Starting phenix.real_space_refine on Mon Dec 30 19:15:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sjr_25164/12_2024/7sjr_25164.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sjr_25164/12_2024/7sjr_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_25164/12_2024/7sjr_25164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sjr_25164/12_2024/7sjr_25164.map" model { file = "/net/cci-nas-00/data/ceres_data/7sjr_25164/12_2024/7sjr_25164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sjr_25164/12_2024/7sjr_25164.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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, 'ARG:plan': 1, 'ASP:plan': 5} 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: 8.07, per 1000 atoms: 0.59 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: 3.65 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 4.58 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: 4.62 Time building geometry restraints manager: 4.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 5700 1.42 - 1.64: 8222 1.64 - 1.85: 67 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 14001 Sorted by residual: bond pdb=" O3A ANP A1103 " pdb=" PB ANP A1103 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.29e+01 bond pdb=" N3B ANP A1103 " pdb=" PG ANP A1103 " ideal model delta sigma weight residual 1.795 1.689 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" O5' ANP A1103 " pdb=" PA ANP A1103 " ideal model delta sigma weight residual 1.655 1.578 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" O3G ANP A1103 " pdb=" PG ANP A1103 " ideal model delta sigma weight residual 1.528 1.578 -0.050 2.00e-02 2.50e+03 6.25e+00 bond pdb=" O2B ANP A1103 " pdb=" PB ANP A1103 " ideal model delta sigma weight residual 1.508 1.555 -0.047 2.00e-02 2.50e+03 5.46e+00 ... (remaining 13996 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.11: 19141 4.11 - 8.22: 68 8.22 - 12.33: 5 12.33 - 16.44: 0 16.44 - 20.54: 1 Bond angle restraints: 19215 Sorted by residual: angle pdb=" PB ANP A1103 " pdb=" N3B ANP A1103 " pdb=" PG ANP A1103 " ideal model delta sigma weight residual 126.95 106.41 20.54 3.00e+00 1.11e-01 4.69e+01 angle pdb=" C VAL B 643 " pdb=" N GLU B 644 " pdb=" CA GLU B 644 " ideal model delta sigma weight residual 123.93 131.87 -7.94 1.54e+00 4.22e-01 2.66e+01 angle pdb=" O1B ANP A1103 " pdb=" PB ANP A1103 " pdb=" O2B ANP A1103 " ideal model delta sigma weight residual 120.08 108.69 11.39 3.00e+00 1.11e-01 1.44e+01 angle pdb=" C GLU B 807 " pdb=" N HIS B 808 " pdb=" CA HIS B 808 " ideal model delta sigma weight residual 121.54 128.54 -7.00 1.91e+00 2.74e-01 1.34e+01 angle pdb=" N GLY B 804 " pdb=" CA GLY B 804 " pdb=" C GLY B 804 " ideal model delta sigma weight residual 111.12 117.51 -6.39 1.89e+00 2.80e-01 1.14e+01 ... (remaining 19210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 8082 35.86 - 71.71: 255 71.71 - 107.57: 18 107.57 - 143.43: 1 143.43 - 179.28: 7 Dihedral angle restraints: 8363 sinusoidal: 3484 harmonic: 4879 Sorted by residual: dihedral pdb=" CA SER B 783 " pdb=" C SER B 783 " pdb=" N GLU B 784 " pdb=" CA GLU B 784 " ideal model delta harmonic sigma weight residual 180.00 155.09 24.91 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA GLN A 472 " pdb=" C GLN A 472 " pdb=" N PRO A 473 " pdb=" CA PRO A 473 " ideal model delta harmonic sigma weight residual 180.00 155.23 24.77 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" O1A ANP A1103 " pdb=" O3A ANP A1103 " pdb=" PA ANP A1103 " pdb=" PB ANP A1103 " ideal model delta sinusoidal sigma weight residual 83.11 -90.53 173.64 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 8360 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1869 0.056 - 0.113: 343 0.113 - 0.169: 44 0.169 - 0.225: 2 0.225 - 0.281: 1 Chirality restraints: 2259 Sorted by residual: chirality pdb=" C3' ANP A1103 " pdb=" C2' ANP A1103 " pdb=" C4' ANP A1103 " pdb=" O3' ANP A1103 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CB ILE B 395 " pdb=" CA ILE B 395 " pdb=" CG1 ILE B 395 " pdb=" CG2 ILE B 395 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.65e-01 chirality pdb=" CB ILE A 450 " pdb=" CA ILE A 450 " pdb=" CG1 ILE A 450 " pdb=" CG2 ILE A 450 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.38e-01 ... (remaining 2256 not shown) Planarity restraints: 2377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 497 " 0.018 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP B 497 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP B 497 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP B 497 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 497 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 497 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 497 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 497 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 497 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 497 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 781 " 0.043 5.00e-02 4.00e+02 6.60e-02 6.96e+00 pdb=" N PRO B 782 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 782 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 782 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 357 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.09e+00 pdb=" C TRP B 357 " -0.043 2.00e-02 2.50e+03 pdb=" O TRP B 357 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG B 358 " 0.014 2.00e-02 2.50e+03 ... (remaining 2374 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 101 2.50 - 3.10: 10216 3.10 - 3.70: 20544 3.70 - 4.30: 27264 4.30 - 4.90: 45197 Nonbonded interactions: 103322 Sorted by model distance: nonbonded pdb=" NE2 HIS A 833 " pdb="MG MG A1101 " model vdw 1.895 2.250 nonbonded pdb=" OD2 ASP A 920 " pdb="MG MG A1101 " model vdw 2.051 2.170 nonbonded pdb=" O VAL A 624 " pdb=" OG SER A 701 " model vdw 2.200 3.040 nonbonded pdb=" OG1 THR A 348 " pdb=" OG1 THR A 712 " model vdw 2.211 3.040 nonbonded pdb=" OG1 THR B 689 " pdb=" OE1 GLN B 690 " model vdw 2.225 3.040 ... (remaining 103317 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 37.940 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.145 14001 Z= 0.357 Angle : 0.787 20.544 19215 Z= 0.419 Chirality : 0.045 0.281 2259 Planarity : 0.005 0.066 2377 Dihedral : 17.634 179.282 5183 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 0.08 % Allowed : 0.53 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.21), 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 TRP 0.053 0.002 TRP B 497 HIS 0.007 0.001 HIS B 665 PHE 0.021 0.002 PHE B 685 TYR 0.016 0.002 TYR A 200 ARG 0.014 0.001 ARG B 572 *********************** 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 : 1.452 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: 0.2594 time to fit residues: 52.7619 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 : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 6.9990 chunk 131 optimal weight: 0.2980 chunk 73 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 52 optimal weight: 0.5980 chunk 82 optimal weight: 6.9990 chunk 101 optimal weight: 20.0000 chunk 158 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 HIS ** B 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14001 Z= 0.272 Angle : 0.684 9.984 19215 Z= 0.349 Chirality : 0.043 0.164 2259 Planarity : 0.005 0.048 2377 Dihedral : 17.271 178.738 2257 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 1.36 % Allowed : 9.55 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.21), residues: 1645 helix: 0.54 (0.18), residues: 862 sheet: -2.00 (0.48), residues: 124 loop : -2.43 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 497 HIS 0.006 0.001 HIS B 665 PHE 0.015 0.002 PHE B 685 TYR 0.028 0.002 TYR A 522 ARG 0.004 0.000 ARG B 128 *********************** 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 135 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 1.546 Fit side-chains REVERT: A 674 MET cc_start: 0.8016 (tmm) cc_final: 0.7661 (tmm) REVERT: A 677 MET cc_start: 0.8160 (mtp) cc_final: 0.7873 (mtp) outliers start: 18 outliers final: 12 residues processed: 131 average time/residue: 0.2303 time to fit residues: 47.1956 Evaluate side-chains 104 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 808 HIS Chi-restraints excluded: chain A residue 357 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 171 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 GLN A 122 GLN A 775 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14001 Z= 0.312 Angle : 0.668 11.123 19215 Z= 0.340 Chirality : 0.043 0.172 2259 Planarity : 0.005 0.044 2377 Dihedral : 17.190 179.634 2257 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 2.42 % Allowed : 14.17 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.21), residues: 1645 helix: 0.63 (0.18), residues: 869 sheet: -1.99 (0.48), residues: 128 loop : -2.42 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 497 HIS 0.009 0.001 HIS B 625 PHE 0.015 0.002 PHE B 685 TYR 0.013 0.002 TYR A 200 ARG 0.003 0.000 ARG B 572 *********************** 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 133 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 1.504 Fit side-chains revert: symmetry clash REVERT: B 301 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8710 (mp) REVERT: A 533 LEU cc_start: 0.8649 (pt) cc_final: 0.8319 (mt) REVERT: A 674 MET cc_start: 0.8059 (tmm) cc_final: 0.7658 (tmm) REVERT: A 677 MET cc_start: 0.8210 (mtp) cc_final: 0.7865 (mtp) outliers start: 32 outliers final: 18 residues processed: 128 average time/residue: 0.2607 time to fit residues: 50.6148 Evaluate side-chains 108 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 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 681 SER Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 357 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.7980 chunk 119 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 75 optimal weight: 0.0980 chunk 106 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 168 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14001 Z= 0.193 Angle : 0.595 11.203 19215 Z= 0.302 Chirality : 0.040 0.147 2259 Planarity : 0.004 0.039 2377 Dihedral : 16.908 178.313 2257 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.95 % Allowed : 15.91 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.21), residues: 1645 helix: 0.87 (0.18), residues: 871 sheet: -1.90 (0.50), residues: 119 loop : -2.32 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 497 HIS 0.005 0.001 HIS B 625 PHE 0.010 0.001 PHE A 879 TYR 0.014 0.001 TYR A 200 ARG 0.003 0.000 ARG A 657 *********************** 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 157 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 118 time to evaluate : 1.512 Fit side-chains revert: symmetry clash REVERT: B 581 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7538 (tm-30) REVERT: A 533 LEU cc_start: 0.8726 (pt) cc_final: 0.8484 (mp) REVERT: A 674 MET cc_start: 0.8001 (tmm) cc_final: 0.7766 (tmm) REVERT: A 677 MET cc_start: 0.8244 (mtp) cc_final: 0.7961 (mtp) outliers start: 39 outliers final: 21 residues processed: 152 average time/residue: 0.2181 time to fit residues: 51.7503 Evaluate side-chains 118 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain A residue 357 THR 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 95 optimal weight: 8.9990 chunk 2 optimal weight: 0.0070 chunk 125 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 150 optimal weight: 9.9990 chunk 42 optimal weight: 0.0030 chunk 56 optimal weight: 4.9990 overall best weight: 2.0012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14001 Z= 0.255 Angle : 0.614 11.611 19215 Z= 0.311 Chirality : 0.041 0.175 2259 Planarity : 0.004 0.042 2377 Dihedral : 16.904 176.466 2257 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.50 % Allowed : 18.64 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.21), residues: 1645 helix: 0.96 (0.18), residues: 873 sheet: -1.75 (0.50), residues: 119 loop : -2.30 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 497 HIS 0.005 0.001 HIS B 665 PHE 0.012 0.001 PHE B 685 TYR 0.017 0.001 TYR A 200 ARG 0.003 0.000 ARG B 276 *********************** 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 137 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 1.364 Fit side-chains REVERT: B 270 GLN cc_start: 0.6947 (pm20) cc_final: 0.6491 (pt0) REVERT: B 353 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8732 (mp) REVERT: B 581 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7622 (tm-30) REVERT: A 483 ASP cc_start: 0.8072 (m-30) cc_final: 0.7863 (m-30) REVERT: A 674 MET cc_start: 0.8008 (tmm) cc_final: 0.7646 (tmm) REVERT: A 677 MET cc_start: 0.8287 (mtp) cc_final: 0.7889 (mtp) outliers start: 33 outliers final: 26 residues processed: 130 average time/residue: 0.2506 time to fit residues: 50.2938 Evaluate side-chains 123 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 1.578 ------------------------------------------------------------------------------- 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 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 526 ASP Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 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 1014 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 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 : 0.004 0.038 14001 Z= 0.250 Angle : 0.604 11.538 19215 Z= 0.306 Chirality : 0.040 0.164 2259 Planarity : 0.004 0.043 2377 Dihedral : 16.852 176.621 2257 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.71 % Allowed : 18.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.22), residues: 1645 helix: 1.07 (0.18), residues: 879 sheet: -1.73 (0.49), residues: 129 loop : -2.24 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 497 HIS 0.004 0.001 HIS A 872 PHE 0.013 0.001 PHE B 685 TYR 0.018 0.001 TYR A 200 ARG 0.009 0.000 ARG A 736 *********************** 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 154 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 105 time to evaluate : 1.596 Fit side-chains REVERT: B 353 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8714 (mp) REVERT: B 581 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7541 (tm-30) REVERT: A 183 ARG cc_start: 0.7522 (mpp80) cc_final: 0.7282 (mtp85) REVERT: A 525 TRP cc_start: 0.7741 (t60) cc_final: 0.7201 (t60) REVERT: A 674 MET cc_start: 0.8024 (tmm) cc_final: 0.7638 (tmm) outliers start: 49 outliers final: 33 residues processed: 146 average time/residue: 0.2469 time to fit residues: 55.8163 Evaluate side-chains 129 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 95 time to evaluate : 1.528 ------------------------------------------------------------------------------- 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 275 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 526 ASP Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 278 THR 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 461 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 103 optimal weight: 9.9990 chunk 66 optimal weight: 0.2980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14001 Z= 0.224 Angle : 0.603 11.340 19215 Z= 0.304 Chirality : 0.040 0.218 2259 Planarity : 0.004 0.043 2377 Dihedral : 16.793 176.407 2257 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.95 % Allowed : 20.08 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.22), residues: 1645 helix: 1.14 (0.18), residues: 879 sheet: -1.71 (0.49), residues: 130 loop : -2.23 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 497 HIS 0.004 0.001 HIS A 872 PHE 0.012 0.001 PHE B 685 TYR 0.017 0.001 TYR A 200 ARG 0.006 0.000 ARG A 736 *********************** 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 146 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 107 time to evaluate : 1.435 Fit side-chains REVERT: B 270 GLN cc_start: 0.6728 (pm20) cc_final: 0.6370 (pt0) REVERT: B 353 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8703 (mp) REVERT: B 581 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7517 (tm-30) REVERT: A 183 ARG cc_start: 0.7538 (mpp80) cc_final: 0.7294 (mtp85) REVERT: A 674 MET cc_start: 0.8041 (tmm) cc_final: 0.7647 (tmm) REVERT: A 677 MET cc_start: 0.8282 (mtp) cc_final: 0.8026 (mtp) outliers start: 39 outliers final: 30 residues processed: 142 average time/residue: 0.2452 time to fit residues: 53.7560 Evaluate side-chains 130 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 1.570 ------------------------------------------------------------------------------- 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 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 612 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 118 THR Chi-restraints excluded: chain A residue 278 THR 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 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 100 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 131 optimal weight: 6.9990 chunk 152 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14001 Z= 0.228 Angle : 0.604 11.338 19215 Z= 0.304 Chirality : 0.040 0.193 2259 Planarity : 0.004 0.044 2377 Dihedral : 16.777 176.362 2257 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.41 % Allowed : 20.45 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.22), residues: 1645 helix: 1.20 (0.18), residues: 878 sheet: -1.69 (0.49), residues: 130 loop : -2.20 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 497 HIS 0.004 0.001 HIS A 872 PHE 0.012 0.001 PHE B 685 TYR 0.015 0.001 TYR A 200 ARG 0.004 0.000 ARG A 736 *********************** 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 146 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 101 time to evaluate : 1.487 Fit side-chains REVERT: B 270 GLN cc_start: 0.6877 (pm20) cc_final: 0.6387 (pt0) REVERT: B 353 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8699 (mp) REVERT: B 581 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7505 (tm-30) REVERT: B 767 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8919 (pp) REVERT: A 183 ARG cc_start: 0.7562 (mpp80) cc_final: 0.7356 (mtp85) REVERT: A 204 MET cc_start: 0.7199 (tpp) cc_final: 0.6690 (tpp) REVERT: A 525 TRP cc_start: 0.7728 (t60) cc_final: 0.7230 (t60) REVERT: A 632 MET cc_start: 0.7569 (mmm) cc_final: 0.7210 (mmt) REVERT: A 674 MET cc_start: 0.8040 (tmm) cc_final: 0.7641 (tmm) REVERT: A 677 MET cc_start: 0.8276 (mtp) cc_final: 0.7983 (mtp) outliers start: 45 outliers final: 36 residues processed: 139 average time/residue: 0.2250 time to fit residues: 49.0575 Evaluate side-chains 132 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 94 time to evaluate : 1.459 ------------------------------------------------------------------------------- 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 275 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 433 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 612 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 B residue 767 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 278 THR 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 461 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 880 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 645 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14001 Z= 0.289 Angle : 0.641 11.313 19215 Z= 0.321 Chirality : 0.041 0.179 2259 Planarity : 0.005 0.043 2377 Dihedral : 16.843 176.903 2257 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.11 % Allowed : 20.61 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.22), residues: 1645 helix: 1.17 (0.18), residues: 875 sheet: -1.75 (0.49), residues: 130 loop : -2.24 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 497 HIS 0.004 0.001 HIS B 665 PHE 0.014 0.001 PHE B 302 TYR 0.031 0.002 TYR A 522 ARG 0.004 0.000 ARG A 736 *********************** 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 138 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 97 time to evaluate : 1.375 Fit side-chains REVERT: B 270 GLN cc_start: 0.6946 (pm20) cc_final: 0.6544 (pt0) REVERT: B 581 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7541 (tm-30) REVERT: A 183 ARG cc_start: 0.7570 (mpp80) cc_final: 0.7350 (mtp85) REVERT: A 204 MET cc_start: 0.7214 (tpp) cc_final: 0.6693 (tpp) REVERT: A 525 TRP cc_start: 0.7703 (t60) cc_final: 0.7228 (t60) REVERT: A 632 MET cc_start: 0.7571 (mmm) cc_final: 0.7181 (mmt) REVERT: A 674 MET cc_start: 0.8072 (tmm) cc_final: 0.7540 (tmm) REVERT: A 677 MET cc_start: 0.8310 (mtp) cc_final: 0.8021 (mtp) outliers start: 41 outliers final: 37 residues processed: 133 average time/residue: 0.2253 time to fit residues: 47.0553 Evaluate side-chains 132 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 95 time to evaluate : 1.403 ------------------------------------------------------------------------------- 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 275 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 612 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 695 LEU 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 278 THR 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 461 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 880 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 114 optimal weight: 0.9990 chunk 173 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 84 optimal weight: 0.5980 chunk 109 optimal weight: 5.9990 chunk 147 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14001 Z= 0.199 Angle : 0.603 11.223 19215 Z= 0.301 Chirality : 0.040 0.182 2259 Planarity : 0.004 0.043 2377 Dihedral : 16.749 176.097 2257 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.65 % Allowed : 21.21 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.22), residues: 1645 helix: 1.28 (0.18), residues: 878 sheet: -1.66 (0.49), residues: 130 loop : -2.16 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 497 HIS 0.004 0.001 HIS A 872 PHE 0.010 0.001 PHE B 685 TYR 0.017 0.001 TYR A 200 ARG 0.004 0.000 ARG A 736 ********************** 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 140 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 1.436 Fit side-chains REVERT: B 270 GLN cc_start: 0.6883 (pm20) cc_final: 0.6502 (pt0) REVERT: B 581 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7475 (tm-30) REVERT: B 767 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8914 (pp) REVERT: A 204 MET cc_start: 0.7364 (tpp) cc_final: 0.6804 (tpp) REVERT: A 525 TRP cc_start: 0.7714 (t60) cc_final: 0.7268 (t60) REVERT: A 632 MET cc_start: 0.7606 (mmm) cc_final: 0.7259 (mmt) REVERT: A 674 MET cc_start: 0.8028 (tmm) cc_final: 0.7691 (tmm) REVERT: A 677 MET cc_start: 0.8265 (mtp) cc_final: 0.7956 (mtp) outliers start: 35 outliers final: 32 residues processed: 136 average time/residue: 0.2203 time to fit residues: 46.7029 Evaluate side-chains 129 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 96 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 397 CYS Chi-restraints excluded: chain B residue 416 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 625 HIS Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 730 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 278 THR 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 720 LEU Chi-restraints excluded: chain A residue 880 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 141 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.125166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.098634 restraints weight = 25056.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.097331 restraints weight = 22485.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.098629 restraints weight = 23375.527| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14001 Z= 0.188 Angle : 0.590 11.093 19215 Z= 0.295 Chirality : 0.039 0.177 2259 Planarity : 0.004 0.044 2377 Dihedral : 16.681 176.070 2257 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.73 % Allowed : 21.36 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.22), residues: 1645 helix: 1.37 (0.18), residues: 881 sheet: -1.65 (0.50), residues: 124 loop : -2.09 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 497 HIS 0.004 0.001 HIS A 872 PHE 0.009 0.001 PHE B 685 TYR 0.027 0.001 TYR A 522 ARG 0.004 0.000 ARG A 736 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2156.19 seconds wall clock time: 40 minutes 37.43 seconds (2437.43 seconds total)