Starting phenix.real_space_refine on Wed May 14 23:12:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dgd_30671/05_2025/7dgd_30671_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dgd_30671/05_2025/7dgd_30671.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dgd_30671/05_2025/7dgd_30671.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dgd_30671/05_2025/7dgd_30671.map" model { file = "/net/cci-nas-00/data/ceres_data/7dgd_30671/05_2025/7dgd_30671_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dgd_30671/05_2025/7dgd_30671_neut.cif" } resolution = 3.96 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= -0.001 sd= 0.022 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: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 7958 2.51 5 N 2074 2.21 5 O 2251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 6194 Classifications: {'peptide': 786} Link IDs: {'PTRANS': 34, 'TRANS': 751} Chain breaks: 1 Chain: "B" Number of atoms: 6187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 6187 Classifications: {'peptide': 786} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 751} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 7.14, per 1000 atoms: 0.58 Number of scatterers: 12381 At special positions: 0 Unit cell: (119.85, 95.88, 186.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 98 16.00 O 2251 8.00 N 2074 7.00 C 7958 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 67 " - pdb=" SG CYS A 109 " distance=2.04 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 291 " distance=2.05 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS A 432 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 544 " distance=2.04 Simple disulfide: pdb=" SG CYS A 528 " - pdb=" SG CYS A 547 " distance=2.03 Simple disulfide: pdb=" SG CYS A 550 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 565 " - pdb=" SG CYS A 578 " distance=2.04 Simple disulfide: pdb=" SG CYS A 657 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B 67 " - pdb=" SG CYS B 109 " distance=2.04 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 394 " distance=2.04 Simple disulfide: pdb=" SG CYS B 432 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 544 " distance=2.05 Simple disulfide: pdb=" SG CYS B 528 " - pdb=" SG CYS B 547 " distance=2.04 Simple disulfide: pdb=" SG CYS B 550 " - pdb=" SG CYS B 562 " distance=2.05 Simple disulfide: pdb=" SG CYS B 565 " - pdb=" SG CYS B 578 " distance=2.03 Simple disulfide: pdb=" SG CYS B 657 " - pdb=" SG CYS B 746 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.7 seconds 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2944 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 15 sheets defined 46.7% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.886A pdb=" N GLU A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 92 removed outlier: 4.469A pdb=" N LEU A 86 " --> pdb=" O MET A 82 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 132 removed outlier: 4.010A pdb=" N GLU A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE A 122 " --> pdb=" O GLN A 118 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 176 removed outlier: 4.563A pdb=" N LEU A 174 " --> pdb=" O GLN A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 removed outlier: 3.719A pdb=" N LEU A 192 " --> pdb=" O SER A 189 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP A 194 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 221 removed outlier: 3.954A pdb=" N GLN A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 249 removed outlier: 4.037A pdb=" N GLU A 238 " --> pdb=" O GLY A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 292 through 306 Processing helix chain 'A' and resid 317 through 321 removed outlier: 3.690A pdb=" N ALA A 321 " --> pdb=" O ASP A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 355 removed outlier: 4.102A pdb=" N ASP A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TYR A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 357 No H-bonds generated for 'chain 'A' and resid 356 through 357' Processing helix chain 'A' and resid 358 through 362 removed outlier: 4.004A pdb=" N ASN A 362 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 407 through 409 No H-bonds generated for 'chain 'A' and resid 407 through 409' Processing helix chain 'A' and resid 410 through 422 removed outlier: 4.054A pdb=" N ILE A 414 " --> pdb=" O MET A 410 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 431 removed outlier: 3.911A pdb=" N HIS A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 456 removed outlier: 4.065A pdb=" N ASP A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 576 removed outlier: 4.001A pdb=" N THR A 576 " --> pdb=" O ALA A 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 573 through 576' Processing helix chain 'A' and resid 593 through 615 removed outlier: 3.616A pdb=" N ILE A 613 " --> pdb=" O PHE A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 626 Processing helix chain 'A' and resid 627 through 649 removed outlier: 4.305A pdb=" N CYS A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) Proline residue: A 645 - end of helix removed outlier: 3.799A pdb=" N ILE A 649 " --> pdb=" O PRO A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 689 removed outlier: 3.563A pdb=" N SER A 668 " --> pdb=" O VAL A 664 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 685 " --> pdb=" O ARG A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 713 removed outlier: 4.299A pdb=" N LEU A 713 " --> pdb=" O ILE A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 728 removed outlier: 4.310A pdb=" N GLN A 717 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU A 718 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET A 727 " --> pdb=" O THR A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 770 removed outlier: 3.662A pdb=" N VAL A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) Proline residue: A 756 - end of helix Processing helix chain 'A' and resid 772 through 776 removed outlier: 3.910A pdb=" N ARG A 775 " --> pdb=" O PHE A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 808 removed outlier: 3.790A pdb=" N TYR A 786 " --> pdb=" O ASN A 782 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE A 797 " --> pdb=" O THR A 793 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL A 802 " --> pdb=" O TRP A 798 " (cutoff:3.500A) Proline residue: A 803 - end of helix Processing helix chain 'A' and resid 810 through 837 removed outlier: 4.024A pdb=" N THR A 814 " --> pdb=" O TYR A 810 " (cutoff:3.500A) Proline residue: A 833 - end of helix Processing helix chain 'B' and resid 75 through 87 removed outlier: 3.597A pdb=" N VAL B 79 " --> pdb=" O GLY B 75 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA B 81 " --> pdb=" O GLN B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 125 through 132 Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 207 through 220 removed outlier: 3.765A pdb=" N GLN B 211 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B 219 " --> pdb=" O MET B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 252 Processing helix chain 'B' and resid 266 through 278 removed outlier: 3.626A pdb=" N LEU B 274 " --> pdb=" O PHE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 307 removed outlier: 3.711A pdb=" N VAL B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 Processing helix chain 'B' and resid 347 through 356 removed outlier: 3.790A pdb=" N ASP B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR B 353 " --> pdb=" O SER B 349 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS B 356 " --> pdb=" O ASP B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 377 Processing helix chain 'B' and resid 409 through 431 removed outlier: 4.019A pdb=" N ILE B 414 " --> pdb=" O MET B 410 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN B 415 " --> pdb=" O GLY B 411 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N HIS B 429 " --> pdb=" O GLN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 455 Processing helix chain 'B' and resid 509 through 512 Processing helix chain 'B' and resid 572 through 576 removed outlier: 4.061A pdb=" N THR B 576 " --> pdb=" O ALA B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 613 removed outlier: 4.038A pdb=" N ALA B 596 " --> pdb=" O GLU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 649 removed outlier: 4.064A pdb=" N CYS B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU B 635 " --> pdb=" O CYS B 631 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU B 640 " --> pdb=" O ALA B 636 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY B 641 " --> pdb=" O GLY B 637 " (cutoff:3.500A) Proline residue: B 645 - end of helix removed outlier: 3.801A pdb=" N ILE B 649 " --> pdb=" O PRO B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 689 removed outlier: 4.409A pdb=" N SER B 667 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N SER B 668 " --> pdb=" O VAL B 664 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU B 675 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE B 682 " --> pdb=" O LYS B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 726 removed outlier: 3.585A pdb=" N ILE B 708 " --> pdb=" O TRP B 704 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B 713 " --> pdb=" O ILE B 709 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL B 721 " --> pdb=" O GLN B 717 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU B 724 " --> pdb=" O LEU B 720 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE B 725 " --> pdb=" O VAL B 721 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE B 726 " --> pdb=" O VAL B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 755 Processing helix chain 'B' and resid 756 through 770 removed outlier: 4.109A pdb=" N LEU B 762 " --> pdb=" O GLY B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 800 removed outlier: 3.915A pdb=" N ILE B 796 " --> pdb=" O TYR B 792 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE B 797 " --> pdb=" O THR B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 808 removed outlier: 4.118A pdb=" N ILE B 804 " --> pdb=" O ALA B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 829 removed outlier: 4.081A pdb=" N VAL B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA B 826 " --> pdb=" O SER B 822 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 827 " --> pdb=" O VAL B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 839 Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 41 removed outlier: 6.631A pdb=" N VAL A 45 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLU A 104 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE A 47 " --> pdb=" O GLU A 104 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE A 46 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLY A 158 " --> pdb=" O ILE A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 182 through 184 removed outlier: 3.538A pdb=" N LEU A 202 " --> pdb=" O GLN A 182 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 229 through 231 removed outlier: 6.974A pdb=" N VAL A 230 " --> pdb=" O PHE A 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 337 through 342 removed outlier: 3.866A pdb=" N GLY A 337 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET A 482 " --> pdb=" O THR A 339 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TYR A 479 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N THR A 499 " --> pdb=" O TYR A 479 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE A 481 " --> pdb=" O VAL A 497 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 533 through 535 Processing sheet with id=AA6, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA7, first strand: chain 'A' and resid 569 through 571 removed outlier: 4.371A pdb=" N TRP A 570 " --> pdb=" O GLU A 579 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A 579 " --> pdb=" O TRP A 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 41 removed outlier: 6.424A pdb=" N VAL B 45 " --> pdb=" O GLY B 102 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N GLU B 104 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE B 47 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ILE B 46 " --> pdb=" O GLY B 158 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N ILE B 160 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY B 48 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N ILE B 183 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL B 159 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLN B 182 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 254 through 258 removed outlier: 6.145A pdb=" N VAL B 227 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N HIS B 257 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N VAL B 288 " --> pdb=" O TYR B 226 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N SER B 228 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N PHE B 290 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL B 230 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL B 287 " --> pdb=" O ILE B 315 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 341 through 342 removed outlier: 3.513A pdb=" N LYS B 341 " --> pdb=" O ASP B 480 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 458 through 460 removed outlier: 3.642A pdb=" N PHE B 459 " --> pdb=" O VAL B 467 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL B 467 " --> pdb=" O PHE B 459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 484 through 486 Processing sheet with id=AB4, first strand: chain 'B' and resid 533 through 535 Processing sheet with id=AB5, first strand: chain 'B' and resid 554 through 558 removed outlier: 3.868A pdb=" N GLN B 557 " --> pdb=" O THR B 561 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N THR B 561 " --> pdb=" O GLN B 557 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 732 through 733 removed outlier: 3.584A pdb=" N ILE B 733 " --> pdb=" O ILE B 745 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE B 745 " --> pdb=" O ILE B 733 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 469 hydrogen bonds defined for protein. 1371 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.42 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2753 1.34 - 1.47: 3594 1.47 - 1.59: 6173 1.59 - 1.71: 0 1.71 - 1.84: 138 Bond restraints: 12658 Sorted by residual: bond pdb=" CD GLU B 80 " pdb=" OE1 GLU B 80 " ideal model delta sigma weight residual 1.249 1.364 -0.115 1.90e-02 2.77e+03 3.65e+01 bond pdb=" CG ASP B 208 " pdb=" OD2 ASP B 208 " ideal model delta sigma weight residual 1.249 1.361 -0.112 1.90e-02 2.77e+03 3.49e+01 bond pdb=" CA VAL A 802 " pdb=" CB VAL A 802 " ideal model delta sigma weight residual 1.537 1.557 -0.021 5.00e-03 4.00e+04 1.69e+01 bond pdb=" CA PRO B 729 " pdb=" C PRO B 729 " ideal model delta sigma weight residual 1.517 1.551 -0.034 9.30e-03 1.16e+04 1.31e+01 bond pdb=" CA VAL A 62 " pdb=" C VAL A 62 " ideal model delta sigma weight residual 1.524 1.562 -0.037 1.05e-02 9.07e+03 1.26e+01 ... (remaining 12653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 12597 2.18 - 4.36: 3778 4.36 - 6.54: 723 6.54 - 8.72: 66 8.72 - 10.91: 7 Bond angle restraints: 17171 Sorted by residual: angle pdb=" N VAL B 309 " pdb=" CA VAL B 309 " pdb=" C VAL B 309 " ideal model delta sigma weight residual 110.42 117.61 -7.19 9.60e-01 1.09e+00 5.60e+01 angle pdb=" CA ASP B 92 " pdb=" CB ASP B 92 " pdb=" CG ASP B 92 " ideal model delta sigma weight residual 112.60 119.69 -7.09 1.00e+00 1.00e+00 5.03e+01 angle pdb=" C VAL A 308 " pdb=" N VAL A 309 " pdb=" CA VAL A 309 " ideal model delta sigma weight residual 120.56 128.80 -8.24 1.26e+00 6.30e-01 4.28e+01 angle pdb=" CA ASP B 318 " pdb=" CB ASP B 318 " pdb=" CG ASP B 318 " ideal model delta sigma weight residual 112.60 119.06 -6.46 1.00e+00 1.00e+00 4.17e+01 angle pdb=" CA ASN B 387 " pdb=" CB ASN B 387 " pdb=" CG ASN B 387 " ideal model delta sigma weight residual 112.60 118.91 -6.31 1.00e+00 1.00e+00 3.98e+01 ... (remaining 17166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 6783 17.20 - 34.40: 644 34.40 - 51.60: 147 51.60 - 68.79: 41 68.79 - 85.99: 17 Dihedral angle restraints: 7632 sinusoidal: 3053 harmonic: 4579 Sorted by residual: dihedral pdb=" CB CYS A 524 " pdb=" SG CYS A 524 " pdb=" SG CYS A 544 " pdb=" CB CYS A 544 " ideal model delta sinusoidal sigma weight residual 93.00 167.38 -74.38 1 1.00e+01 1.00e-02 7.01e+01 dihedral pdb=" CA SER A 589 " pdb=" C SER A 589 " pdb=" N ASN A 590 " pdb=" CA ASN A 590 " ideal model delta harmonic sigma weight residual 180.00 142.29 37.71 0 5.00e+00 4.00e-02 5.69e+01 dihedral pdb=" CA THR A 499 " pdb=" C THR A 499 " pdb=" N TRP A 500 " pdb=" CA TRP A 500 " ideal model delta harmonic sigma weight residual 180.00 145.81 34.19 0 5.00e+00 4.00e-02 4.68e+01 ... (remaining 7629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1246 0.104 - 0.208: 533 0.208 - 0.312: 144 0.312 - 0.415: 26 0.415 - 0.519: 5 Chirality restraints: 1954 Sorted by residual: chirality pdb=" CB THR B 607 " pdb=" CA THR B 607 " pdb=" OG1 THR B 607 " pdb=" CG2 THR B 607 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.52 2.00e-01 2.50e+01 6.74e+00 chirality pdb=" CA GLU A 72 " pdb=" N GLU A 72 " pdb=" C GLU A 72 " pdb=" CB GLU A 72 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" CB THR B 611 " pdb=" CA THR B 611 " pdb=" OG1 THR B 611 " pdb=" CG2 THR B 611 " both_signs ideal model delta sigma weight residual False 2.55 2.11 0.44 2.00e-01 2.50e+01 4.87e+00 ... (remaining 1951 not shown) Planarity restraints: 2163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 353 " 0.188 2.00e-02 2.50e+03 1.04e-01 2.17e+02 pdb=" CG TYR A 353 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR A 353 " -0.093 2.00e-02 2.50e+03 pdb=" CD2 TYR A 353 " -0.082 2.00e-02 2.50e+03 pdb=" CE1 TYR A 353 " -0.057 2.00e-02 2.50e+03 pdb=" CE2 TYR A 353 " -0.068 2.00e-02 2.50e+03 pdb=" CZ TYR A 353 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 353 " 0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 672 " 0.158 2.00e-02 2.50e+03 8.39e-02 1.41e+02 pdb=" CG TYR A 672 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR A 672 " -0.085 2.00e-02 2.50e+03 pdb=" CD2 TYR A 672 " -0.070 2.00e-02 2.50e+03 pdb=" CE1 TYR A 672 " -0.033 2.00e-02 2.50e+03 pdb=" CE2 TYR A 672 " -0.045 2.00e-02 2.50e+03 pdb=" CZ TYR A 672 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR A 672 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 770 " 0.113 2.00e-02 2.50e+03 5.91e-02 6.98e+01 pdb=" CG TYR A 770 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 770 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR A 770 " -0.071 2.00e-02 2.50e+03 pdb=" CE1 TYR A 770 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 770 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 770 " 0.017 2.00e-02 2.50e+03 pdb=" OH TYR A 770 " 0.065 2.00e-02 2.50e+03 ... (remaining 2160 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 2 2.52 - 3.12: 7579 3.12 - 3.71: 19449 3.71 - 4.31: 25982 4.31 - 4.90: 42319 Nonbonded interactions: 95331 Sorted by model distance: nonbonded pdb=" O LEU B 281 " pdb=" CG ARG B 285 " model vdw 1.930 3.440 nonbonded pdb=" O LEU B 281 " pdb=" CD ARG B 285 " model vdw 2.083 3.440 nonbonded pdb=" O ARG B 521 " pdb=" N VAL B 523 " model vdw 2.569 3.120 nonbonded pdb=" OG SER B 517 " pdb=" N GLY B 518 " model vdw 2.570 3.120 nonbonded pdb=" N TRP A 570 " pdb=" O TRP A 570 " model vdw 2.587 2.496 ... (remaining 95326 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 35 through 225 or (resid 226 and (name N or name CA or nam \ e C or name O or name CB )) or resid 227 through 839)) selection = chain 'B' } 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: 0.610 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 28.170 Find NCS groups from input model: 0.360 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: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5286 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 : 0.015 0.115 12675 Z= 0.899 Angle : 2.083 10.905 17205 Z= 1.400 Chirality : 0.121 0.519 1954 Planarity : 0.013 0.104 2163 Dihedral : 15.162 85.992 4637 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.90 % Allowed : 9.21 % Favored : 89.90 % Rotamer: Outliers : 3.87 % Allowed : 8.18 % Favored : 87.95 % Cbeta Deviations : 0.68 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.20 % 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: -4.26 (0.17), residues: 1564 helix: -2.39 (0.16), residues: 662 sheet: -2.84 (0.45), residues: 99 loop : -3.28 (0.18), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.017 TRP B 320 HIS 0.022 0.004 HIS B 383 PHE 0.097 0.022 PHE B 350 TYR 0.188 0.021 TYR A 353 ARG 0.006 0.001 ARG B 285 Details of bonding type rmsd hydrogen bonds : bond 0.22300 ( 469) hydrogen bonds : angle 8.83360 ( 1371) SS BOND : bond 0.00940 ( 17) SS BOND : angle 2.02619 ( 34) covalent geometry : bond 0.01512 (12658) covalent geometry : angle 2.08284 (17171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 170 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 HIS cc_start: 0.6008 (OUTLIER) cc_final: 0.5343 (p-80) REVERT: A 420 MET cc_start: 0.6674 (tpt) cc_final: 0.6359 (tpp) REVERT: A 427 MET cc_start: 0.6341 (ttm) cc_final: 0.5973 (ttm) REVERT: A 727 MET cc_start: 0.6833 (tpt) cc_final: 0.6149 (ppp) REVERT: B 291 CYS cc_start: 0.7752 (m) cc_final: 0.7271 (m) REVERT: B 318 ASP cc_start: 0.5207 (t0) cc_final: 0.4898 (t0) outliers start: 53 outliers final: 13 residues processed: 216 average time/residue: 0.2388 time to fit residues: 73.8296 Evaluate side-chains 117 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 746 CYS Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 547 CYS Chi-restraints excluded: chain B residue 657 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 141 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 173 ASN A 182 GLN A 231 HIS A 250 GLN A 365 ASN A 387 ASN A 485 GLN A 506 ASN ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 776 ASN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN B 173 ASN B 182 GLN B 223 ASN ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 HIS ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 ASN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 809 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.144520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.108526 restraints weight = 31392.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.106960 restraints weight = 21780.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.108204 restraints weight = 18614.812| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12675 Z= 0.181 Angle : 0.814 10.044 17205 Z= 0.420 Chirality : 0.048 0.206 1954 Planarity : 0.005 0.061 2163 Dihedral : 7.424 59.594 1737 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.99 % Favored : 91.94 % Rotamer: Outliers : 4.60 % Allowed : 11.83 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.91 (0.19), residues: 1564 helix: -0.94 (0.18), residues: 680 sheet: -2.85 (0.38), residues: 124 loop : -2.73 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 500 HIS 0.006 0.001 HIS A 428 PHE 0.032 0.002 PHE A 599 TYR 0.022 0.002 TYR A 672 ARG 0.007 0.001 ARG A 304 Details of bonding type rmsd hydrogen bonds : bond 0.04993 ( 469) hydrogen bonds : angle 5.46925 ( 1371) SS BOND : bond 0.00380 ( 17) SS BOND : angle 1.77020 ( 34) covalent geometry : bond 0.00402 (12658) covalent geometry : angle 0.81102 (17171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 107 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 HIS cc_start: 0.6484 (OUTLIER) cc_final: 0.5031 (p-80) REVERT: A 90 ASN cc_start: 0.6819 (t0) cc_final: 0.6514 (t0) REVERT: A 303 MET cc_start: 0.7350 (mtp) cc_final: 0.6909 (mtp) REVERT: A 414 ILE cc_start: 0.6995 (mm) cc_final: 0.6526 (mm) REVERT: B 318 ASP cc_start: 0.7086 (t0) cc_final: 0.6833 (t0) REVERT: B 410 MET cc_start: 0.7227 (tpp) cc_final: 0.6964 (mmm) REVERT: B 514 MET cc_start: 0.5374 (OUTLIER) cc_final: 0.4854 (pmm) REVERT: B 614 PHE cc_start: 0.7906 (t80) cc_final: 0.7623 (t80) REVERT: B 632 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.8451 (m-10) REVERT: B 639 PHE cc_start: 0.8005 (m-80) cc_final: 0.7442 (m-80) REVERT: B 731 MET cc_start: 0.6981 (mmm) cc_final: 0.6434 (mpp) REVERT: B 827 LEU cc_start: 0.8407 (tp) cc_final: 0.7924 (mt) REVERT: B 830 MET cc_start: 0.7643 (mmm) cc_final: 0.6920 (mmm) outliers start: 63 outliers final: 33 residues processed: 160 average time/residue: 0.2015 time to fit residues: 50.5171 Evaluate side-chains 127 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 500 TRP Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 746 CYS Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 459 PHE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 547 CYS Chi-restraints excluded: chain B residue 557 GLN Chi-restraints excluded: chain B residue 632 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 89 optimal weight: 0.1980 chunk 51 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 66 optimal weight: 30.0000 chunk 148 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 overall best weight: 6.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 118 GLN ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 ASN ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 ASN ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 HIS ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 706 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.134715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.096034 restraints weight = 32619.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.094467 restraints weight = 26012.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.095484 restraints weight = 22726.880| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.089 12675 Z= 0.378 Angle : 0.977 12.858 17205 Z= 0.510 Chirality : 0.053 0.228 1954 Planarity : 0.007 0.068 2163 Dihedral : 7.803 57.835 1729 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.08 % Favored : 87.85 % Rotamer: Outliers : 5.55 % Allowed : 14.46 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.96 (0.19), residues: 1564 helix: -0.92 (0.19), residues: 676 sheet: -2.38 (0.40), residues: 114 loop : -2.93 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 570 HIS 0.008 0.002 HIS A 496 PHE 0.034 0.003 PHE A 599 TYR 0.040 0.003 TYR A 185 ARG 0.009 0.001 ARG A 106 Details of bonding type rmsd hydrogen bonds : bond 0.05885 ( 469) hydrogen bonds : angle 5.76321 ( 1371) SS BOND : bond 0.00643 ( 17) SS BOND : angle 2.21590 ( 34) covalent geometry : bond 0.00859 (12658) covalent geometry : angle 0.97319 (17171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 93 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ILE cc_start: 0.4983 (OUTLIER) cc_final: 0.4631 (mm) REVERT: A 90 ASN cc_start: 0.6959 (t0) cc_final: 0.6752 (t0) REVERT: A 153 LYS cc_start: 0.8700 (mttt) cc_final: 0.8258 (mtpt) REVERT: A 403 ASN cc_start: 0.9046 (t0) cc_final: 0.8812 (t0) REVERT: A 420 MET cc_start: 0.7745 (tpp) cc_final: 0.7370 (tpp) REVERT: A 438 LEU cc_start: 0.7400 (mt) cc_final: 0.7127 (pt) REVERT: B 291 CYS cc_start: 0.8242 (m) cc_final: 0.8007 (m) REVERT: B 317 SER cc_start: 0.8190 (OUTLIER) cc_final: 0.7786 (t) REVERT: B 403 ASN cc_start: 0.8529 (t0) cc_final: 0.8179 (t0) REVERT: B 410 MET cc_start: 0.8361 (tpp) cc_final: 0.8037 (mmm) REVERT: B 639 PHE cc_start: 0.8007 (m-80) cc_final: 0.7641 (m-80) REVERT: B 700 PHE cc_start: 0.6435 (m-80) cc_final: 0.6161 (m-80) REVERT: B 731 MET cc_start: 0.7289 (mmm) cc_final: 0.6523 (mpp) REVERT: B 827 LEU cc_start: 0.8420 (tp) cc_final: 0.7907 (mt) REVERT: B 830 MET cc_start: 0.7401 (mmm) cc_final: 0.6783 (mmm) outliers start: 76 outliers final: 50 residues processed: 158 average time/residue: 0.2358 time to fit residues: 56.9922 Evaluate side-chains 130 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 78 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 367 TRP Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 500 TRP Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 746 CYS Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 557 GLN Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 632 TYR Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 798 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 88 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 83 optimal weight: 0.0970 chunk 90 optimal weight: 0.8980 chunk 53 optimal weight: 0.0170 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 HIS A 660 GLN B 182 GLN B 343 GLN ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.144348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.113387 restraints weight = 31515.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.112142 restraints weight = 23818.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.113757 restraints weight = 18960.756| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6306 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12675 Z= 0.133 Angle : 0.727 9.911 17205 Z= 0.370 Chirality : 0.045 0.206 1954 Planarity : 0.005 0.058 2163 Dihedral : 6.480 51.940 1726 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.80 % Favored : 92.14 % Rotamer: Outliers : 3.51 % Allowed : 17.09 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -2.33 (0.20), residues: 1564 helix: -0.44 (0.19), residues: 683 sheet: -2.00 (0.41), residues: 119 loop : -2.57 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 570 HIS 0.005 0.001 HIS A 422 PHE 0.029 0.001 PHE A 599 TYR 0.025 0.001 TYR B 236 ARG 0.008 0.001 ARG B 203 Details of bonding type rmsd hydrogen bonds : bond 0.04092 ( 469) hydrogen bonds : angle 5.10775 ( 1371) SS BOND : bond 0.00363 ( 17) SS BOND : angle 1.70423 ( 34) covalent geometry : bond 0.00288 (12658) covalent geometry : angle 0.72411 (17171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 101 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8067 (ttp) cc_final: 0.7752 (ttp) REVERT: A 153 LYS cc_start: 0.8543 (mttt) cc_final: 0.8280 (mtpt) REVERT: A 290 PHE cc_start: 0.7129 (OUTLIER) cc_final: 0.6255 (m-80) REVERT: A 303 MET cc_start: 0.6089 (mtp) cc_final: 0.5826 (mtp) REVERT: A 422 HIS cc_start: 0.6823 (OUTLIER) cc_final: 0.5853 (t-90) REVERT: A 500 TRP cc_start: 0.8398 (OUTLIER) cc_final: 0.7578 (t-100) REVERT: A 731 MET cc_start: 0.7161 (mmp) cc_final: 0.6936 (mmp) REVERT: B 201 PHE cc_start: 0.5776 (t80) cc_final: 0.5465 (t80) REVERT: B 236 TYR cc_start: 0.7046 (t80) cc_final: 0.6829 (t80) REVERT: B 241 MET cc_start: 0.7120 (tpp) cc_final: 0.6679 (tpp) REVERT: B 482 MET cc_start: 0.7596 (mmm) cc_final: 0.6856 (mtt) REVERT: B 514 MET cc_start: 0.5024 (OUTLIER) cc_final: 0.4464 (pmm) REVERT: B 632 TYR cc_start: 0.8815 (t80) cc_final: 0.8608 (m-10) REVERT: B 639 PHE cc_start: 0.7616 (m-80) cc_final: 0.7215 (m-80) REVERT: B 718 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.7074 (pp) REVERT: B 727 MET cc_start: 0.5703 (ppp) cc_final: 0.4946 (ppp) REVERT: B 731 MET cc_start: 0.6090 (mmm) cc_final: 0.5805 (mpp) REVERT: B 827 LEU cc_start: 0.8078 (tp) cc_final: 0.7628 (mt) REVERT: B 830 MET cc_start: 0.6500 (mmm) cc_final: 0.6046 (mmm) outliers start: 48 outliers final: 27 residues processed: 141 average time/residue: 0.2123 time to fit residues: 46.3012 Evaluate side-chains 114 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 422 HIS Chi-restraints excluded: chain A residue 500 TRP Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 718 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 103 optimal weight: 0.0050 chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 111 optimal weight: 20.0000 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN B 362 ASN ** B 406 GLN ** 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 = 0.4632 r_free = 0.4632 target = 0.144633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.107482 restraints weight = 30897.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.106721 restraints weight = 18269.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.108263 restraints weight = 14445.826| |-----------------------------------------------------------------------------| r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12675 Z= 0.127 Angle : 0.695 8.954 17205 Z= 0.350 Chirality : 0.043 0.200 1954 Planarity : 0.004 0.052 2163 Dihedral : 6.087 52.349 1725 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.25 % Favored : 91.69 % Rotamer: Outliers : 3.65 % Allowed : 17.75 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -2.09 (0.20), residues: 1564 helix: -0.26 (0.19), residues: 692 sheet: -1.76 (0.42), residues: 130 loop : -2.45 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 570 HIS 0.017 0.001 HIS A 422 PHE 0.023 0.001 PHE A 599 TYR 0.018 0.001 TYR A 672 ARG 0.006 0.000 ARG B 203 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 469) hydrogen bonds : angle 4.98654 ( 1371) SS BOND : bond 0.00539 ( 17) SS BOND : angle 1.56426 ( 34) covalent geometry : bond 0.00273 (12658) covalent geometry : angle 0.69216 (17171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 90 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8045 (ttp) cc_final: 0.7766 (ttp) REVERT: A 170 GLN cc_start: 0.7824 (mp10) cc_final: 0.6714 (tt0) REVERT: A 290 PHE cc_start: 0.7236 (OUTLIER) cc_final: 0.6512 (m-80) REVERT: A 303 MET cc_start: 0.6440 (mtp) cc_final: 0.6129 (mtp) REVERT: A 420 MET cc_start: 0.7451 (tpp) cc_final: 0.7131 (tpp) REVERT: A 731 MET cc_start: 0.7863 (mmp) cc_final: 0.7314 (mmm) REVERT: A 830 MET cc_start: 0.6994 (tpp) cc_final: 0.6678 (mmm) REVERT: B 160 ILE cc_start: 0.6833 (OUTLIER) cc_final: 0.6414 (mm) REVERT: B 236 TYR cc_start: 0.7013 (t80) cc_final: 0.6654 (t80) REVERT: B 241 MET cc_start: 0.7286 (tpp) cc_final: 0.6764 (tpp) REVERT: B 469 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.8147 (m-80) REVERT: B 482 MET cc_start: 0.7717 (mmm) cc_final: 0.7037 (mtt) REVERT: B 514 MET cc_start: 0.5359 (OUTLIER) cc_final: 0.4821 (pmm) REVERT: B 614 PHE cc_start: 0.6825 (t80) cc_final: 0.6363 (t80) REVERT: B 632 TYR cc_start: 0.8881 (t80) cc_final: 0.8596 (m-10) REVERT: B 639 PHE cc_start: 0.7898 (m-80) cc_final: 0.7440 (m-80) REVERT: B 731 MET cc_start: 0.7235 (mmm) cc_final: 0.6724 (mpp) REVERT: B 827 LEU cc_start: 0.8428 (tp) cc_final: 0.7982 (mt) REVERT: B 830 MET cc_start: 0.7066 (mmm) cc_final: 0.6475 (mmm) outliers start: 50 outliers final: 30 residues processed: 132 average time/residue: 0.1962 time to fit residues: 40.3099 Evaluate side-chains 115 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 81 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 367 TRP Chi-restraints excluded: chain A residue 500 TRP Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 556 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 31 optimal weight: 5.9990 chunk 6 optimal weight: 0.3980 chunk 128 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 110 optimal weight: 0.6980 chunk 64 optimal weight: 0.0980 chunk 120 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN B 182 GLN B 362 ASN ** B 406 GLN ** 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 = 0.4595 r_free = 0.4595 target = 0.142042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.111608 restraints weight = 31439.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.109557 restraints weight = 25306.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.111105 restraints weight = 21374.166| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6366 moved from start: 0.5591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12675 Z= 0.144 Angle : 0.698 9.980 17205 Z= 0.350 Chirality : 0.044 0.186 1954 Planarity : 0.004 0.048 2163 Dihedral : 6.045 53.238 1725 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.25 % Favored : 91.69 % Rotamer: Outliers : 3.65 % Allowed : 17.82 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -1.95 (0.20), residues: 1564 helix: -0.12 (0.19), residues: 686 sheet: -1.71 (0.41), residues: 139 loop : -2.38 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 570 HIS 0.003 0.001 HIS A 111 PHE 0.019 0.001 PHE A 599 TYR 0.018 0.001 TYR A 672 ARG 0.004 0.000 ARG B 203 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 469) hydrogen bonds : angle 4.94235 ( 1371) SS BOND : bond 0.00311 ( 17) SS BOND : angle 1.61151 ( 34) covalent geometry : bond 0.00325 (12658) covalent geometry : angle 0.69537 (17171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 88 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 SER cc_start: 0.7011 (OUTLIER) cc_final: 0.6532 (p) REVERT: A 82 MET cc_start: 0.8057 (ttp) cc_final: 0.7841 (ttp) REVERT: A 116 LEU cc_start: 0.6299 (OUTLIER) cc_final: 0.6080 (mp) REVERT: A 303 MET cc_start: 0.6271 (mtp) cc_final: 0.6039 (mtp) REVERT: A 420 MET cc_start: 0.7643 (tpp) cc_final: 0.7180 (tpp) REVERT: A 731 MET cc_start: 0.6985 (mmp) cc_final: 0.6468 (mmp) REVERT: A 830 MET cc_start: 0.6670 (tpp) cc_final: 0.6398 (mmm) REVERT: B 160 ILE cc_start: 0.6751 (OUTLIER) cc_final: 0.6372 (mm) REVERT: B 236 TYR cc_start: 0.7292 (t80) cc_final: 0.7084 (t80) REVERT: B 241 MET cc_start: 0.7343 (tpp) cc_final: 0.6788 (tpp) REVERT: B 403 ASN cc_start: 0.8351 (t0) cc_final: 0.8080 (t0) REVERT: B 514 MET cc_start: 0.5280 (OUTLIER) cc_final: 0.4686 (pmm) REVERT: B 614 PHE cc_start: 0.6790 (t80) cc_final: 0.6564 (t80) REVERT: B 639 PHE cc_start: 0.7588 (m-80) cc_final: 0.7173 (m-80) REVERT: B 718 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.7027 (pp) REVERT: B 830 MET cc_start: 0.6352 (mmm) cc_final: 0.6028 (mmm) outliers start: 50 outliers final: 33 residues processed: 131 average time/residue: 0.1880 time to fit residues: 39.1153 Evaluate side-chains 116 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 78 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 367 TRP Chi-restraints excluded: chain A residue 500 TRP Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 367 TRP Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 718 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 35 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 138 optimal weight: 20.0000 chunk 154 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 73 optimal weight: 30.0000 chunk 12 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** B 406 GLN ** 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 = 0.4598 r_free = 0.4598 target = 0.141990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.105422 restraints weight = 30721.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.103969 restraints weight = 19817.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.105554 restraints weight = 16408.899| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.5904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12675 Z= 0.164 Angle : 0.720 9.417 17205 Z= 0.363 Chirality : 0.044 0.181 1954 Planarity : 0.005 0.048 2163 Dihedral : 6.117 53.822 1725 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.08 % Favored : 90.86 % Rotamer: Outliers : 4.16 % Allowed : 18.26 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -2.01 (0.20), residues: 1564 helix: -0.18 (0.19), residues: 690 sheet: -1.70 (0.42), residues: 139 loop : -2.44 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 570 HIS 0.003 0.001 HIS A 55 PHE 0.016 0.002 PHE A 599 TYR 0.018 0.002 TYR A 185 ARG 0.003 0.000 ARG B 203 Details of bonding type rmsd hydrogen bonds : bond 0.03993 ( 469) hydrogen bonds : angle 4.93552 ( 1371) SS BOND : bond 0.00369 ( 17) SS BOND : angle 1.95261 ( 34) covalent geometry : bond 0.00376 (12658) covalent geometry : angle 0.71559 (17171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 88 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 SER cc_start: 0.6581 (OUTLIER) cc_final: 0.5632 (p) REVERT: A 82 MET cc_start: 0.8110 (ttp) cc_final: 0.7891 (ttp) REVERT: A 116 LEU cc_start: 0.6359 (OUTLIER) cc_final: 0.6150 (mp) REVERT: A 290 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.6702 (m-80) REVERT: A 303 MET cc_start: 0.6488 (mtp) cc_final: 0.6176 (mtp) REVERT: A 420 MET cc_start: 0.7688 (tpp) cc_final: 0.7417 (tpp) REVERT: A 469 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.7931 (m-80) REVERT: A 614 PHE cc_start: 0.7027 (t80) cc_final: 0.6780 (t80) REVERT: A 731 MET cc_start: 0.7387 (mmp) cc_final: 0.6950 (mmm) REVERT: A 760 ASN cc_start: 0.7274 (m-40) cc_final: 0.6850 (m110) REVERT: A 830 MET cc_start: 0.6961 (tpp) cc_final: 0.6366 (mmm) REVERT: B 160 ILE cc_start: 0.6539 (OUTLIER) cc_final: 0.6333 (mm) REVERT: B 241 MET cc_start: 0.7321 (tpp) cc_final: 0.6798 (tpp) REVERT: B 403 ASN cc_start: 0.8582 (t0) cc_final: 0.8289 (t0) REVERT: B 469 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7888 (m-80) REVERT: B 639 PHE cc_start: 0.7798 (m-80) cc_final: 0.7412 (m-80) REVERT: B 718 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7150 (pp) REVERT: B 830 MET cc_start: 0.6689 (mmm) cc_final: 0.6184 (mmm) outliers start: 57 outliers final: 36 residues processed: 137 average time/residue: 0.2089 time to fit residues: 43.8888 Evaluate side-chains 122 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 79 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 367 TRP Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 500 TRP Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 367 TRP Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 718 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 128 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 138 optimal weight: 30.0000 chunk 40 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** 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 = 0.4584 r_free = 0.4584 target = 0.141103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.104290 restraints weight = 31318.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.103001 restraints weight = 22396.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.104141 restraints weight = 17096.048| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12675 Z= 0.151 Angle : 0.710 12.885 17205 Z= 0.355 Chirality : 0.044 0.253 1954 Planarity : 0.004 0.048 2163 Dihedral : 5.948 53.957 1723 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.76 % Favored : 91.18 % Rotamer: Outliers : 3.73 % Allowed : 18.55 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -2.00 (0.20), residues: 1564 helix: -0.13 (0.19), residues: 690 sheet: -1.84 (0.41), residues: 144 loop : -2.45 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 570 HIS 0.003 0.001 HIS A 55 PHE 0.016 0.001 PHE A 599 TYR 0.018 0.001 TYR B 792 ARG 0.006 0.000 ARG B 203 Details of bonding type rmsd hydrogen bonds : bond 0.03906 ( 469) hydrogen bonds : angle 4.88510 ( 1371) SS BOND : bond 0.00301 ( 17) SS BOND : angle 1.61745 ( 34) covalent geometry : bond 0.00346 (12658) covalent geometry : angle 0.70724 (17171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 84 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 SER cc_start: 0.6562 (OUTLIER) cc_final: 0.5714 (p) REVERT: A 116 LEU cc_start: 0.6449 (OUTLIER) cc_final: 0.6245 (mp) REVERT: A 290 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.6628 (m-80) REVERT: A 303 MET cc_start: 0.6516 (mtp) cc_final: 0.6148 (mtp) REVERT: A 420 MET cc_start: 0.7669 (tpp) cc_final: 0.7354 (tpp) REVERT: A 514 MET cc_start: 0.3688 (ppp) cc_final: 0.3232 (tmm) REVERT: A 614 PHE cc_start: 0.7046 (t80) cc_final: 0.6773 (t80) REVERT: A 731 MET cc_start: 0.7269 (mmp) cc_final: 0.6802 (mmp) REVERT: A 760 ASN cc_start: 0.7169 (m-40) cc_final: 0.6798 (m110) REVERT: A 830 MET cc_start: 0.6838 (tpp) cc_final: 0.6334 (mmm) REVERT: B 241 MET cc_start: 0.7350 (tpp) cc_final: 0.6741 (tpp) REVERT: B 403 ASN cc_start: 0.8478 (t0) cc_final: 0.8239 (t0) REVERT: B 469 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.8085 (m-80) REVERT: B 639 PHE cc_start: 0.7667 (m-80) cc_final: 0.7311 (m-80) REVERT: B 718 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6901 (pp) REVERT: B 830 MET cc_start: 0.6743 (mmm) cc_final: 0.6191 (mmm) outliers start: 51 outliers final: 36 residues processed: 126 average time/residue: 0.1934 time to fit residues: 38.6389 Evaluate side-chains 119 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 78 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 367 TRP Chi-restraints excluded: chain A residue 500 TRP Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 367 TRP Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 514 MET Chi-restraints excluded: chain B residue 524 CYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 572 ASN Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 718 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.515 > 50: distance: 50 - 55: 20.995 distance: 55 - 56: 14.353 distance: 56 - 57: 21.038 distance: 56 - 59: 33.604 distance: 57 - 58: 22.492 distance: 57 - 66: 23.697 distance: 59 - 60: 6.647 distance: 60 - 61: 4.694 distance: 61 - 62: 7.850 distance: 62 - 63: 14.934 distance: 63 - 64: 9.199 distance: 63 - 65: 19.306 distance: 66 - 67: 28.119 distance: 67 - 68: 3.379 distance: 67 - 70: 34.877 distance: 68 - 74: 12.514 distance: 69 - 96: 26.930 distance: 70 - 71: 18.202 distance: 71 - 72: 14.719 distance: 71 - 73: 16.408 distance: 74 - 75: 8.871 distance: 75 - 76: 12.319 distance: 75 - 78: 22.322 distance: 76 - 77: 7.400 distance: 76 - 80: 3.513 distance: 77 - 102: 19.872 distance: 78 - 79: 24.673 distance: 81 - 82: 10.101 distance: 81 - 84: 6.121 distance: 82 - 83: 27.703 distance: 82 - 88: 11.335 distance: 83 - 110: 32.964 distance: 84 - 85: 11.427 distance: 85 - 86: 17.052 distance: 85 - 87: 20.930 distance: 88 - 89: 7.056 distance: 89 - 90: 4.800 distance: 89 - 92: 5.193 distance: 90 - 91: 11.433 distance: 90 - 96: 6.303 distance: 91 - 121: 19.037 distance: 92 - 93: 7.598 distance: 92 - 94: 14.523 distance: 93 - 95: 19.107 distance: 96 - 97: 3.913 distance: 97 - 98: 11.303 distance: 97 - 100: 9.766 distance: 98 - 99: 14.277 distance: 98 - 102: 15.723 distance: 100 - 101: 29.856 distance: 102 - 103: 9.665 distance: 103 - 104: 10.880 distance: 103 - 106: 7.182 distance: 104 - 105: 13.092 distance: 104 - 110: 7.566 distance: 106 - 107: 11.225 distance: 106 - 108: 27.101 distance: 107 - 109: 16.605 distance: 110 - 111: 9.458 distance: 111 - 112: 6.949 distance: 111 - 114: 20.919 distance: 112 - 113: 9.757 distance: 112 - 121: 20.255 distance: 114 - 115: 28.066 distance: 115 - 116: 19.203 distance: 116 - 117: 11.603 distance: 117 - 118: 9.774 distance: 118 - 119: 18.555 distance: 118 - 120: 20.045 distance: 121 - 122: 24.555 distance: 122 - 123: 14.624 distance: 122 - 125: 10.269 distance: 125 - 126: 23.314 distance: 126 - 127: 27.426 distance: 126 - 128: 18.786 distance: 129 - 130: 16.806 distance: 130 - 131: 11.969 distance: 130 - 133: 16.956 distance: 131 - 132: 9.784 distance: 131 - 136: 21.757 distance: 133 - 134: 21.715 distance: 133 - 135: 9.657