C VAL B 158 " pdb=" N CYS B 159 " ideal model delta sigma weight residual 1.325 1.310 0.015 1.25e-02 6.40e+03 1.47e+00 bond pdb=" CA ASP B 250 " pdb=" CB ASP B 250 " ideal model delta sigma weight residual 1.530 1.550 -0.020 1.69e-02 3.50e+03 1.39e+00 ... (remaining 14986 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 19884 1.90 - 3.80: 374 3.80 - 5.69: 40 5.69 - 7.59: 12 7.59 - 9.49: 2 Bond angle restraints: 20312 Sorted by residual: angle pdb=" N VAL A 377 " pdb=" CA VAL A 377 " pdb=" C VAL A 377 " ideal model delta sigma weight residual 113.53 109.56 3.97 9.80e-01 1.04e+00 1.64e+01 angle pdb=" N VAL A 140 " pdb=" CA VAL A 140 " pdb=" C VAL A 140 " ideal model delta sigma weight residual 112.96 109.24 3.72 1.00e+00 1.00e+00 1.38e+01 angle pdb=" CA ASP A 142 " pdb=" CB ASP A 142 " pdb=" CG ASP A 142 " ideal model delta sigma weight residual 112.60 116.07 -3.47 1.00e+00 1.00e+00 1.20e+01 angle pdb=" CA MET A 833 " pdb=" CB MET A 833 " pdb=" CG MET A 833 " ideal model delta sigma weight residual 114.10 120.65 -6.55 2.00e+00 2.50e-01 1.07e+01 angle pdb=" CB MET A 833 " pdb=" CG MET A 833 " pdb=" SD MET A 833 " ideal model delta sigma weight residual 112.70 122.19 -9.49 3.00e+00 1.11e-01 1.00e+01 ... (remaining 20307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 7873 18.06 - 36.11: 917 36.11 - 54.17: 233 54.17 - 72.22: 33 72.22 - 90.28: 22 Dihedral angle restraints: 9078 sinusoidal: 3782 harmonic: 5296 Sorted by residual: dihedral pdb=" CB CYS G 7 " pdb=" SG CYS G 7 " pdb=" SG CYS G 62 " pdb=" CB CYS G 62 " ideal model delta sinusoidal sigma weight residual 93.00 -176.72 -90.28 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS B 288 " pdb=" SG CYS B 288 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -172.30 86.30 1 1.00e+01 1.00e-02 8.98e+01 dihedral pdb=" CB CYS A 169 " pdb=" SG CYS A 169 " pdb=" SG CYS A 188 " pdb=" CB CYS A 188 " ideal model delta sinusoidal sigma weight residual 93.00 178.90 -85.90 1 1.00e+01 1.00e-02 8.91e+01 ... (remaining 9075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1393 0.034 - 0.068: 537 0.068 - 0.102: 186 0.102 - 0.136: 85 0.136 - 0.169: 6 Chirality restraints: 2207 Sorted by residual: chirality pdb=" CA ILE A 95 " pdb=" N ILE A 95 " pdb=" C ILE A 95 " pdb=" CB ILE A 95 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA ILE B 119 " pdb=" N ILE B 119 " pdb=" C ILE B 119 " pdb=" CB ILE B 119 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CG LEU F 15 " pdb=" CB LEU F 15 " pdb=" CD1 LEU F 15 " pdb=" CD2 LEU F 15 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 2204 not shown) Planarity restraints: 2621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 250 " -0.012 2.00e-02 2.50e+03 2.45e-02 5.98e+00 pdb=" C ASP B 250 " 0.042 2.00e-02 2.50e+03 pdb=" O ASP B 250 " -0.016 2.00e-02 2.50e+03 pdb=" N TRP B 251 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 142 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C ASP A 142 " 0.040 2.00e-02 2.50e+03 pdb=" O ASP A 142 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN A 143 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 580 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" C THR B 580 " 0.039 2.00e-02 2.50e+03 pdb=" O THR B 580 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR B 581 " -0.013 2.00e-02 2.50e+03 ... (remaining 2618 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 446 2.68 - 3.24: 14248 3.24 - 3.79: 22884 3.79 - 4.35: 29909 4.35 - 4.90: 48842 Nonbonded interactions: 116329 Sorted by model distance: nonbonded pdb=" O ILE B 29 " pdb=" OG1 THR B 58 " model vdw 2.130 3.040 nonbonded pdb=" OH TYR A 144 " pdb=" OE2 GLU B 700 " model vdw 2.152 3.040 nonbonded pdb=" OG SER B 880 " pdb=" OH TYR B 884 " model vdw 2.160 3.040 nonbonded pdb=" O GLY G 56 " pdb=" OH TYR G 74 " model vdw 2.161 3.040 nonbonded pdb=" O GLN F 60 " pdb=" OG SER F 64 " model vdw 2.162 3.040 ... (remaining 116324 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 1 through 406 or resid 408 through 910)) selection = chain 'B' } ncs_group { reference = (chain 'D' and (resid 4 through 26 or resid 56 through 76)) selection = (chain 'E' and (resid 4 through 26 or resid 56 through 76)) selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.240 Process input model: 36.000 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 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 : 0.004 0.041 15037 Z= 0.173 Angle : 0.633 9.489 20404 Z= 0.342 Chirality : 0.044 0.169 2207 Planarity : 0.004 0.034 2621 Dihedral : 15.908 89.022 5522 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.12 % Allowed : 21.99 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.65 (0.20), residues: 1769 helix: -0.70 (0.31), residues: 292 sheet: -0.80 (0.29), residues: 333 loop : -1.32 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 634 HIS 0.005 0.001 HIS B 440 PHE 0.014 0.001 PHE A 778 TYR 0.025 0.001 TYR G 16 ARG 0.006 0.000 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.16920 ( 356) hydrogen bonds : angle 8.17039 ( 936) SS BOND : bond 0.00320 ( 46) SS BOND : angle 0.99125 ( 92) covalent geometry : bond 0.00390 (14991) covalent geometry : angle 0.63136 (20312) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 1.684 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 100 average time/residue: 0.2237 time to fit residues: 36.4585 Evaluate side-chains 94 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 634 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 161 optimal weight: 40.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN A 90 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 ASN A 624 ASN A 860 HIS B 90 ASN B 108 ASN ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN F 70 GLN F 76 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.116323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.075669 restraints weight = 39656.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.078128 restraints weight = 21634.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.079697 restraints weight = 15393.783| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 15037 Z= 0.298 Angle : 0.678 7.289 20404 Z= 0.350 Chirality : 0.047 0.169 2207 Planarity : 0.004 0.038 2621 Dihedral : 5.068 39.085 1980 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.91 % Favored : 91.92 % Rotamer: Outliers : 2.91 % Allowed : 20.78 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.78 (0.20), residues: 1769 helix: -0.78 (0.30), residues: 295 sheet: -1.00 (0.29), residues: 338 loop : -1.38 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 634 HIS 0.008 0.001 HIS B 440 PHE 0.016 0.002 PHE A 567 TYR 0.031 0.002 TYR D 74 ARG 0.005 0.000 ARG B 345 Details of bonding type rmsd hydrogen bonds : bond 0.04578 ( 356) hydrogen bonds : angle 6.74834 ( 936) SS BOND : bond 0.00367 ( 46) SS BOND : angle 0.95667 ( 92) covalent geometry : bond 0.00700 (14991) covalent geometry : angle 0.67639 (20312) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 94 time to evaluate : 1.740 Fit side-chains REVERT: A 102 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8526 (mttp) REVERT: A 899 TRP cc_start: 0.9270 (m100) cc_final: 0.8966 (m100) REVERT: B 119 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8671 (mm) REVERT: B 577 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7600 (pm20) REVERT: B 846 LEU cc_start: 0.9783 (OUTLIER) cc_final: 0.9485 (mt) REVERT: B 899 TRP cc_start: 0.9198 (m100) cc_final: 0.8889 (m100) REVERT: D 68 LEU cc_start: 0.8902 (tp) cc_final: 0.8665 (tt) REVERT: E 15 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8942 (mm) outliers start: 48 outliers final: 23 residues processed: 132 average time/residue: 0.2516 time to fit residues: 53.5016 Evaluate side-chains 112 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 577 GLU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 634 TRP Chi-restraints excluded: chain B residue 792 SER Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain F residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 174 optimal weight: 0.0770 chunk 124 optimal weight: 0.8980 chunk 63 optimal weight: 0.0980 chunk 100 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN B 143 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.118814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.079035 restraints weight = 39668.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.081688 restraints weight = 20931.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.083369 restraints weight = 14580.116| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15037 Z= 0.114 Angle : 0.569 6.922 20404 Z= 0.295 Chirality : 0.043 0.152 2207 Planarity : 0.004 0.040 2621 Dihedral : 4.811 40.935 1980 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.79 % Allowed : 20.53 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.61 (0.20), residues: 1769 helix: -0.63 (0.30), residues: 296 sheet: -0.83 (0.29), residues: 341 loop : -1.28 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 183 HIS 0.003 0.001 HIS B 440 PHE 0.016 0.001 PHE B 707 TYR 0.024 0.001 TYR E 74 ARG 0.009 0.000 ARG F 22 Details of bonding type rmsd hydrogen bonds : bond 0.03983 ( 356) hydrogen bonds : angle 6.30938 ( 936) SS BOND : bond 0.00251 ( 46) SS BOND : angle 0.71431 ( 92) covalent geometry : bond 0.00265 (14991) covalent geometry : angle 0.56826 (20312) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 104 time to evaluate : 1.684 Fit side-chains revert: symmetry clash REVERT: A 899 TRP cc_start: 0.9251 (m100) cc_final: 0.8746 (m100) REVERT: B 119 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8649 (mm) REVERT: B 377 VAL cc_start: 0.8708 (OUTLIER) cc_final: 0.8507 (t) REVERT: B 846 LEU cc_start: 0.9765 (OUTLIER) cc_final: 0.9512 (mt) REVERT: B 899 TRP cc_start: 0.9101 (m100) cc_final: 0.8587 (m100) REVERT: D 68 LEU cc_start: 0.8848 (tp) cc_final: 0.8548 (tt) outliers start: 46 outliers final: 16 residues processed: 138 average time/residue: 0.2124 time to fit residues: 48.5354 Evaluate side-chains 113 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 518 PHE Chi-restraints excluded: chain B residue 555 MET Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 634 TRP Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain F residue 9 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 47 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 136 optimal weight: 0.0470 chunk 82 optimal weight: 0.9990 chunk 140 optimal weight: 0.0980 chunk 76 optimal weight: 50.0000 chunk 177 optimal weight: 0.3980 chunk 102 optimal weight: 1.9990 chunk 152 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 overall best weight: 0.4880 ------------------------------------------------------------------------------- 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 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.114802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.075256 restraints weight = 38355.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.077751 restraints weight = 23872.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.080201 restraints weight = 15982.216| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15037 Z= 0.107 Angle : 0.552 7.051 20404 Z= 0.284 Chirality : 0.043 0.150 2207 Planarity : 0.003 0.037 2621 Dihedral : 4.669 42.792 1980 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.03 % Allowed : 20.78 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.55 (0.20), residues: 1769 helix: -0.70 (0.29), residues: 303 sheet: -0.75 (0.29), residues: 337 loop : -1.23 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 634 HIS 0.002 0.000 HIS A 247 PHE 0.015 0.001 PHE F 25 TYR 0.020 0.001 TYR E 74 ARG 0.004 0.000 ARG F 22 Details of bonding type rmsd hydrogen bonds : bond 0.03695 ( 356) hydrogen bonds : angle 5.96511 ( 936) SS BOND : bond 0.00218 ( 46) SS BOND : angle 0.59299 ( 92) covalent geometry : bond 0.00251 (14991) covalent geometry : angle 0.55168 (20312) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 102 time to evaluate : 1.603 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.8262 (mmm) cc_final: 0.8061 (mmm) REVERT: A 899 TRP cc_start: 0.8921 (m100) cc_final: 0.8004 (m100) REVERT: B 102 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8625 (mttp) REVERT: B 899 TRP cc_start: 0.8521 (m100) cc_final: 0.7882 (m100) REVERT: E 15 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8846 (mm) REVERT: E 21 GLU cc_start: 0.7042 (pm20) cc_final: 0.6732 (pm20) outliers start: 50 outliers final: 24 residues processed: 141 average time/residue: 0.2221 time to fit residues: 51.2383 Evaluate side-chains 121 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 555 MET Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 634 TRP Chi-restraints excluded: chain B residue 788 CYS Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 71 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 72 optimal weight: 0.0970 chunk 100 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 78 optimal weight: 30.0000 chunk 31 optimal weight: 2.9990 chunk 142 optimal weight: 0.0370 chunk 74 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 GLN B 108 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.113624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.075411 restraints weight = 38619.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.077011 restraints weight = 23963.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.076561 restraints weight = 17386.409| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15037 Z= 0.164 Angle : 0.570 7.169 20404 Z= 0.292 Chirality : 0.044 0.164 2207 Planarity : 0.004 0.037 2621 Dihedral : 4.675 44.397 1980 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.97 % Allowed : 21.87 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.50 (0.20), residues: 1769 helix: -0.50 (0.30), residues: 295 sheet: -0.74 (0.29), residues: 341 loop : -1.24 (0.19), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 634 HIS 0.004 0.001 HIS B 440 PHE 0.015 0.001 PHE A 567 TYR 0.023 0.001 TYR E 16 ARG 0.003 0.000 ARG B 865 Details of bonding type rmsd hydrogen bonds : bond 0.03770 ( 356) hydrogen bonds : angle 5.92219 ( 936) SS BOND : bond 0.00244 ( 46) SS BOND : angle 0.72928 ( 92) covalent geometry : bond 0.00396 (14991) covalent geometry : angle 0.56916 (20312) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 94 time to evaluate : 1.822 Fit side-chains REVERT: A 102 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8728 (mttp) REVERT: A 238 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8757 (p) REVERT: A 899 TRP cc_start: 0.8837 (m100) cc_final: 0.7968 (m100) REVERT: B 102 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8653 (mttp) REVERT: B 899 TRP cc_start: 0.8275 (m100) cc_final: 0.7802 (m100) REVERT: E 15 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8878 (mm) outliers start: 49 outliers final: 30 residues processed: 132 average time/residue: 0.2881 time to fit residues: 62.9183 Evaluate side-chains 122 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 88 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 634 TRP Chi-restraints excluded: chain B residue 788 CYS Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 71 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 1.9990 chunk 134 optimal weight: 0.0070 chunk 18 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 142 optimal weight: 0.0030 chunk 101 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 160 optimal weight: 20.0000 chunk 139 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 overall best weight: 2.0014 ------------------------------------------------------------------------------- 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 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.117786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.081641 restraints weight = 40058.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.082064 restraints weight = 25251.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.083253 restraints weight = 17333.102| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15037 Z= 0.208 Angle : 0.597 7.366 20404 Z= 0.305 Chirality : 0.045 0.150 2207 Planarity : 0.004 0.040 2621 Dihedral : 4.760 46.328 1980 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 3.33 % Allowed : 21.62 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.57 (0.20), residues: 1769 helix: -0.49 (0.30), residues: 293 sheet: -0.83 (0.29), residues: 348 loop : -1.28 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 183 HIS 0.004 0.001 HIS B 440 PHE 0.019 0.001 PHE A 567 TYR 0.021 0.002 TYR E 74 ARG 0.003 0.000 ARG B 345 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 356) hydrogen bonds : angle 5.95434 ( 936) SS BOND : bond 0.00353 ( 46) SS BOND : angle 0.84965 ( 92) covalent geometry : bond 0.00493 (14991) covalent geometry : angle 0.59584 (20312) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 88 time to evaluate : 1.734 Fit side-chains REVERT: A 102 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8521 (mttm) REVERT: A 899 TRP cc_start: 0.8936 (m100) cc_final: 0.8175 (m100) REVERT: B 102 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8663 (mttm) REVERT: B 899 TRP cc_start: 0.8464 (m100) cc_final: 0.8033 (m100) REVERT: E 15 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.9013 (mm) outliers start: 55 outliers final: 36 residues processed: 131 average time/residue: 0.2120 time to fit residues: 46.0862 Evaluate side-chains 124 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 85 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 634 TRP Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 788 CYS Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 71 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 58 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 29 optimal weight: 0.0170 chunk 140 optimal weight: 0.0050 overall best weight: 1.0036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.118692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.080765 restraints weight = 40243.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.083548 restraints weight = 22987.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.084156 restraints weight = 15761.066| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15037 Z= 0.135 Angle : 0.575 12.366 20404 Z= 0.293 Chirality : 0.044 0.150 2207 Planarity : 0.004 0.039 2621 Dihedral : 4.718 46.689 1980 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.03 % Allowed : 21.56 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.51 (0.20), residues: 1769 helix: -0.49 (0.30), residues: 294 sheet: -0.72 (0.29), residues: 337 loop : -1.27 (0.19), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 634 HIS 0.003 0.001 HIS B 440 PHE 0.013 0.001 PHE A 567 TYR 0.026 0.001 TYR E 74 ARG 0.003 0.000 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 356) hydrogen bonds : angle 5.85669 ( 936) SS BOND : bond 0.00265 ( 46) SS BOND : angle 1.54047 ( 92) covalent geometry : bond 0.00327 (14991) covalent geometry : angle 0.56734 (20312) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 94 time to evaluate : 1.714 Fit side-chains revert: symmetry clash REVERT: A 102 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8677 (mttp) REVERT: A 238 VAL cc_start: 0.9047 (OUTLIER) cc_final: 0.8722 (p) REVERT: A 899 TRP cc_start: 0.9103 (m100) cc_final: 0.8345 (m100) REVERT: B 899 TRP cc_start: 0.8679 (m100) cc_final: 0.8251 (m100) REVERT: E 15 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8969 (mm) REVERT: E 21 GLU cc_start: 0.7329 (pm20) cc_final: 0.6909 (pm20) outliers start: 50 outliers final: 36 residues processed: 131 average time/residue: 0.2110 time to fit residues: 45.8194 Evaluate side-chains 123 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 84 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 778 PHE Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 634 TRP Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 788 CYS Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain G residue 71 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 45 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 124 optimal weight: 0.2980 chunk 133 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 117 optimal weight: 0.1980 chunk 159 optimal weight: 40.0000 chunk 43 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.119421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.081989 restraints weight = 39764.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.084857 restraints weight = 23199.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.084924 restraints weight = 16334.327| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15037 Z= 0.114 Angle : 0.564 8.270 20404 Z= 0.287 Chirality : 0.044 0.148 2207 Planarity : 0.003 0.038 2621 Dihedral : 4.626 46.575 1980 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.67 % Allowed : 21.68 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.42 (0.20), residues: 1769 helix: -0.44 (0.31), residues: 295 sheet: -0.48 (0.31), residues: 312 loop : -1.25 (0.19), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 183 HIS 0.002 0.001 HIS B 440 PHE 0.014 0.001 PHE A 707 TYR 0.026 0.001 TYR E 74 ARG 0.002 0.000 ARG B 345 Details of bonding type rmsd hydrogen bonds : bond 0.03518 ( 356) hydrogen bonds : angle 5.74699 ( 936) SS BOND : bond 0.00221 ( 46) SS BOND : angle 1.04590 ( 92) covalent geometry : bond 0.00274 (14991) covalent geometry : angle 0.56046 (20312) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 100 time to evaluate : 1.621 Fit side-chains REVERT: A 38 MET cc_start: 0.8231 (mmm) cc_final: 0.7961 (mmm) REVERT: A 41 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8826 (p) REVERT: A 102 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8700 (mttp) REVERT: A 238 VAL cc_start: 0.9010 (OUTLIER) cc_final: 0.8690 (p) REVERT: A 899 TRP cc_start: 0.9128 (m100) cc_final: 0.8405 (m100) REVERT: B 41 THR cc_start: 0.8847 (OUTLIER) cc_final: 0.8629 (p) REVERT: B 102 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8633 (mttp) REVERT: B 700 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7789 (tm-30) REVERT: B 899 TRP cc_start: 0.8732 (m100) cc_final: 0.8289 (m100) REVERT: E 21 GLU cc_start: 0.7268 (pm20) cc_final: 0.6958 (pm20) outliers start: 44 outliers final: 31 residues processed: 133 average time/residue: 0.2068 time to fit residues: 45.7369 Evaluate side-chains 125 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 89 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 634 TRP Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 788 CYS Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain G residue 71 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 HIS B 624 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.117995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.082912 restraints weight = 40255.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.083967 restraints weight = 22604.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.083586 restraints weight = 16556.615| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15037 Z= 0.184 Angle : 0.588 9.251 20404 Z= 0.299 Chirality : 0.045 0.183 2207 Planarity : 0.004 0.038 2621 Dihedral : 4.681 47.079 1980 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.03 % Allowed : 21.56 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.49 (0.20), residues: 1769 helix: -0.49 (0.30), residues: 296 sheet: -0.65 (0.30), residues: 324 loop : -1.26 (0.19), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 183 HIS 0.004 0.001 HIS B 440 PHE 0.017 0.001 PHE B 567 TYR 0.032 0.002 TYR E 74 ARG 0.003 0.000 ARG B 345 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 356) hydrogen bonds : angle 5.79901 ( 936) SS BOND : bond 0.00290 ( 46) SS BOND : angle 0.98025 ( 92) covalent geometry : bond 0.00439 (14991) covalent geometry : angle 0.58589 (20312) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 86 time to evaluate : 1.647 Fit side-chains REVERT: A 41 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8931 (p) REVERT: A 102 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8684 (mttp) REVERT: A 238 VAL cc_start: 0.9031 (OUTLIER) cc_final: 0.8703 (p) REVERT: A 899 TRP cc_start: 0.8721 (m100) cc_final: 0.8039 (m100) REVERT: B 41 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8743 (p) REVERT: B 102 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8647 (mttp) REVERT: B 899 TRP cc_start: 0.8141 (m100) cc_final: 0.7817 (m100) REVERT: E 15 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8985 (mm) REVERT: E 21 GLU cc_start: 0.7458 (pm20) cc_final: 0.7163 (pm20) outliers start: 50 outliers final: 39 residues processed: 126 average time/residue: 0.2028 time to fit residues: 42.2996 Evaluate side-chains 126 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 81 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 778 PHE Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 11 MET Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 634 TRP Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 788 CYS Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain G residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 50 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 78 optimal weight: 30.0000 chunk 69 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.117486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.081908 restraints weight = 40127.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.082754 restraints weight = 23271.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.082030 restraints weight = 18547.966| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 15037 Z= 0.226 Angle : 0.629 9.567 20404 Z= 0.319 Chirality : 0.046 0.188 2207 Planarity : 0.004 0.039 2621 Dihedral : 4.802 47.736 1980 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.85 % Allowed : 21.80 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.59 (0.20), residues: 1769 helix: -0.58 (0.30), residues: 295 sheet: -0.68 (0.30), residues: 324 loop : -1.33 (0.19), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 183 HIS 0.005 0.001 HIS B 440 PHE 0.019 0.001 PHE B 567 TYR 0.036 0.002 TYR E 74 ARG 0.003 0.000 ARG B 345 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 356) hydrogen bonds : angle 5.89905 ( 936) SS BOND : bond 0.00345 ( 46) SS BOND : angle 1.01862 ( 92) covalent geometry : bond 0.00537 (14991) covalent geometry : angle 0.62625 (20312) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3538 Ramachandran restraints generated. 1769 Oldfield, 0 Emsley, 1769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 84 time to evaluate : 1.540 Fit side-chains REVERT: A 41 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.8979 (p) REVERT: A 102 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8519 (mttm) REVERT: A 238 VAL cc_start: 0.9017 (OUTLIER) cc_final: 0.8690 (p) REVERT: A 899 TRP cc_start: 0.8885 (m100) cc_final: 0.8239 (m100) REVERT: B 41 THR cc_start: 0.8948 (OUTLIER) cc_final: 0.8745 (p) REVERT: B 102 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8666 (mttp) REVERT: B 899 TRP cc_start: 0.8239 (m100) cc_final: 0.7953 (m100) REVERT: E 15 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.9004 (mm) REVERT: E 21 GLU cc_start: 0.7430 (pm20) cc_final: 0.7230 (pm20) REVERT: G 57 ILE cc_start: 0.8794 (mp) cc_final: 0.8538 (tp) outliers start: 47 outliers final: 39 residues processed: 122 average time/residue: 0.1985 time to fit residues: 40.2939 Evaluate side-chains 126 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 81 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 313 GLN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 634 TRP Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain A residue 778 PHE Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 634 TRP Chi-restraints excluded: chain B residue 717 VAL Chi-restraints excluded: chain B residue 788 CYS Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain G residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 155 optimal weight: 8.9990 chunk 129 optimal weight: 0.9990 chunk 77 optimal weight: 20.0000 chunk 144 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 chunk 149 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 4 optimal weight: 0.0370 chunk 150 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.118992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.080427 restraints weight = 40020.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.083095 restraints weight = 20805.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.084818 restraints weight = 14417.868| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15037 Z= 0.114 Angle : 0.577 9.296 20404 Z= 0.293 Chirality : 0.044 0.161 2207 Planarity : 0.004 0.039 2621 Dihedral : 4.671 47.392 1980 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.48 % Allowed : 22.11 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -1.49 (0.20), residues: 1769 helix: -0.58 (0.30), residues: 301 sheet: -0.57 (0.30), residues: 319 loop : -1.26 (0.19), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 634 HIS 0.003 0.001 HIS B 440 PHE 0.015 0.001 PHE A 707 TYR 0.029 0.001 TYR E 74 ARG 0.008 0.000 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.03582 ( 356) hydrogen bonds : angle 5.74712 ( 936) SS BOND : bond 0.00312 ( 46) SS BOND : angle 0.75338 ( 92) covalent geometry : bond 0.00268 (14991) covalent geometry : angle 0.57656 (20312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5015.00 seconds wall clock time: 89 minutes 32.45 seconds (5372.45 seconds total)