Starting phenix.real_space_refine on Sun Aug 24 05:57:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ez0_28725/08_2025/8ez0_28725_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ez0_28725/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ez0_28725/08_2025/8ez0_28725_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ez0_28725/08_2025/8ez0_28725_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ez0_28725/08_2025/8ez0_28725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ez0_28725/08_2025/8ez0_28725.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.80, per 1000 atoms: 0.26 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: 1.17 Conformation dependent library (CDL) restraints added in 644.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.64 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: 1.95 Time building geometry restraints manager: 1.64 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.020 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.220 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.530 ------------------------------------------------------------------------------- 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 : 13.62 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (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 ARG 0.006 0.000 ARG B 181 TYR 0.025 0.001 TYR G 16 PHE 0.014 0.001 PHE A 778 TRP 0.030 0.002 TRP A 634 HIS 0.005 0.001 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00390 (14991) covalent geometry : angle 0.63136 (20312) SS BOND : bond 0.00320 ( 46) SS BOND : angle 0.99125 ( 92) hydrogen bonds : bond 0.16920 ( 356) hydrogen bonds : angle 8.17039 ( 936) *********************** 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 : 0.489 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 100 average time/residue: 0.0966 time to fit residues: 15.8462 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 : 0.592 ------------------------------------------------------------------------------- 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 98 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 20.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 295 ASN ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN F 70 GLN F 76 ASN G 76 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.116858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.076397 restraints weight = 39730.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.078896 restraints weight = 21515.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.080520 restraints weight = 15206.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.081497 restraints weight = 12501.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.082034 restraints weight = 11161.522| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 15037 Z= 0.267 Angle : 0.652 7.289 20404 Z= 0.337 Chirality : 0.046 0.167 2207 Planarity : 0.004 0.035 2621 Dihedral : 4.985 38.641 1980 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.86 % Favored : 92.09 % Rotamer: Outliers : 2.42 % Allowed : 20.84 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.20), residues: 1769 helix: -0.75 (0.30), residues: 295 sheet: -0.96 (0.29), residues: 335 loop : -1.36 (0.19), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 345 TYR 0.024 0.002 TYR D 74 PHE 0.015 0.002 PHE F 25 TRP 0.017 0.001 TRP B 634 HIS 0.008 0.001 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00628 (14991) covalent geometry : angle 0.65055 (20312) SS BOND : bond 0.00373 ( 46) SS BOND : angle 0.90071 ( 92) hydrogen bonds : bond 0.04683 ( 356) hydrogen bonds : angle 6.73140 ( 936) *********************** 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 135 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 95 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 360 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8808 (mt) REVERT: A 899 TRP cc_start: 0.9222 (m100) cc_final: 0.8903 (m100) REVERT: B 110 MET cc_start: 0.7802 (pmm) cc_final: 0.7576 (ptp) REVERT: B 119 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8701 (mm) REVERT: B 846 LEU cc_start: 0.9780 (OUTLIER) cc_final: 0.9481 (mt) REVERT: B 899 TRP cc_start: 0.9134 (m100) cc_final: 0.8812 (m100) REVERT: D 68 LEU cc_start: 0.8911 (tp) cc_final: 0.8655 (tt) REVERT: E 15 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8903 (mm) outliers start: 40 outliers final: 16 residues processed: 127 average time/residue: 0.1012 time to fit residues: 20.7192 Evaluate side-chains 105 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 360 LEU 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 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 360 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 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 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 79 optimal weight: 20.0000 chunk 65 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 175 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.113148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.073258 restraints weight = 38795.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.075518 restraints weight = 23766.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.076341 restraints weight = 16377.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.076850 restraints weight = 15033.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.076718 restraints weight = 14055.392| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15037 Z= 0.167 Angle : 0.576 6.977 20404 Z= 0.299 Chirality : 0.044 0.153 2207 Planarity : 0.004 0.042 2621 Dihedral : 4.870 42.225 1980 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.03 % Allowed : 20.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.20), residues: 1769 helix: -0.69 (0.30), residues: 296 sheet: -0.96 (0.28), residues: 350 loop : -1.31 (0.19), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 704 TYR 0.026 0.001 TYR D 74 PHE 0.015 0.001 PHE F 25 TRP 0.019 0.001 TRP B 183 HIS 0.004 0.001 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00394 (14991) covalent geometry : angle 0.57494 (20312) SS BOND : bond 0.00297 ( 46) SS BOND : angle 0.70517 ( 92) hydrogen bonds : bond 0.04116 ( 356) hydrogen bonds : angle 6.37191 ( 936) *********************** 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 145 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 95 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8586 (mttp) REVERT: A 899 TRP cc_start: 0.8813 (m100) cc_final: 0.8290 (m100) REVERT: B 119 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8645 (mm) REVERT: B 846 LEU cc_start: 0.9647 (OUTLIER) cc_final: 0.9417 (mt) REVERT: B 899 TRP cc_start: 0.8604 (m100) cc_final: 0.8068 (m100) REVERT: D 68 LEU cc_start: 0.8873 (tp) cc_final: 0.8600 (tt) outliers start: 50 outliers final: 18 residues processed: 133 average time/residue: 0.1033 time to fit residues: 22.1190 Evaluate side-chains 106 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 102 LYS 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 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 119 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 240 THR 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 54 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 108 ASN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.114072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.074212 restraints weight = 38479.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.076965 restraints weight = 23922.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.078197 restraints weight = 16026.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.078639 restraints weight = 15274.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.078499 restraints weight = 12857.603| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15037 Z= 0.123 Angle : 0.556 7.557 20404 Z= 0.287 Chirality : 0.043 0.152 2207 Planarity : 0.004 0.039 2621 Dihedral : 4.747 43.643 1980 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.03 % Allowed : 20.84 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.20), residues: 1769 helix: -0.56 (0.30), residues: 295 sheet: -0.88 (0.29), residues: 346 loop : -1.26 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 704 TYR 0.021 0.001 TYR D 74 PHE 0.015 0.001 PHE F 25 TRP 0.016 0.001 TRP B 634 HIS 0.003 0.001 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00291 (14991) covalent geometry : angle 0.55540 (20312) SS BOND : bond 0.00211 ( 46) SS BOND : angle 0.63870 ( 92) hydrogen bonds : bond 0.03742 ( 356) hydrogen bonds : angle 6.01714 ( 936) *********************** 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 : 0.565 Fit side-chains revert: symmetry clash REVERT: A 102 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8571 (mttp) REVERT: A 899 TRP cc_start: 0.8916 (m100) cc_final: 0.8006 (m100) REVERT: B 102 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8643 (mttp) REVERT: B 119 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8650 (mm) REVERT: B 899 TRP cc_start: 0.8530 (m100) cc_final: 0.7898 (m100) REVERT: D 68 LEU cc_start: 0.8850 (tp) cc_final: 0.8537 (tt) REVERT: E 15 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8871 (mm) REVERT: E 21 GLU cc_start: 0.7142 (pm20) cc_final: 0.6812 (pm20) REVERT: G 70 GLN cc_start: 0.8692 (mt0) cc_final: 0.8316 (pt0) outliers start: 50 outliers final: 23 residues processed: 140 average time/residue: 0.0882 time to fit residues: 19.9876 Evaluate side-chains 122 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 102 LYS 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 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 119 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 376 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 6 optimal weight: 0.9980 chunk 75 optimal weight: 20.0000 chunk 118 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 113 optimal weight: 0.0980 chunk 160 optimal weight: 5.9990 chunk 101 optimal weight: 0.3980 chunk 48 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4049 r_free = 0.4049 target = 0.114643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.075726 restraints weight = 38725.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.077500 restraints weight = 25233.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.079403 restraints weight = 17117.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.079467 restraints weight = 15674.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.079138 restraints weight = 14042.983| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15037 Z= 0.111 Angle : 0.551 7.567 20404 Z= 0.283 Chirality : 0.043 0.150 2207 Planarity : 0.003 0.038 2621 Dihedral : 4.628 44.806 1980 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.67 % Allowed : 21.38 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.20), residues: 1769 helix: -0.58 (0.30), residues: 301 sheet: -0.72 (0.29), residues: 341 loop : -1.21 (0.19), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 865 TYR 0.021 0.001 TYR D 74 PHE 0.017 0.001 PHE F 25 TRP 0.016 0.001 TRP B 634 HIS 0.003 0.001 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00263 (14991) covalent geometry : angle 0.55026 (20312) SS BOND : bond 0.00208 ( 46) SS BOND : angle 0.61959 ( 92) hydrogen bonds : bond 0.03581 ( 356) hydrogen bonds : angle 5.78610 ( 936) *********************** 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 146 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 102 time to evaluate : 0.589 Fit side-chains REVERT: A 102 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8647 (mttp) REVERT: A 238 VAL cc_start: 0.9089 (OUTLIER) cc_final: 0.8795 (p) REVERT: A 899 TRP cc_start: 0.8970 (m100) cc_final: 0.8122 (m100) REVERT: B 119 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8640 (mm) REVERT: B 899 TRP cc_start: 0.8486 (m100) cc_final: 0.7989 (m100) REVERT: E 15 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8848 (mm) REVERT: G 70 GLN cc_start: 0.8664 (mt0) cc_final: 0.8241 (pt0) outliers start: 44 outliers final: 24 residues processed: 136 average time/residue: 0.0852 time to fit residues: 19.4999 Evaluate side-chains 117 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 334 THR Chi-restraints excluded: chain A residue 377 VAL 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 119 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 436 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 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 35 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 58 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 85 optimal weight: 0.0040 chunk 57 optimal weight: 2.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- 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** A 440 HIS 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 = 0.4159 r_free = 0.4159 target = 0.118773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.080060 restraints weight = 39926.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.082698 restraints weight = 20894.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.084385 restraints weight = 14554.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.085385 restraints weight = 11825.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.085991 restraints weight = 10510.031| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15037 Z= 0.160 Angle : 0.571 8.158 20404 Z= 0.290 Chirality : 0.044 0.150 2207 Planarity : 0.004 0.038 2621 Dihedral : 4.625 45.913 1980 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.15 % Allowed : 21.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.20), residues: 1769 helix: -0.50 (0.30), residues: 295 sheet: -0.84 (0.29), residues: 351 loop : -1.21 (0.19), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 345 TYR 0.021 0.001 TYR D 74 PHE 0.015 0.001 PHE A 567 TRP 0.019 0.001 TRP B 183 HIS 0.003 0.001 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00382 (14991) covalent geometry : angle 0.57013 (20312) SS BOND : bond 0.00403 ( 46) SS BOND : angle 0.67440 ( 92) hydrogen bonds : bond 0.03696 ( 356) hydrogen bonds : angle 5.77158 ( 936) *********************** 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 142 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 90 time to evaluate : 0.496 Fit side-chains REVERT: A 102 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8530 (mttp) REVERT: A 899 TRP cc_start: 0.9322 (m100) cc_final: 0.8606 (m100) REVERT: B 102 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8615 (mttp) REVERT: B 119 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8609 (mm) REVERT: B 899 TRP cc_start: 0.8972 (m100) cc_final: 0.8481 (m100) REVERT: E 15 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8993 (mm) REVERT: G 70 GLN cc_start: 0.8669 (mt0) cc_final: 0.8372 (pt0) outliers start: 52 outliers final: 35 residues processed: 130 average time/residue: 0.0850 time to fit residues: 18.8197 Evaluate side-chains 130 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 91 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE 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 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 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 57 ILE Chi-restraints excluded: chain B residue 102 LYS 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 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 436 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 57 ILE 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 48 optimal weight: 1.9990 chunk 156 optimal weight: 30.0000 chunk 139 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.117421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.078897 restraints weight = 39846.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.081470 restraints weight = 23736.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.081812 restraints weight = 16605.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.082809 restraints weight = 14792.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.082884 restraints weight = 12636.244| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 15037 Z= 0.221 Angle : 0.606 8.391 20404 Z= 0.310 Chirality : 0.045 0.178 2207 Planarity : 0.004 0.040 2621 Dihedral : 4.780 47.596 1980 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.15 % Allowed : 21.26 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.20), residues: 1769 helix: -0.52 (0.30), residues: 293 sheet: -0.78 (0.29), residues: 337 loop : -1.29 (0.19), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 345 TYR 0.027 0.002 TYR D 74 PHE 0.019 0.001 PHE A 567 TRP 0.014 0.001 TRP B 634 HIS 0.005 0.001 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00524 (14991) covalent geometry : angle 0.60485 (20312) SS BOND : bond 0.00322 ( 46) SS BOND : angle 0.77087 ( 92) hydrogen bonds : bond 0.03896 ( 356) hydrogen bonds : angle 5.88996 ( 936) *********************** 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 140 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 88 time to evaluate : 0.611 Fit side-chains REVERT: A 102 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8502 (mttm) REVERT: A 899 TRP cc_start: 0.9174 (m100) cc_final: 0.8441 (m100) REVERT: B 102 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8619 (mttm) REVERT: B 119 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8619 (mm) REVERT: B 899 TRP cc_start: 0.8737 (m100) cc_final: 0.8328 (m100) REVERT: E 21 GLU cc_start: 0.7346 (pm20) cc_final: 0.6956 (pm20) outliers start: 52 outliers final: 34 residues processed: 129 average time/residue: 0.0929 time to fit residues: 20.0764 Evaluate side-chains 117 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 80 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 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 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 57 ILE Chi-restraints excluded: chain B residue 102 LYS 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 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 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 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 120 optimal weight: 0.9980 chunk 165 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 172 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 167 optimal weight: 0.5980 chunk 32 optimal weight: 0.0170 overall best weight: 1.1222 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.118482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.079585 restraints weight = 39982.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.082202 restraints weight = 20981.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.083888 restraints weight = 14651.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.084926 restraints weight = 11949.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.085358 restraints weight = 10607.416| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15037 Z= 0.141 Angle : 0.590 12.378 20404 Z= 0.300 Chirality : 0.044 0.175 2207 Planarity : 0.004 0.040 2621 Dihedral : 4.750 47.457 1980 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.67 % Allowed : 22.05 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.20), residues: 1769 helix: -0.51 (0.31), residues: 294 sheet: -0.68 (0.30), residues: 329 loop : -1.27 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 22 TYR 0.028 0.001 TYR E 74 PHE 0.012 0.001 PHE A 707 TRP 0.015 0.001 TRP B 634 HIS 0.003 0.001 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00338 (14991) covalent geometry : angle 0.58066 (20312) SS BOND : bond 0.00252 ( 46) SS BOND : angle 1.68331 ( 92) hydrogen bonds : bond 0.03636 ( 356) hydrogen bonds : angle 5.80029 ( 936) *********************** 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 136 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 92 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8651 (mttp) REVERT: A 238 VAL cc_start: 0.9051 (OUTLIER) cc_final: 0.8716 (p) REVERT: A 899 TRP cc_start: 0.9406 (m100) cc_final: 0.8745 (m100) REVERT: B 119 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8564 (mm) REVERT: B 899 TRP cc_start: 0.9075 (m100) cc_final: 0.8617 (m100) REVERT: E 21 GLU cc_start: 0.7277 (pm20) cc_final: 0.7016 (pm20) REVERT: G 70 GLN cc_start: 0.8652 (mt0) cc_final: 0.8298 (pt0) outliers start: 44 outliers final: 36 residues processed: 126 average time/residue: 0.0729 time to fit residues: 15.1521 Evaluate side-chains 125 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 86 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE 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 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 508 LYS 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 57 ILE Chi-restraints excluded: chain B residue 102 LYS 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 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 426 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 F residue 57 ILE 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 39 optimal weight: 0.5980 chunk 136 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4164 r_free = 0.4164 target = 0.118965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.083156 restraints weight = 39898.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.084225 restraints weight = 23075.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.084889 restraints weight = 15996.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.085357 restraints weight = 16280.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.085193 restraints weight = 13714.518| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15037 Z= 0.126 Angle : 0.583 10.732 20404 Z= 0.294 Chirality : 0.044 0.170 2207 Planarity : 0.004 0.039 2621 Dihedral : 4.679 47.337 1980 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.85 % Allowed : 21.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.20), residues: 1769 helix: -0.58 (0.30), residues: 295 sheet: -0.73 (0.30), residues: 336 loop : -1.22 (0.19), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 22 TYR 0.029 0.001 TYR E 74 PHE 0.013 0.001 PHE A 707 TRP 0.024 0.001 TRP B 183 HIS 0.003 0.001 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00304 (14991) covalent geometry : angle 0.57811 (20312) SS BOND : bond 0.00268 ( 46) SS BOND : angle 1.25977 ( 92) hydrogen bonds : bond 0.03561 ( 356) hydrogen bonds : angle 5.72099 ( 936) *********************** 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 140 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 93 time to evaluate : 0.620 Fit side-chains REVERT: A 102 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8620 (mttp) REVERT: A 238 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8628 (p) REVERT: A 899 TRP cc_start: 0.8978 (m100) cc_final: 0.8287 (m100) REVERT: B 41 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8619 (p) REVERT: B 102 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8651 (mttp) REVERT: B 119 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8539 (mm) REVERT: B 178 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8269 (t80) REVERT: B 899 TRP cc_start: 0.8393 (m100) cc_final: 0.8004 (m100) REVERT: E 21 GLU cc_start: 0.7258 (pm20) cc_final: 0.7053 (pm20) REVERT: G 70 GLN cc_start: 0.8673 (mt0) cc_final: 0.8195 (pt0) outliers start: 47 outliers final: 36 residues processed: 131 average time/residue: 0.0824 time to fit residues: 18.1207 Evaluate side-chains 131 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 89 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 238 VAL Chi-restraints excluded: chain A residue 262 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 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 119 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 240 THR 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 75 CYS Chi-restraints excluded: chain F residue 57 ILE 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 137 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 75 optimal weight: 30.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.116436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.080932 restraints weight = 40128.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.081924 restraints weight = 23288.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.081386 restraints weight = 17510.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.081748 restraints weight = 17969.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.081742 restraints weight = 16709.510| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 15037 Z= 0.277 Angle : 0.666 10.098 20404 Z= 0.338 Chirality : 0.047 0.198 2207 Planarity : 0.004 0.040 2621 Dihedral : 4.937 48.564 1980 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.67 % Allowed : 22.05 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.20), residues: 1769 helix: -0.69 (0.30), residues: 292 sheet: -0.88 (0.29), residues: 339 loop : -1.40 (0.19), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 181 TYR 0.045 0.002 TYR E 74 PHE 0.022 0.002 PHE B 567 TRP 0.013 0.002 TRP B 634 HIS 0.005 0.001 HIS B 187 Details of bonding type rmsd covalent geometry : bond 0.00656 (14991) covalent geometry : angle 0.66265 (20312) SS BOND : bond 0.00348 ( 46) SS BOND : angle 1.24264 ( 92) hydrogen bonds : bond 0.04049 ( 356) hydrogen bonds : angle 5.96876 ( 936) ********************** 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 124 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 80 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7651 (pmm) cc_final: 0.7400 (ptp) REVERT: A 508 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7877 (ttpt) REVERT: A 899 TRP cc_start: 0.8611 (m100) cc_final: 0.8064 (m100) REVERT: B 119 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8711 (mm) REVERT: B 178 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.7917 (t80) REVERT: G 57 ILE cc_start: 0.8789 (mp) cc_final: 0.8385 (tp) REVERT: G 70 GLN cc_start: 0.8646 (mt0) cc_final: 0.8214 (pt0) outliers start: 44 outliers final: 39 residues processed: 118 average time/residue: 0.0844 time to fit residues: 16.7097 Evaluate side-chains 120 residues out of total 1651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 78 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 175 ASN Chi-restraints excluded: chain A residue 262 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 508 LYS 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 57 ILE Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 240 THR 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 695 LEU 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 F residue 57 ILE 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 168 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 chunk 63 optimal weight: 0.0980 chunk 108 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 159 optimal weight: 40.0000 chunk 100 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 624 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.118746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.083367 restraints weight = 39613.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.083698 restraints weight = 23113.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.084341 restraints weight = 16082.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.084885 restraints weight = 16879.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.084785 restraints weight = 13882.561| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15037 Z= 0.123 Angle : 0.595 11.146 20404 Z= 0.301 Chirality : 0.044 0.181 2207 Planarity : 0.004 0.041 2621 Dihedral : 4.767 48.070 1980 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.42 % Allowed : 22.29 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.20), residues: 1769 helix: -0.59 (0.30), residues: 294 sheet: -0.75 (0.30), residues: 332 loop : -1.29 (0.19), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 181 TYR 0.033 0.001 TYR D 74 PHE 0.014 0.001 PHE A 707 TRP 0.034 0.002 TRP B 183 HIS 0.003 0.001 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00294 (14991) covalent geometry : angle 0.59232 (20312) SS BOND : bond 0.00237 ( 46) SS BOND : angle 0.99492 ( 92) hydrogen bonds : bond 0.03597 ( 356) hydrogen bonds : angle 5.78572 ( 936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2390.74 seconds wall clock time: 42 minutes 7.65 seconds (2527.65 seconds total)