Starting phenix.real_space_refine on Wed Feb 4 23:12:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sjr_25164/02_2026/7sjr_25164.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sjr_25164/02_2026/7sjr_25164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sjr_25164/02_2026/7sjr_25164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sjr_25164/02_2026/7sjr_25164.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sjr_25164/02_2026/7sjr_25164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sjr_25164/02_2026/7sjr_25164.map" } resolution = 3.8 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 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 38 5.49 5 Mg 1 5.21 5 S 44 5.16 5 C 8437 2.51 5 N 2518 2.21 5 O 2654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13696 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 802, 6056 Classifications: {'peptide': 802} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 50, 'TRANS': 751} Chain breaks: 11 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 6885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 911, 6885 Classifications: {'peptide': 911} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 50, 'TRANS': 860} Chain breaks: 21 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 715 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain breaks: 1 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {' MG': 1, 'ANP': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12877 SG CYS A1030 45.987 45.214 59.684 1.00 21.76 S ATOM 12920 SG CYS A1036 48.104 39.890 57.626 1.00 19.87 S ATOM 12858 SG CYS A1027 45.045 43.486 55.074 1.00 25.39 S ATOM 11241 SG CYS A 807 41.638 40.092 59.852 1.00 18.07 S Time building chain proxies: 3.29, per 1000 atoms: 0.24 Number of scatterers: 13696 At special positions: 0 Unit cell: (145.768, 104.272, 112.784, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 44 16.00 P 38 15.00 Mg 1 11.99 O 2654 8.00 N 2518 7.00 C 8437 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.42 Conformation dependent library (CDL) restraints added in 522.4 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1102 " pdb="FE4 SF4 A1102 " - pdb=" SG CYS A 807 " pdb="FE3 SF4 A1102 " - pdb=" SG CYS A1027 " pdb="FE1 SF4 A1102 " - pdb=" SG CYS A1030 " pdb="FE2 SF4 A1102 " - pdb=" SG CYS A1036 " Number of angles added : 12 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3180 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 8 sheets defined 53.3% alpha, 4.3% beta 5 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'B' and resid 14 through 22 removed outlier: 3.504A pdb=" N LEU B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.093A pdb=" N VAL B 34 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 67 Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 80 through 101 removed outlier: 3.897A pdb=" N GLY B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA B 101 " --> pdb=" O ARG B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 131 Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 144 through 159 removed outlier: 3.607A pdb=" N LEU B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TRP B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN B 150 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASP B 154 " --> pdb=" O GLN B 150 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS B 157 " --> pdb=" O TYR B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 187 removed outlier: 3.661A pdb=" N ALA B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU B 185 " --> pdb=" O GLY B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 206 removed outlier: 3.577A pdb=" N LEU B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 249 Proline residue: B 237 - end of helix Processing helix chain 'B' and resid 253 through 268 Processing helix chain 'B' and resid 268 through 279 removed outlier: 4.405A pdb=" N GLY B 272 " --> pdb=" O PHE B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.852A pdb=" N ILE B 296 " --> pdb=" O HIS B 292 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 297 " --> pdb=" O ALA B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 removed outlier: 4.773A pdb=" N THR B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 Processing helix chain 'B' and resid 402 through 425 removed outlier: 3.618A pdb=" N ALA B 421 " --> pdb=" O ALA B 417 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 450 removed outlier: 3.694A pdb=" N ALA B 445 " --> pdb=" O ALA B 441 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA B 450 " --> pdb=" O GLU B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 481 Processing helix chain 'B' and resid 484 through 493 removed outlier: 3.983A pdb=" N ARG B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 514 Processing helix chain 'B' and resid 523 through 530 Processing helix chain 'B' and resid 539 through 544 removed outlier: 4.304A pdb=" N ALA B 543 " --> pdb=" O CYS B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 572 removed outlier: 4.249A pdb=" N GLU B 559 " --> pdb=" O PRO B 555 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 590 removed outlier: 3.800A pdb=" N ALA B 584 " --> pdb=" O PRO B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 599 removed outlier: 4.122A pdb=" N ARG B 597 " --> pdb=" O ASP B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 623 Processing helix chain 'B' and resid 632 through 643 Processing helix chain 'B' and resid 729 through 759 removed outlier: 3.844A pdb=" N SER B 736 " --> pdb=" O SER B 732 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 745 " --> pdb=" O SER B 741 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG B 746 " --> pdb=" O LEU B 742 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG B 752 " --> pdb=" O ASP B 748 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU B 753 " --> pdb=" O GLU B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 794 Processing helix chain 'B' and resid 839 through 853 Processing helix chain 'B' and resid 863 through 877 removed outlier: 3.752A pdb=" N ARG B 877 " --> pdb=" O ALA B 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 46 removed outlier: 3.618A pdb=" N LEU A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL A 40 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS A 46 " --> pdb=" O THR A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 77 removed outlier: 3.685A pdb=" N ALA A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 106 Processing helix chain 'A' and resid 119 through 134 Processing helix chain 'A' and resid 148 through 153 removed outlier: 4.077A pdb=" N THR A 153 " --> pdb=" O PRO A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 171 removed outlier: 3.604A pdb=" N ALA A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 185 Processing helix chain 'A' and resid 187 through 203 removed outlier: 3.731A pdb=" N LEU A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 239 removed outlier: 3.917A pdb=" N GLU A 233 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 247 Processing helix chain 'A' and resid 257 through 260 removed outlier: 3.537A pdb=" N LEU A 260 " --> pdb=" O ALA A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 257 through 260' Processing helix chain 'A' and resid 261 through 272 Processing helix chain 'A' and resid 316 through 329 removed outlier: 4.105A pdb=" N ARG A 329 " --> pdb=" O GLY A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 374 removed outlier: 3.916A pdb=" N GLY A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 403 removed outlier: 4.009A pdb=" N ARG A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 435 removed outlier: 3.509A pdb=" N LEU A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 446 removed outlier: 5.035A pdb=" N VAL A 443 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA A 444 " --> pdb=" O SER A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 469 removed outlier: 4.149A pdb=" N GLN A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 487 Processing helix chain 'A' and resid 495 through 514 removed outlier: 4.027A pdb=" N THR A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU A 503 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP A 514 " --> pdb=" O ALA A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 548 through 571 Processing helix chain 'A' and resid 578 through 582 removed outlier: 4.231A pdb=" N ASP A 582 " --> pdb=" O ARG A 578 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 578 through 582' Processing helix chain 'A' and resid 640 through 649 removed outlier: 3.703A pdb=" N ASP A 646 " --> pdb=" O GLN A 642 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A 647 " --> pdb=" O HIS A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 678 removed outlier: 4.047A pdb=" N ARG A 671 " --> pdb=" O ALA A 667 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LEU A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 673 " --> pdb=" O GLU A 669 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 678 " --> pdb=" O MET A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 711 removed outlier: 4.207A pdb=" N ALA A 705 " --> pdb=" O SER A 701 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU A 706 " --> pdb=" O PRO A 702 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TRP A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 740 removed outlier: 4.040A pdb=" N GLY A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA A 737 " --> pdb=" O GLY A 733 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N CYS A 740 " --> pdb=" O ARG A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 774 through 778 Processing helix chain 'A' and resid 797 through 805 removed outlier: 3.619A pdb=" N GLN A 802 " --> pdb=" O PRO A 798 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 816 Processing helix chain 'A' and resid 823 through 838 removed outlier: 3.823A pdb=" N THR A 827 " --> pdb=" O ASP A 823 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY A 829 " --> pdb=" O ARG A 825 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 838 " --> pdb=" O ALA A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 855 removed outlier: 3.577A pdb=" N VAL A 847 " --> pdb=" O GLU A 843 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASN A 848 " --> pdb=" O SER A 844 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU A 849 " --> pdb=" O GLN A 845 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL A 853 " --> pdb=" O GLU A 849 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP A 855 " --> pdb=" O GLU A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 887 removed outlier: 3.664A pdb=" N ASP A 866 " --> pdb=" O LYS A 862 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN A 867 " --> pdb=" O TRP A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 962 Processing helix chain 'A' and resid 996 through 1014 removed outlier: 4.354A pdb=" N GLU A1002 " --> pdb=" O ASP A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1029 removed outlier: 4.001A pdb=" N ALA A1028 " --> pdb=" O ASN A1025 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN A1029 " --> pdb=" O GLY A1026 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 115 through 118 removed outlier: 3.834A pdb=" N THR B 115 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR B 313 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL B 43 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N LEU B 353 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE B 45 " --> pdb=" O LEU B 353 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 141 through 142 removed outlier: 5.977A pdb=" N ARG B 141 " --> pdb=" O MET B 252 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 395 through 398 Processing sheet with id=AA4, first strand: chain 'B' and resid 432 through 433 removed outlier: 7.088A pdb=" N ALA B 432 " --> pdb=" O ALA B 676 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 90 through 92 removed outlier: 5.653A pdb=" N LEU A 58 " --> pdb=" O ARG A 92 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU A 57 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASP A 255 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU A 59 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL A 279 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 354 removed outlier: 3.509A pdb=" N THR A 350 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 688 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA A 383 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N MET A 382 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N LEU A 606 " --> pdb=" O MET A 382 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL A 384 " --> pdb=" O LEU A 606 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 898 through 900 Processing sheet with id=AA8, first strand: chain 'A' and resid 921 through 923 removed outlier: 3.999A pdb=" N ARG A 921 " --> pdb=" O VAL A 933 " (cutoff:3.500A) 568 hydrogen bonds defined for protein. 1674 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 11 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 5700 1.42 - 1.64: 8222 1.64 - 1.85: 67 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 14001 Sorted by residual: bond pdb=" O3A ANP A1103 " pdb=" PB ANP A1103 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.29e+01 bond pdb=" N3B ANP A1103 " pdb=" PG ANP A1103 " ideal model delta sigma weight residual 1.795 1.689 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" O5' ANP A1103 " pdb=" PA ANP A1103 " ideal model delta sigma weight residual 1.655 1.578 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" O3G ANP A1103 " pdb=" PG ANP A1103 " ideal model delta sigma weight residual 1.528 1.578 -0.050 2.00e-02 2.50e+03 6.25e+00 bond pdb=" O2B ANP A1103 " pdb=" PB ANP A1103 " ideal model delta sigma weight residual 1.508 1.555 -0.047 2.00e-02 2.50e+03 5.46e+00 ... (remaining 13996 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.11: 19141 4.11 - 8.22: 68 8.22 - 12.33: 5 12.33 - 16.44: 0 16.44 - 20.54: 1 Bond angle restraints: 19215 Sorted by residual: angle pdb=" PB ANP A1103 " pdb=" N3B ANP A1103 " pdb=" PG ANP A1103 " ideal model delta sigma weight residual 126.95 106.41 20.54 3.00e+00 1.11e-01 4.69e+01 angle pdb=" C VAL B 643 " pdb=" N GLU B 644 " pdb=" CA GLU B 644 " ideal model delta sigma weight residual 123.93 131.87 -7.94 1.54e+00 4.22e-01 2.66e+01 angle pdb=" O1B ANP A1103 " pdb=" PB ANP A1103 " pdb=" O2B ANP A1103 " ideal model delta sigma weight residual 120.08 108.69 11.39 3.00e+00 1.11e-01 1.44e+01 angle pdb=" C GLU B 807 " pdb=" N HIS B 808 " pdb=" CA HIS B 808 " ideal model delta sigma weight residual 121.54 128.54 -7.00 1.91e+00 2.74e-01 1.34e+01 angle pdb=" N GLY B 804 " pdb=" CA GLY B 804 " pdb=" C GLY B 804 " ideal model delta sigma weight residual 111.12 117.51 -6.39 1.89e+00 2.80e-01 1.14e+01 ... (remaining 19210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 8082 35.86 - 71.71: 255 71.71 - 107.57: 18 107.57 - 143.43: 1 143.43 - 179.28: 7 Dihedral angle restraints: 8363 sinusoidal: 3484 harmonic: 4879 Sorted by residual: dihedral pdb=" CA SER B 783 " pdb=" C SER B 783 " pdb=" N GLU B 784 " pdb=" CA GLU B 784 " ideal model delta harmonic sigma weight residual 180.00 155.09 24.91 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA GLN A 472 " pdb=" C GLN A 472 " pdb=" N PRO A 473 " pdb=" CA PRO A 473 " ideal model delta harmonic sigma weight residual 180.00 155.23 24.77 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" O1A ANP A1103 " pdb=" O3A ANP A1103 " pdb=" PA ANP A1103 " pdb=" PB ANP A1103 " ideal model delta sinusoidal sigma weight residual 83.11 -90.53 173.64 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 8360 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1869 0.056 - 0.113: 343 0.113 - 0.169: 44 0.169 - 0.225: 2 0.225 - 0.281: 1 Chirality restraints: 2259 Sorted by residual: chirality pdb=" C3' ANP A1103 " pdb=" C2' ANP A1103 " pdb=" C4' ANP A1103 " pdb=" O3' ANP A1103 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CB ILE B 395 " pdb=" CA ILE B 395 " pdb=" CG1 ILE B 395 " pdb=" CG2 ILE B 395 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.65e-01 chirality pdb=" CB ILE A 450 " pdb=" CA ILE A 450 " pdb=" CG1 ILE A 450 " pdb=" CG2 ILE A 450 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.38e-01 ... (remaining 2256 not shown) Planarity restraints: 2377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 497 " 0.018 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP B 497 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP B 497 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP B 497 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 497 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 497 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 497 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 497 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 497 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 497 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 781 " 0.043 5.00e-02 4.00e+02 6.60e-02 6.96e+00 pdb=" N PRO B 782 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 782 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 782 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 357 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.09e+00 pdb=" C TRP B 357 " -0.043 2.00e-02 2.50e+03 pdb=" O TRP B 357 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG B 358 " 0.014 2.00e-02 2.50e+03 ... (remaining 2374 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 101 2.50 - 3.10: 10216 3.10 - 3.70: 20544 3.70 - 4.30: 27264 4.30 - 4.90: 45197 Nonbonded interactions: 103322 Sorted by model distance: nonbonded pdb=" NE2 HIS A 833 " pdb="MG MG A1101 " model vdw 1.895 2.250 nonbonded pdb=" OD2 ASP A 920 " pdb="MG MG A1101 " model vdw 2.051 2.170 nonbonded pdb=" O VAL A 624 " pdb=" OG SER A 701 " model vdw 2.200 3.040 nonbonded pdb=" OG1 THR A 348 " pdb=" OG1 THR A 712 " model vdw 2.211 3.040 nonbonded pdb=" OG1 THR B 689 " pdb=" OE1 GLN B 690 " model vdw 2.225 3.040 ... (remaining 103317 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.070 Find NCS groups from input model: 0.100 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:1.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 0.005 0.145 14005 Z= 0.242 Angle : 0.897 43.732 19227 Z= 0.421 Chirality : 0.045 0.281 2259 Planarity : 0.005 0.066 2377 Dihedral : 17.634 179.282 5183 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 0.08 % Allowed : 0.53 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.61 (0.21), residues: 1645 helix: 0.21 (0.18), residues: 828 sheet: -2.08 (0.47), residues: 126 loop : -2.49 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 572 TYR 0.016 0.002 TYR A 200 PHE 0.021 0.002 PHE B 685 TRP 0.053 0.002 TRP B 497 HIS 0.007 0.001 HIS B 665 Details of bonding type rmsd covalent geometry : bond 0.00549 (14001) covalent geometry : angle 0.78698 (19215) hydrogen bonds : bond 0.16988 ( 579) hydrogen bonds : angle 6.45389 ( 1696) metal coordination : bond 0.00836 ( 4) metal coordination : angle 17.21749 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.542 Fit side-chains REVERT: B 258 MET cc_start: 0.8579 (tpt) cc_final: 0.7956 (tpt) outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 0.1190 time to fit residues: 24.4854 Evaluate side-chains 95 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.0050 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 HIS ** B 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 GLN ** A 775 HIS ** 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 = 0.3622 r_free = 0.3622 target = 0.125160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.098478 restraints weight = 25278.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.097324 restraints weight = 21531.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.098342 restraints weight = 23280.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.098896 restraints weight = 15990.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.099242 restraints weight = 14469.150| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14005 Z= 0.137 Angle : 0.755 35.306 19227 Z= 0.336 Chirality : 0.042 0.176 2259 Planarity : 0.005 0.042 2377 Dihedral : 17.121 179.193 2257 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 1.21 % Allowed : 8.33 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.11 (0.21), residues: 1645 helix: 0.59 (0.18), residues: 870 sheet: -1.84 (0.50), residues: 118 loop : -2.39 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 128 TYR 0.030 0.002 TYR A 522 PHE 0.016 0.001 PHE A 879 TRP 0.016 0.001 TRP B 497 HIS 0.006 0.001 HIS A 872 Details of bonding type rmsd covalent geometry : bond 0.00298 (14001) covalent geometry : angle 0.65696 (19215) hydrogen bonds : bond 0.04338 ( 579) hydrogen bonds : angle 4.41764 ( 1696) metal coordination : bond 0.00488 ( 4) metal coordination : angle 14.90913 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.651 Fit side-chains REVERT: B 274 GLN cc_start: 0.7997 (tp40) cc_final: 0.7786 (tp40) REVERT: A 674 MET cc_start: 0.8110 (tmm) cc_final: 0.7802 (tmm) REVERT: A 677 MET cc_start: 0.8278 (mtp) cc_final: 0.8004 (mtp) outliers start: 16 outliers final: 11 residues processed: 138 average time/residue: 0.1064 time to fit residues: 23.0477 Evaluate side-chains 104 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 808 HIS Chi-restraints excluded: chain A residue 357 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 165 optimal weight: 6.9990 chunk 156 optimal weight: 0.7980 chunk 138 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 chunk 111 optimal weight: 0.0970 chunk 125 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 58 optimal weight: 0.0050 chunk 121 optimal weight: 4.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 ASN B 673 GLN A 643 HIS ** A 775 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.125982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.099616 restraints weight = 25293.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.098654 restraints weight = 21760.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.099737 restraints weight = 23138.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.100183 restraints weight = 16515.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.100532 restraints weight = 14984.847| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14005 Z= 0.120 Angle : 0.690 32.978 19227 Z= 0.300 Chirality : 0.040 0.179 2259 Planarity : 0.004 0.037 2377 Dihedral : 16.852 178.117 2257 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.80 % Allowed : 12.88 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.83 (0.21), residues: 1645 helix: 0.82 (0.18), residues: 879 sheet: -1.74 (0.50), residues: 119 loop : -2.29 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 295 TYR 0.015 0.001 TYR A 200 PHE 0.012 0.001 PHE A 879 TRP 0.019 0.001 TRP B 497 HIS 0.005 0.001 HIS A 872 Details of bonding type rmsd covalent geometry : bond 0.00268 (14001) covalent geometry : angle 0.59279 (19215) hydrogen bonds : bond 0.03623 ( 579) hydrogen bonds : angle 3.99337 ( 1696) metal coordination : bond 0.00448 ( 4) metal coordination : angle 14.13056 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: B 581 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7579 (tm-30) REVERT: A 533 LEU cc_start: 0.8802 (pt) cc_final: 0.8518 (mp) REVERT: A 677 MET cc_start: 0.8267 (mtp) cc_final: 0.7771 (mtp) outliers start: 37 outliers final: 20 residues processed: 147 average time/residue: 0.1122 time to fit residues: 25.0811 Evaluate side-chains 123 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 932 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 172 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 164 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 99 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 85 optimal weight: 20.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.120249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.093289 restraints weight = 25617.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.092847 restraints weight = 21666.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.093547 restraints weight = 24377.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.094163 restraints weight = 17157.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.094500 restraints weight = 14907.329| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 14005 Z= 0.282 Angle : 0.827 39.814 19227 Z= 0.367 Chirality : 0.045 0.183 2259 Planarity : 0.005 0.042 2377 Dihedral : 17.132 178.714 2257 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 3.18 % Allowed : 15.98 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.97 (0.21), residues: 1645 helix: 0.73 (0.18), residues: 873 sheet: -2.22 (0.49), residues: 124 loop : -2.27 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 477 TYR 0.017 0.002 TYR B 755 PHE 0.023 0.002 PHE B 302 TRP 0.042 0.002 TRP B 497 HIS 0.007 0.002 HIS B 665 Details of bonding type rmsd covalent geometry : bond 0.00664 (14001) covalent geometry : angle 0.71869 (19215) hydrogen bonds : bond 0.04626 ( 579) hydrogen bonds : angle 4.43306 ( 1696) metal coordination : bond 0.01656 ( 4) metal coordination : angle 16.40648 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 98 time to evaluate : 0.520 Fit side-chains REVERT: B 581 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7692 (tm-30) REVERT: A 533 LEU cc_start: 0.8835 (pt) cc_final: 0.8547 (mp) REVERT: A 674 MET cc_start: 0.8011 (tmm) cc_final: 0.7716 (tmm) REVERT: A 677 MET cc_start: 0.8477 (mtp) cc_final: 0.8044 (mtp) REVERT: A 859 TYR cc_start: 0.9163 (OUTLIER) cc_final: 0.8890 (m-80) outliers start: 42 outliers final: 27 residues processed: 134 average time/residue: 0.1094 time to fit residues: 22.7046 Evaluate side-chains 114 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain A residue 99 PHE Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 859 TYR Chi-restraints excluded: chain A residue 932 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 126 optimal weight: 10.0000 chunk 147 optimal weight: 0.0470 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 98 optimal weight: 20.0000 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.125093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.098482 restraints weight = 25440.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.097792 restraints weight = 22002.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.098826 restraints weight = 22908.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.099317 restraints weight = 15811.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.099584 restraints weight = 14483.516| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14005 Z= 0.118 Angle : 0.687 32.578 19227 Z= 0.296 Chirality : 0.039 0.158 2259 Planarity : 0.004 0.042 2377 Dihedral : 16.813 175.121 2257 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.58 % Allowed : 18.03 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.63 (0.22), residues: 1645 helix: 1.03 (0.18), residues: 878 sheet: -1.77 (0.50), residues: 120 loop : -2.24 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 657 TYR 0.012 0.001 TYR A 200 PHE 0.011 0.001 PHE A 879 TRP 0.028 0.001 TRP B 497 HIS 0.005 0.001 HIS A 872 Details of bonding type rmsd covalent geometry : bond 0.00259 (14001) covalent geometry : angle 0.58217 (19215) hydrogen bonds : bond 0.03350 ( 579) hydrogen bonds : angle 3.86693 ( 1696) metal coordination : bond 0.00420 ( 4) metal coordination : angle 14.57971 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: B 581 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7484 (tm-30) REVERT: A 525 TRP cc_start: 0.7770 (t60) cc_final: 0.7246 (t60) REVERT: A 677 MET cc_start: 0.8364 (mtp) cc_final: 0.7889 (mtp) outliers start: 34 outliers final: 24 residues processed: 134 average time/residue: 0.1081 time to fit residues: 22.4411 Evaluate side-chains 119 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 430 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 9 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 145 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 152 optimal weight: 5.9990 chunk 42 optimal weight: 0.0570 overall best weight: 2.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.121307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.094644 restraints weight = 25377.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.094168 restraints weight = 22430.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.094632 restraints weight = 28108.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.095420 restraints weight = 18159.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.095700 restraints weight = 15226.522| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14005 Z= 0.214 Angle : 0.754 36.641 19227 Z= 0.329 Chirality : 0.042 0.162 2259 Planarity : 0.005 0.042 2377 Dihedral : 16.911 177.250 2257 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 3.33 % Allowed : 18.71 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.66 (0.22), residues: 1645 helix: 1.01 (0.18), residues: 873 sheet: -1.85 (0.48), residues: 129 loop : -2.23 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 657 TYR 0.016 0.002 TYR A 200 PHE 0.017 0.002 PHE B 685 TRP 0.037 0.002 TRP B 497 HIS 0.005 0.001 HIS B 665 Details of bonding type rmsd covalent geometry : bond 0.00505 (14001) covalent geometry : angle 0.64552 (19215) hydrogen bonds : bond 0.04084 ( 579) hydrogen bonds : angle 4.13831 ( 1696) metal coordination : bond 0.01263 ( 4) metal coordination : angle 15.63071 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 94 time to evaluate : 0.547 Fit side-chains REVERT: B 581 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7591 (tm-30) REVERT: A 677 MET cc_start: 0.8386 (mtp) cc_final: 0.8181 (mtp) outliers start: 44 outliers final: 35 residues processed: 131 average time/residue: 0.1057 time to fit residues: 21.7098 Evaluate side-chains 123 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 88 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 110 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 49 optimal weight: 0.4980 chunk 17 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.122233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.095846 restraints weight = 25432.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.094665 restraints weight = 22842.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.095922 restraints weight = 24567.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.096415 restraints weight = 16866.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.096755 restraints weight = 15470.439| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14005 Z= 0.172 Angle : 0.729 35.540 19227 Z= 0.314 Chirality : 0.041 0.163 2259 Planarity : 0.004 0.041 2377 Dihedral : 16.878 176.946 2257 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.41 % Allowed : 19.92 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.60 (0.22), residues: 1645 helix: 1.08 (0.18), residues: 873 sheet: -1.83 (0.48), residues: 129 loop : -2.23 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 736 TYR 0.017 0.001 TYR A 200 PHE 0.013 0.001 PHE B 685 TRP 0.030 0.002 TRP B 497 HIS 0.004 0.001 HIS B 665 Details of bonding type rmsd covalent geometry : bond 0.00405 (14001) covalent geometry : angle 0.61851 (19215) hydrogen bonds : bond 0.03765 ( 579) hydrogen bonds : angle 4.01665 ( 1696) metal coordination : bond 0.00867 ( 4) metal coordination : angle 15.44022 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 99 time to evaluate : 0.524 Fit side-chains REVERT: B 581 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7554 (tm-30) REVERT: A 525 TRP cc_start: 0.7867 (t60) cc_final: 0.7270 (t60) REVERT: A 677 MET cc_start: 0.8390 (mtp) cc_final: 0.8163 (mtp) outliers start: 45 outliers final: 32 residues processed: 137 average time/residue: 0.1083 time to fit residues: 22.8771 Evaluate side-chains 126 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 55 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 12 optimal weight: 0.0060 chunk 103 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 137 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 5 optimal weight: 0.0980 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 625 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.127712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.101848 restraints weight = 25068.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.100576 restraints weight = 21934.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.101813 restraints weight = 23663.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.102438 restraints weight = 15890.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.102757 restraints weight = 14428.890| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14005 Z= 0.110 Angle : 0.678 29.142 19227 Z= 0.293 Chirality : 0.039 0.234 2259 Planarity : 0.004 0.039 2377 Dihedral : 16.657 174.609 2257 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.73 % Allowed : 20.98 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.33 (0.22), residues: 1645 helix: 1.31 (0.18), residues: 878 sheet: -1.80 (0.49), residues: 125 loop : -2.11 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 736 TYR 0.014 0.001 TYR A 200 PHE 0.009 0.001 PHE A 879 TRP 0.014 0.001 TRP B 497 HIS 0.005 0.001 HIS A 872 Details of bonding type rmsd covalent geometry : bond 0.00240 (14001) covalent geometry : angle 0.58494 (19215) hydrogen bonds : bond 0.02944 ( 579) hydrogen bonds : angle 3.64846 ( 1696) metal coordination : bond 0.00434 ( 4) metal coordination : angle 13.75502 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 0.478 Fit side-chains REVERT: B 581 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7391 (tm-30) REVERT: A 525 TRP cc_start: 0.7671 (t60) cc_final: 0.7240 (t60) outliers start: 36 outliers final: 26 residues processed: 152 average time/residue: 0.1122 time to fit residues: 26.3653 Evaluate side-chains 128 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 915 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 51 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 121 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 157 optimal weight: 8.9990 chunk 151 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.124108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.097393 restraints weight = 25487.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.096385 restraints weight = 22378.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.097488 restraints weight = 23886.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.098132 restraints weight = 15868.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.098437 restraints weight = 14297.115| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14005 Z= 0.158 Angle : 0.726 32.170 19227 Z= 0.317 Chirality : 0.041 0.187 2259 Planarity : 0.004 0.041 2377 Dihedral : 16.719 176.056 2257 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.20 % Allowed : 22.27 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.30 (0.22), residues: 1645 helix: 1.32 (0.18), residues: 880 sheet: -1.79 (0.49), residues: 124 loop : -2.10 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 736 TYR 0.014 0.001 TYR A 200 PHE 0.012 0.001 PHE B 685 TRP 0.028 0.001 TRP B 497 HIS 0.017 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00373 (14001) covalent geometry : angle 0.63039 (19215) hydrogen bonds : bond 0.03496 ( 579) hydrogen bonds : angle 3.83543 ( 1696) metal coordination : bond 0.00805 ( 4) metal coordination : angle 14.40522 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.484 Fit side-chains REVERT: B 581 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7528 (tm-30) REVERT: A 525 TRP cc_start: 0.7782 (t60) cc_final: 0.7270 (t60) outliers start: 29 outliers final: 25 residues processed: 126 average time/residue: 0.0964 time to fit residues: 18.6865 Evaluate side-chains 121 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 915 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 127 optimal weight: 0.9980 chunk 130 optimal weight: 0.0060 chunk 160 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 105 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.126484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.099740 restraints weight = 25234.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.099134 restraints weight = 21657.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.100129 restraints weight = 23083.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.100777 restraints weight = 15509.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.101032 restraints weight = 14007.854| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14005 Z= 0.116 Angle : 0.693 30.443 19227 Z= 0.300 Chirality : 0.039 0.179 2259 Planarity : 0.004 0.039 2377 Dihedral : 16.635 175.625 2257 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.12 % Allowed : 22.65 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.20 (0.22), residues: 1645 helix: 1.39 (0.18), residues: 880 sheet: -1.77 (0.49), residues: 125 loop : -2.03 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 671 TYR 0.013 0.001 TYR A 200 PHE 0.008 0.001 PHE A 879 TRP 0.020 0.001 TRP B 497 HIS 0.005 0.001 HIS A 872 Details of bonding type rmsd covalent geometry : bond 0.00266 (14001) covalent geometry : angle 0.59825 (19215) hydrogen bonds : bond 0.03078 ( 579) hydrogen bonds : angle 3.69541 ( 1696) metal coordination : bond 0.00311 ( 4) metal coordination : angle 13.97671 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3290 Ramachandran restraints generated. 1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.571 Fit side-chains REVERT: B 581 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7443 (tm-30) REVERT: B 767 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8891 (pp) REVERT: A 525 TRP cc_start: 0.7624 (t60) cc_final: 0.7200 (t60) outliers start: 28 outliers final: 25 residues processed: 130 average time/residue: 0.1121 time to fit residues: 22.6603 Evaluate side-chains 127 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 915 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 21 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 113 optimal weight: 0.2980 chunk 159 optimal weight: 0.0020 chunk 117 optimal weight: 0.5980 chunk 19 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.126400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.100039 restraints weight = 25305.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.099302 restraints weight = 22515.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.100330 restraints weight = 25842.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.101071 restraints weight = 17314.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.101347 restraints weight = 15375.067| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14005 Z= 0.121 Angle : 0.688 30.265 19227 Z= 0.298 Chirality : 0.039 0.167 2259 Planarity : 0.004 0.039 2377 Dihedral : 16.609 176.151 2257 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.05 % Allowed : 22.95 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.13 (0.22), residues: 1645 helix: 1.44 (0.18), residues: 880 sheet: -1.69 (0.50), residues: 124 loop : -1.99 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 736 TYR 0.014 0.001 TYR B 13 PHE 0.008 0.001 PHE B 685 TRP 0.023 0.001 TRP B 497 HIS 0.004 0.001 HIS A 872 Details of bonding type rmsd covalent geometry : bond 0.00282 (14001) covalent geometry : angle 0.59394 (19215) hydrogen bonds : bond 0.03130 ( 579) hydrogen bonds : angle 3.69515 ( 1696) metal coordination : bond 0.00424 ( 4) metal coordination : angle 13.90275 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1822.33 seconds wall clock time: 32 minutes 19.38 seconds (1939.38 seconds total)