Starting phenix.real_space_refine on Sat Sep 12 04:44:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sjr_25164/09_2026/7sjr_25164.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sjr_25164/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7sjr_25164/09_2026/7sjr_25164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sjr_25164/09_2026/7sjr_25164.map" model { file = "/net/cci-nas-00/data/ceres_data/7sjr_25164/09_2026/7sjr_25164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sjr_25164/09_2026/7sjr_25164.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7sjr_25164/09_2026/7sjr_25164.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sjr_25164/09_2026/7sjr_25164.cif" } 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-2.2.1-6174/lib/python3.11/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: 2.99, per 1000 atoms: 0.22 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: 1.19 Conformation dependent library (CDL) restraints added in 603.9 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: 1.38 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: 2.00 Time building geometry restraints manager: 1.53 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=" C3' DT C 40 " pdb=" C2' DT C 40 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DC C 15 " pdb=" C2' DC C 15 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.95e+00 ... (remaining 13996 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.11: 19140 4.11 - 8.22: 69 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=" N3 DT C 56 " pdb=" C4 DT C 56 " pdb=" O4 DT C 56 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT C 48 " pdb=" C4 DT C 48 " pdb=" O4 DT C 48 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT C 2 " pdb=" C4 DT C 2 " pdb=" O4 DT C 2 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 ... (remaining 19210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 8057 35.86 - 71.71: 252 71.71 - 107.57: 18 107.57 - 143.43: 1 143.43 - 179.28: 7 Dihedral angle restraints: 8335 sinusoidal: 3456 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 8332 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1847 0.056 - 0.113: 358 0.113 - 0.169: 50 0.169 - 0.225: 3 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=" C3' DT C 55 " pdb=" C4' DT C 55 " pdb=" O3' DT C 55 " pdb=" C2' DT C 55 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.08e+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 ... (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: 1.480 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.050 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 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 : 0.006 0.145 14005 Z= 0.296 Angle : 0.915 43.732 19227 Z= 0.478 Chirality : 0.046 0.281 2259 Planarity : 0.005 0.066 2377 Dihedral : 17.577 179.282 5155 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/Z covalent geometry : bond 0.00564 / 0.30 (14001) covalent geometry : angle 0.80825 / 0.48 (19215) hydrogen bonds : bond 0.16988 / 11.72 ( 579) hydrogen bonds : angle 6.45389 / 4.51 ( 1696) metal coordination : bond 0.00836 / 0.43 ( 4) metal coordination : angle 17.21749 / 12.94 ( 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 : 0.515 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: 0.1048 time to fit residues: 21.5824 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 : 0.469 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 HIS ** B 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.124228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.097477 restraints weight = 25266.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.096401 restraints weight = 21684.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.097330 restraints weight = 23617.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.097816 restraints weight = 17140.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.098255 restraints weight = 15301.663| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14005 Z= 0.146 Angle : 0.806 38.179 19227 Z= 0.360 Chirality : 0.046 0.399 2259 Planarity : 0.005 0.046 2377 Dihedral : 17.339 176.130 2229 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 1.14 % Allowed : 8.79 % Favored : 90.08 % 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: -1.20 (0.21), residues: 1645 helix: 0.53 (0.18), residues: 862 sheet: -1.88 (0.50), residues: 118 loop : -2.41 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 572 TYR 0.020 0.002 TYR A 522 PHE 0.016 0.002 PHE A 879 TRP 0.020 0.001 TRP B 497 HIS 0.005 0.001 HIS A 872 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (14001) covalent geometry : angle 0.70354 / 0.36 (19215) hydrogen bonds : bond 0.04963 / 3.30 ( 579) hydrogen bonds : angle 4.62472 / 3.28 ( 1696) metal coordination : bond 0.00523 / 0.27 ( 4) metal coordination : angle 15.76604 / 12.19 ( 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 131 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.533 Fit side-chains REVERT: B 274 GLN cc_start: 0.8017 (tp40) cc_final: 0.7788 (tp40) REVERT: B 444 MET cc_start: 0.8998 (tpt) cc_final: 0.8798 (tpt) outliers start: 15 outliers final: 12 residues processed: 126 average time/residue: 0.0934 time to fit residues: 18.4627 Evaluate side-chains 105 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU 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 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 261 ASP Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 429 LEU 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: 3.9990 chunk 138 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 chunk 111 optimal weight: 0.0670 chunk 125 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 166 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 121 optimal weight: 8.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 ASN B 673 GLN A 122 GLN ** A 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.121187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.094862 restraints weight = 25648.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.093674 restraints weight = 23561.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.094583 restraints weight = 27430.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.095172 restraints weight = 18952.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.095472 restraints weight = 16896.732| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 14005 Z= 0.229 Angle : 0.815 40.210 19227 Z= 0.361 Chirality : 0.046 0.368 2259 Planarity : 0.005 0.046 2377 Dihedral : 17.425 178.904 2229 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 2.65 % Allowed : 13.26 % Favored : 84.09 % 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: -1.19 (0.21), residues: 1645 helix: 0.56 (0.18), residues: 867 sheet: -2.04 (0.48), residues: 124 loop : -2.44 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 572 TYR 0.016 0.002 TYR A 200 PHE 0.021 0.002 PHE B 685 TRP 0.027 0.002 TRP B 497 HIS 0.005 0.001 HIS B 679 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 (14001) covalent geometry : angle 0.70622 / 0.36 (19215) hydrogen bonds : bond 0.05016 / 3.43 ( 579) hydrogen bonds : angle 4.63463 / 3.29 ( 1696) metal coordination : bond 0.01255 / 0.64 ( 4) metal coordination : angle 16.28720 / 12.34 ( 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 137 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 102 time to evaluate : 0.466 Fit side-chains REVERT: A 674 MET cc_start: 0.8094 (tmm) cc_final: 0.7678 (tmm) outliers start: 35 outliers final: 20 residues processed: 131 average time/residue: 0.0921 time to fit residues: 19.0691 Evaluate side-chains 113 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 118 THR 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 625 HIS 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 99 PHE Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 366 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: 40.0000 chunk 35 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 142 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 27 optimal weight: 0.0980 chunk 99 optimal weight: 20.0000 chunk 21 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.123273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.096331 restraints weight = 25299.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.095610 restraints weight = 21430.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.096547 restraints weight = 24994.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.097202 restraints weight = 16531.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.097554 restraints weight = 14491.599| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1446 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= 0.144 Angle : 0.748 37.698 19227 Z= 0.326 Chirality : 0.043 0.288 2259 Planarity : 0.005 0.043 2377 Dihedral : 17.262 176.081 2229 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 2.42 % Allowed : 15.98 % Favored : 81.59 % 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: -0.94 (0.21), residues: 1645 helix: 0.80 (0.18), residues: 867 sheet: -1.95 (0.49), residues: 119 loop : -2.37 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 295 TYR 0.017 0.001 TYR A 200 PHE 0.012 0.001 PHE B 302 TRP 0.020 0.001 TRP B 497 HIS 0.006 0.001 HIS B 665 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (14001) covalent geometry : angle 0.63750 / 0.32 (19215) hydrogen bonds : bond 0.04097 / 2.74 ( 579) hydrogen bonds : angle 4.25036 / 3.03 ( 1696) metal coordination : bond 0.00563 / 0.27 ( 4) metal coordination : angle 15.65065 / 12.14 ( 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 138 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 0.484 Fit side-chains REVERT: B 581 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7659 (tm-30) REVERT: A 483 ASP cc_start: 0.8256 (m-30) cc_final: 0.7996 (m-30) REVERT: A 674 MET cc_start: 0.8089 (tmm) cc_final: 0.7770 (tmm) outliers start: 32 outliers final: 24 residues processed: 132 average time/residue: 0.0889 time to fit residues: 18.4485 Evaluate side-chains 114 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 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 148 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 47 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 126 optimal weight: 10.0000 chunk 147 optimal weight: 0.2980 chunk 60 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 113 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 274 GLN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.124400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.097881 restraints weight = 25420.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.097325 restraints weight = 21688.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.098283 restraints weight = 24369.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.098922 restraints weight = 16190.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.099157 restraints weight = 14521.429| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14005 Z= 0.121 Angle : 0.711 35.174 19227 Z= 0.308 Chirality : 0.041 0.241 2259 Planarity : 0.004 0.039 2377 Dihedral : 17.118 178.182 2229 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.65 % Allowed : 18.11 % Favored : 79.24 % 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: -0.74 (0.22), residues: 1645 helix: 0.97 (0.18), residues: 869 sheet: -1.79 (0.50), residues: 119 loop : -2.31 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 736 TYR 0.023 0.001 TYR A 200 PHE 0.010 0.001 PHE B 685 TRP 0.015 0.001 TRP B 497 HIS 0.005 0.001 HIS B 665 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (14001) covalent geometry : angle 0.60454 / 0.31 (19215) hydrogen bonds : bond 0.03665 / 2.44 ( 579) hydrogen bonds : angle 4.01538 / 2.86 ( 1696) metal coordination : bond 0.00440 / 0.21 ( 4) metal coordination : angle 14.99297 / 11.72 ( 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 143 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: B 56 MET cc_start: 0.8247 (mmp) cc_final: 0.8011 (mmt) REVERT: B 353 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8735 (mp) REVERT: B 581 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7542 (tm-30) REVERT: A 533 LEU cc_start: 0.8840 (pt) cc_final: 0.8521 (mp) REVERT: A 674 MET cc_start: 0.8028 (tmm) cc_final: 0.7805 (tmm) outliers start: 35 outliers final: 23 residues processed: 139 average time/residue: 0.0962 time to fit residues: 21.1276 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 : 0.491 ------------------------------------------------------------------------------- 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 281 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 353 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 618 LEU 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 148 LEU Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 736 ARG Chi-restraints excluded: chain A residue 932 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 9 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 87 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 152 optimal weight: 7.9990 chunk 42 optimal weight: 0.3980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 274 GLN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.124647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.098053 restraints weight = 25164.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.097750 restraints weight = 21374.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.098400 restraints weight = 25283.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.099277 restraints weight = 16171.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.099472 restraints weight = 13703.107| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1891 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= 0.121 Angle : 0.703 34.320 19227 Z= 0.304 Chirality : 0.041 0.250 2259 Planarity : 0.004 0.040 2377 Dihedral : 17.024 176.651 2229 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.73 % Allowed : 18.94 % Favored : 78.33 % 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: -0.61 (0.22), residues: 1645 helix: 1.06 (0.18), residues: 877 sheet: -1.84 (0.49), residues: 124 loop : -2.23 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 358 TYR 0.018 0.001 TYR A 200 PHE 0.010 0.001 PHE B 685 TRP 0.019 0.001 TRP A 525 HIS 0.004 0.001 HIS B 665 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (14001) covalent geometry : angle 0.59939 / 0.30 (19215) hydrogen bonds : bond 0.03550 / 2.39 ( 579) hydrogen bonds : angle 3.91147 / 2.78 ( 1696) metal coordination : bond 0.00455 / 0.22 ( 4) metal coordination : angle 14.69126 / 11.48 ( 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 146 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 0.395 Fit side-chains REVERT: B 270 GLN cc_start: 0.6858 (pm20) cc_final: 0.6327 (pt0) REVERT: B 353 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8699 (mp) REVERT: B 581 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7508 (tm-30) REVERT: A 525 TRP cc_start: 0.7798 (t60) cc_final: 0.7235 (t60) REVERT: A 533 LEU cc_start: 0.8807 (pt) cc_final: 0.8529 (mp) REVERT: A 699 LEU cc_start: 0.9027 (mt) cc_final: 0.8826 (mp) outliers start: 36 outliers final: 26 residues processed: 140 average time/residue: 0.1017 time to fit residues: 21.9682 Evaluate side-chains 126 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 353 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 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 148 LEU Chi-restraints excluded: chain A residue 338 HIS 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 932 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 110 optimal weight: 7.9990 chunk 135 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 130 optimal weight: 0.0020 chunk 23 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 8 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 overall best weight: 1.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.123993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.097574 restraints weight = 25319.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.097008 restraints weight = 22068.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.097715 restraints weight = 24697.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.098316 restraints weight = 17115.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.098760 restraints weight = 14959.568| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14005 Z= 0.145 Angle : 0.712 34.722 19227 Z= 0.310 Chirality : 0.042 0.257 2259 Planarity : 0.004 0.038 2377 Dihedral : 17.010 176.083 2229 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 2.80 % Allowed : 19.85 % Favored : 77.35 % 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: -0.57 (0.22), residues: 1645 helix: 1.09 (0.18), residues: 880 sheet: -1.83 (0.49), residues: 124 loop : -2.21 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 358 TYR 0.020 0.001 TYR A 200 PHE 0.012 0.001 PHE B 302 TRP 0.022 0.001 TRP B 497 HIS 0.004 0.001 HIS B 665 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (14001) covalent geometry : angle 0.60841 / 0.31 (19215) hydrogen bonds : bond 0.03618 / 2.44 ( 579) hydrogen bonds : angle 3.95240 / 2.81 ( 1696) metal coordination : bond 0.00690 / 0.34 ( 4) metal coordination : angle 14.82495 / 11.54 ( 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 139 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 102 time to evaluate : 0.506 Fit side-chains REVERT: B 353 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8700 (mp) REVERT: B 581 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7520 (tm-30) REVERT: A 533 LEU cc_start: 0.8789 (pt) cc_final: 0.8508 (mp) outliers start: 37 outliers final: 28 residues processed: 133 average time/residue: 0.1025 time to fit residues: 20.9361 Evaluate side-chains 125 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 353 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 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 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: 0.7980 chunk 91 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 12 optimal weight: 0.0670 chunk 103 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 3 optimal weight: 0.0980 chunk 17 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.124838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.097742 restraints weight = 25211.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.097988 restraints weight = 21526.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.098847 restraints weight = 23242.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.099345 restraints weight = 15961.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.099628 restraints weight = 14164.441| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2062 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= 0.124 Angle : 0.702 33.737 19227 Z= 0.304 Chirality : 0.041 0.266 2259 Planarity : 0.004 0.038 2377 Dihedral : 16.939 175.849 2229 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.88 % Allowed : 20.08 % Favored : 77.05 % 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: -0.49 (0.22), residues: 1645 helix: 1.16 (0.18), residues: 880 sheet: -1.80 (0.49), residues: 124 loop : -2.19 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 358 TYR 0.020 0.001 TYR A 200 PHE 0.010 0.001 PHE B 302 TRP 0.020 0.001 TRP B 497 HIS 0.004 0.001 HIS A 872 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (14001) covalent geometry : angle 0.59962 / 0.30 (19215) hydrogen bonds : bond 0.03443 / 2.31 ( 579) hydrogen bonds : angle 3.84282 / 2.72 ( 1696) metal coordination : bond 0.00466 / 0.22 ( 4) metal coordination : angle 14.61746 / 11.50 ( 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 143 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.481 Fit side-chains REVERT: B 270 GLN cc_start: 0.6711 (pm20) cc_final: 0.6379 (pt0) REVERT: B 353 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8702 (mp) REVERT: B 581 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7507 (tm-30) REVERT: A 483 ASP cc_start: 0.8099 (m-30) cc_final: 0.7865 (m-30) REVERT: A 525 TRP cc_start: 0.7812 (t60) cc_final: 0.7252 (t60) outliers start: 38 outliers final: 29 residues processed: 137 average time/residue: 0.0931 time to fit residues: 19.9171 Evaluate side-chains 125 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 353 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 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 338 HIS 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 880 THR 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: 3.9990 chunk 84 optimal weight: 0.7980 chunk 121 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 158 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 132 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 0.3980 chunk 63 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.125960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.099246 restraints weight = 25343.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.098213 restraints weight = 21800.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.099269 restraints weight = 24039.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.099953 restraints weight = 16167.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.100208 restraints weight = 14505.285| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14005 Z= 0.114 Angle : 0.693 32.639 19227 Z= 0.300 Chirality : 0.041 0.267 2259 Planarity : 0.004 0.038 2377 Dihedral : 16.870 175.479 2229 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.27 % Allowed : 21.14 % Favored : 76.59 % 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: -0.38 (0.22), residues: 1645 helix: 1.25 (0.18), residues: 880 sheet: -1.75 (0.49), residues: 124 loop : -2.15 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 94 TYR 0.018 0.001 TYR A 200 PHE 0.008 0.001 PHE A 879 TRP 0.018 0.001 TRP B 497 HIS 0.005 0.001 HIS A 872 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (14001) covalent geometry : angle 0.59361 / 0.30 (19215) hydrogen bonds : bond 0.03258 / 2.19 ( 579) hydrogen bonds : angle 3.76267 / 2.66 ( 1696) metal coordination : bond 0.00427 / 0.21 ( 4) metal coordination : angle 14.34722 / 11.37 ( 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 139 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.485 Fit side-chains REVERT: B 270 GLN cc_start: 0.6863 (pm20) cc_final: 0.6223 (pt0) REVERT: B 353 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8700 (mp) REVERT: B 581 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7485 (tm-30) REVERT: A 483 ASP cc_start: 0.8119 (m-30) cc_final: 0.7873 (m-30) REVERT: A 525 TRP cc_start: 0.7827 (t60) cc_final: 0.7265 (t60) outliers start: 30 outliers final: 27 residues processed: 135 average time/residue: 0.1009 time to fit residues: 21.3183 Evaluate side-chains 128 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 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 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 353 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 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 357 THR Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 880 THR 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: 0.9990 chunk 130 optimal weight: 0.0010 chunk 160 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 114 optimal weight: 0.2980 chunk 105 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 34 optimal weight: 0.0170 chunk 20 optimal weight: 0.9980 overall best weight: 0.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.127106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.100857 restraints weight = 25139.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.100010 restraints weight = 22239.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.101070 restraints weight = 24132.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.101672 restraints weight = 16240.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.101922 restraints weight = 14876.032| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14005 Z= 0.111 Angle : 0.694 31.664 19227 Z= 0.303 Chirality : 0.040 0.268 2259 Planarity : 0.004 0.037 2377 Dihedral : 16.810 175.287 2229 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.20 % Allowed : 21.21 % Favored : 76.59 % 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: -0.28 (0.22), residues: 1645 helix: 1.33 (0.18), residues: 877 sheet: -1.70 (0.49), residues: 124 loop : -2.09 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 521 TYR 0.014 0.001 TYR A 200 PHE 0.008 0.001 PHE A 879 TRP 0.016 0.001 TRP B 497 HIS 0.005 0.001 HIS A 872 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (14001) covalent geometry : angle 0.59843 / 0.30 (19215) hydrogen bonds : bond 0.03167 / 2.12 ( 579) hydrogen bonds : angle 3.69694 / 2.61 ( 1696) metal coordination : bond 0.00465 / 0.24 ( 4) metal coordination : angle 14.06608 / 11.20 ( 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 136 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.348 Fit side-chains REVERT: B 270 GLN cc_start: 0.6745 (pm20) cc_final: 0.6206 (pt0) REVERT: B 353 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8705 (mp) REVERT: B 581 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7458 (tm-30) REVERT: A 525 TRP cc_start: 0.7622 (t60) cc_final: 0.7167 (t60) outliers start: 29 outliers final: 27 residues processed: 132 average time/residue: 0.0884 time to fit residues: 18.7692 Evaluate side-chains 128 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 353 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 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 357 THR Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 880 THR 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: 0.8980 chunk 44 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.126299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.100064 restraints weight = 25255.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.099235 restraints weight = 22281.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.100589 restraints weight = 23749.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.101204 restraints weight = 16047.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.101571 restraints weight = 14493.263| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14005 Z= 0.121 Angle : 0.696 31.938 19227 Z= 0.303 Chirality : 0.041 0.273 2259 Planarity : 0.004 0.038 2377 Dihedral : 16.793 175.563 2229 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.12 % Allowed : 21.36 % Favored : 76.52 % 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: -0.23 (0.22), residues: 1645 helix: 1.36 (0.18), residues: 879 sheet: -1.69 (0.49), residues: 124 loop : -2.06 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 127 TYR 0.025 0.001 TYR A 522 PHE 0.009 0.001 PHE B 685 TRP 0.019 0.001 TRP B 497 HIS 0.004 0.001 HIS A 872 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (14001) covalent geometry : angle 0.59970 / 0.30 (19215) hydrogen bonds : bond 0.03263 / 2.20 ( 579) hydrogen bonds : angle 3.71489 / 2.62 ( 1696) metal coordination : bond 0.00405 / 0.19 ( 4) metal coordination : angle 14.14270 / 11.23 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1692.84 seconds wall clock time: 30 minutes 3.10 seconds (1803.10 seconds total)