Starting phenix.real_space_refine on Thu Sep 26 06:38:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dgd_30671/09_2024/7dgd_30671_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dgd_30671/09_2024/7dgd_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dgd_30671/09_2024/7dgd_30671.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dgd_30671/09_2024/7dgd_30671.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dgd_30671/09_2024/7dgd_30671_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dgd_30671/09_2024/7dgd_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 7.43, per 1000 atoms: 0.60 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: 2.67 Conformation dependent library (CDL) restraints added in 1.6 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: 1.30 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: 3.58 Time building geometry restraints manager: 3.20 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 28.670 Find NCS groups from input model: 0.400 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.010 ------------------------------------------------------------------------------- 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 12658 Z= 0.985 Angle : 2.083 10.905 17171 Z= 1.401 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 *********************** 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 fitting. rotamer outliers: 53 poor density : 170 time to evaluate : 1.412 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: 0.2454 time to fit residues: 77.0028 Evaluate side-chains 117 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 1.482 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5742 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 12658 Z= 0.270 Angle : 0.811 10.044 17171 Z= 0.419 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 *********************** 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 fitting. rotamer outliers: 63 poor density : 107 time to evaluate : 1.374 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: 0.6890 (OUTLIER) cc_final: 0.5417 (p-80) REVERT: A 414 ILE cc_start: 0.6730 (mm) cc_final: 0.6244 (mm) REVERT: B 410 MET cc_start: 0.7076 (tpp) cc_final: 0.6844 (mmm) REVERT: B 514 MET cc_start: 0.4686 (OUTLIER) cc_final: 0.4091 (pmm) outliers start: 63 outliers final: 33 residues processed: 160 average time/residue: 0.1920 time to fit residues: 48.8426 Evaluate side-chains 122 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 87 time to evaluate : 1.335 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 117 optimal weight: 0.0000 chunk 96 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 141 optimal weight: 30.0000 chunk 153 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 48 optimal weight: 20.0000 chunk 113 optimal weight: 1.9990 overall best weight: 2.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 ASN ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 GLN A 782 ASN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 GLN B 706 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5927 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 12658 Z= 0.306 Angle : 0.779 8.893 17171 Z= 0.404 Chirality : 0.047 0.210 1954 Planarity : 0.005 0.057 2163 Dihedral : 6.982 53.795 1729 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.59 % Favored : 90.35 % Rotamer: Outliers : 4.31 % Allowed : 14.32 % Favored : 81.37 % 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: -2.55 (0.20), residues: 1564 helix: -0.60 (0.19), residues: 688 sheet: -2.39 (0.37), residues: 132 loop : -2.66 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 570 HIS 0.006 0.001 HIS B 374 PHE 0.038 0.002 PHE B 639 TYR 0.026 0.002 TYR A 185 ARG 0.006 0.001 ARG B 203 *********************** 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 150 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 91 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 241 MET cc_start: 0.6297 (tpp) cc_final: 0.6068 (tpp) REVERT: B 291 CYS cc_start: 0.7797 (m) cc_final: 0.7544 (m) outliers start: 59 outliers final: 42 residues processed: 141 average time/residue: 0.1970 time to fit residues: 44.1276 Evaluate side-chains 117 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 75 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS 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 205 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 339 THR 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 445 ILE 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 42 ASP Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 281 LEU 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 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 547 CYS Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 557 GLN Chi-restraints excluded: chain B residue 572 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 142 optimal weight: 0.0980 chunk 150 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6070 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12658 Z= 0.347 Angle : 0.792 9.578 17171 Z= 0.408 Chirality : 0.047 0.194 1954 Planarity : 0.005 0.049 2163 Dihedral : 7.010 53.934 1729 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.42 % Favored : 89.51 % Rotamer: Outliers : 5.41 % Allowed : 15.85 % Favored : 78.74 % 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: -2.50 (0.20), residues: 1564 helix: -0.57 (0.19), residues: 686 sheet: -1.95 (0.40), residues: 132 loop : -2.70 (0.20), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 224 HIS 0.006 0.002 HIS A 55 PHE 0.039 0.002 PHE B 639 TYR 0.029 0.002 TYR B 185 ARG 0.005 0.001 ARG A 221 *********************** 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 166 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 92 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7483 (tt) REVERT: A 420 MET cc_start: 0.7335 (tpp) cc_final: 0.7130 (tpp) REVERT: B 160 ILE cc_start: 0.6384 (OUTLIER) cc_final: 0.5960 (mm) REVERT: B 241 MET cc_start: 0.6335 (tpp) cc_final: 0.6013 (tpp) REVERT: B 291 CYS cc_start: 0.7957 (m) cc_final: 0.7668 (m) REVERT: B 514 MET cc_start: 0.4693 (OUTLIER) cc_final: 0.3869 (pmm) REVERT: B 830 MET cc_start: 0.5470 (mmm) cc_final: 0.5222 (mmm) outliers start: 74 outliers final: 46 residues processed: 155 average time/residue: 0.2027 time to fit residues: 48.7298 Evaluate side-chains 123 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 74 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 183 ILE 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 287 VAL Chi-restraints excluded: chain A residue 308 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 556 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 A residue 731 MET Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 159 VAL 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 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 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 413 VAL Chi-restraints excluded: chain B residue 420 MET 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 556 VAL Chi-restraints excluded: chain B residue 557 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.0370 chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 62 optimal weight: 30.0000 chunk 128 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 135 optimal weight: 30.0000 chunk 38 optimal weight: 0.8980 overall best weight: 2.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN A 422 HIS ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6050 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12658 Z= 0.285 Angle : 0.747 8.695 17171 Z= 0.383 Chirality : 0.046 0.200 1954 Planarity : 0.005 0.050 2163 Dihedral : 6.491 52.182 1723 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.72 % Favored : 90.22 % Rotamer: Outliers : 5.19 % Allowed : 16.65 % Favored : 78.16 % 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: -2.25 (0.20), residues: 1564 helix: -0.35 (0.19), residues: 684 sheet: -1.74 (0.41), residues: 129 loop : -2.59 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 570 HIS 0.004 0.001 HIS A 84 PHE 0.066 0.002 PHE B 639 TYR 0.018 0.001 TYR A 672 ARG 0.006 0.000 ARG B 203 *********************** 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 153 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 82 time to evaluate : 1.423 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: 0.6679 (OUTLIER) cc_final: 0.6066 (p) REVERT: A 182 GLN cc_start: 0.5951 (OUTLIER) cc_final: 0.5471 (pt0) REVERT: A 290 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.6958 (m-80) REVERT: A 417 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7395 (tt) REVERT: A 420 MET cc_start: 0.7505 (tpp) cc_final: 0.7164 (tpp) REVERT: A 422 HIS cc_start: 0.7327 (OUTLIER) cc_final: 0.6507 (t-90) REVERT: B 241 MET cc_start: 0.6718 (tpp) cc_final: 0.6346 (tpp) REVERT: B 291 CYS cc_start: 0.7749 (m) cc_final: 0.7487 (m) REVERT: B 367 TRP cc_start: 0.6365 (OUTLIER) cc_final: 0.3547 (m100) REVERT: B 469 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7802 (m-80) REVERT: B 594 ILE cc_start: 0.6679 (OUTLIER) cc_final: 0.6379 (mm) REVERT: B 718 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6535 (pp) outliers start: 71 outliers final: 43 residues processed: 144 average time/residue: 0.2062 time to fit residues: 47.3157 Evaluate side-chains 129 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 77 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 86 LEU 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 159 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 182 GLN 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 290 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 367 TRP Chi-restraints excluded: chain A residue 417 ILE 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 556 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 A residue 701 MET Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 171 VAL 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 339 THR Chi-restraints excluded: chain B residue 340 ILE 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 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 557 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 4.9990 chunk 135 optimal weight: 30.0000 chunk 29 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 150 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 79 optimal weight: 0.0470 overall best weight: 1.1482 ------------------------------------------------------------------------------- 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 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5961 moved from start: 0.5795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12658 Z= 0.204 Angle : 0.703 8.906 17171 Z= 0.358 Chirality : 0.044 0.212 1954 Planarity : 0.004 0.047 2163 Dihedral : 6.050 51.620 1723 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.38 % Favored : 91.56 % Rotamer: Outliers : 4.31 % Allowed : 18.19 % Favored : 77.50 % 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: -1.99 (0.20), residues: 1564 helix: -0.18 (0.19), residues: 692 sheet: -1.64 (0.42), residues: 136 loop : -2.43 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 570 HIS 0.020 0.001 HIS A 422 PHE 0.022 0.002 PHE B 639 TYR 0.018 0.001 TYR A 672 ARG 0.006 0.000 ARG B 203 *********************** 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 149 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 90 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 SER cc_start: 0.7298 (OUTLIER) cc_final: 0.7003 (p) REVERT: A 170 GLN cc_start: 0.7997 (mp10) cc_final: 0.7286 (tt0) REVERT: A 290 PHE cc_start: 0.7438 (OUTLIER) cc_final: 0.6791 (m-80) REVERT: A 420 MET cc_start: 0.7391 (tpp) cc_final: 0.7152 (tpp) REVERT: A 760 ASN cc_start: 0.6934 (m-40) cc_final: 0.6564 (m110) REVERT: B 160 ILE cc_start: 0.6284 (OUTLIER) cc_final: 0.5891 (mm) REVERT: B 469 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7870 (m-80) REVERT: B 514 MET cc_start: 0.5073 (OUTLIER) cc_final: 0.4510 (pmm) REVERT: B 594 ILE cc_start: 0.6650 (OUTLIER) cc_final: 0.6363 (mm) REVERT: B 830 MET cc_start: 0.5439 (mmm) cc_final: 0.5109 (mmm) outliers start: 59 outliers final: 33 residues processed: 138 average time/residue: 0.1874 time to fit residues: 41.1953 Evaluate side-chains 117 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 78 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 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 190 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 417 ILE 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 556 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 701 MET Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 111 HIS 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 202 LEU Chi-restraints excluded: chain B residue 218 ILE 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 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 594 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 127 optimal weight: 7.9990 chunk 84 optimal weight: 0.6980 chunk 150 optimal weight: 30.0000 chunk 94 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 69 optimal weight: 40.0000 chunk 93 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6009 moved from start: 0.6085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12658 Z= 0.239 Angle : 0.729 12.337 17171 Z= 0.368 Chirality : 0.044 0.215 1954 Planarity : 0.004 0.047 2163 Dihedral : 6.052 52.528 1723 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.21 % Favored : 90.73 % Rotamer: Outliers : 4.46 % Allowed : 18.26 % Favored : 77.28 % 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: -1.92 (0.20), residues: 1564 helix: -0.11 (0.19), residues: 694 sheet: -1.70 (0.42), residues: 139 loop : -2.38 (0.21), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 570 HIS 0.003 0.001 HIS B 231 PHE 0.026 0.002 PHE A 831 TYR 0.019 0.001 TYR B 185 ARG 0.004 0.000 ARG B 203 *********************** 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 148 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 87 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 SER cc_start: 0.7007 (OUTLIER) cc_final: 0.6387 (p) REVERT: A 82 MET cc_start: 0.6964 (OUTLIER) cc_final: 0.6753 (ptp) REVERT: A 170 GLN cc_start: 0.7849 (mp10) cc_final: 0.7134 (tt0) REVERT: A 182 GLN cc_start: 0.5808 (OUTLIER) cc_final: 0.5276 (pt0) REVERT: A 251 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: A 290 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.6685 (m-80) REVERT: A 420 MET cc_start: 0.7484 (tpp) cc_final: 0.5941 (ttm) REVERT: A 760 ASN cc_start: 0.6696 (m-40) cc_final: 0.6325 (m110) REVERT: B 160 ILE cc_start: 0.6076 (OUTLIER) cc_final: 0.5761 (mm) REVERT: B 367 TRP cc_start: 0.6204 (OUTLIER) cc_final: 0.3208 (m100) REVERT: B 469 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7903 (m-80) REVERT: B 514 MET cc_start: 0.4989 (OUTLIER) cc_final: 0.4403 (pmm) REVERT: B 594 ILE cc_start: 0.6691 (OUTLIER) cc_final: 0.6390 (mm) REVERT: B 642 TYR cc_start: 0.5415 (m-80) cc_final: 0.5043 (m-80) REVERT: B 718 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6654 (pp) REVERT: B 830 MET cc_start: 0.5513 (mmm) cc_final: 0.5293 (mmm) REVERT: B 835 MET cc_start: 0.5509 (tmm) cc_final: 0.4338 (tmm) outliers start: 61 outliers final: 36 residues processed: 141 average time/residue: 0.2002 time to fit residues: 43.8234 Evaluate side-chains 124 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 77 time to evaluate : 1.422 ------------------------------------------------------------------------------- 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 82 MET 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 182 GLN Chi-restraints excluded: chain A residue 183 ILE 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 251 GLU 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 417 ILE 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 556 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 701 MET Chi-restraints excluded: chain B residue 111 HIS 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 202 LEU Chi-restraints excluded: chain B residue 218 ILE 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 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 594 ILE Chi-restraints excluded: chain B residue 612 LEU 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 60 optimal weight: 40.0000 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6001 moved from start: 0.6317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12658 Z= 0.234 Angle : 0.730 12.831 17171 Z= 0.366 Chirality : 0.044 0.217 1954 Planarity : 0.004 0.049 2163 Dihedral : 5.945 52.665 1723 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.76 % Favored : 91.18 % Rotamer: Outliers : 4.24 % Allowed : 18.70 % Favored : 77.06 % 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: -1.88 (0.21), residues: 1564 helix: -0.08 (0.20), residues: 696 sheet: -1.83 (0.43), residues: 134 loop : -2.32 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 570 HIS 0.003 0.001 HIS B 231 PHE 0.074 0.002 PHE B 639 TYR 0.021 0.001 TYR B 642 ARG 0.005 0.000 ARG B 203 *********************** 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 138 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 80 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 SER cc_start: 0.6930 (OUTLIER) cc_final: 0.6377 (p) REVERT: A 182 GLN cc_start: 0.5734 (OUTLIER) cc_final: 0.5273 (pt0) REVERT: A 251 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: A 290 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.6701 (m-80) REVERT: A 420 MET cc_start: 0.7387 (tpp) cc_final: 0.5900 (ttm) REVERT: A 514 MET cc_start: 0.4156 (ppp) cc_final: 0.3591 (tmm) REVERT: A 760 ASN cc_start: 0.6677 (m-40) cc_final: 0.6312 (m110) REVERT: B 160 ILE cc_start: 0.6104 (OUTLIER) cc_final: 0.5817 (mm) REVERT: B 241 MET cc_start: 0.6673 (tpp) cc_final: 0.6466 (tpp) REVERT: B 367 TRP cc_start: 0.6303 (OUTLIER) cc_final: 0.3356 (m100) REVERT: B 469 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7923 (m-80) REVERT: B 514 MET cc_start: 0.4739 (OUTLIER) cc_final: 0.4206 (pmm) REVERT: B 594 ILE cc_start: 0.6691 (OUTLIER) cc_final: 0.6396 (mm) REVERT: B 718 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6593 (pp) outliers start: 58 outliers final: 38 residues processed: 129 average time/residue: 0.1857 time to fit residues: 38.1033 Evaluate side-chains 125 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 77 time to evaluate : 1.318 ------------------------------------------------------------------------------- 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 182 GLN Chi-restraints excluded: chain A residue 183 ILE 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 251 GLU Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 339 THR 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 556 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 A residue 701 MET Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 159 VAL 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 218 ILE Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 339 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 92 optimal weight: 0.5980 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 GLN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 660 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6145 moved from start: 0.6664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 12658 Z= 0.381 Angle : 0.833 14.464 17171 Z= 0.422 Chirality : 0.048 0.197 1954 Planarity : 0.005 0.051 2163 Dihedral : 6.493 54.641 1723 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.74 % Favored : 89.19 % Rotamer: Outliers : 4.31 % Allowed : 19.21 % Favored : 76.48 % 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: -2.14 (0.20), residues: 1564 helix: -0.31 (0.19), residues: 695 sheet: -1.74 (0.43), residues: 129 loop : -2.49 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 224 HIS 0.005 0.001 HIS A 111 PHE 0.039 0.003 PHE A 831 TYR 0.030 0.002 TYR B 200 ARG 0.004 0.001 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 9 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 fitting. rotamer outliers: 59 poor density : 79 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.7120 (mtm) cc_final: 0.6746 (mtm) REVERT: A 251 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7622 (mp0) REVERT: A 420 MET cc_start: 0.7491 (tpp) cc_final: 0.6245 (ttm) REVERT: A 514 MET cc_start: 0.4074 (ppp) cc_final: 0.3522 (tmm) REVERT: A 760 ASN cc_start: 0.6728 (m-40) cc_final: 0.6366 (m110) REVERT: B 160 ILE cc_start: 0.6259 (OUTLIER) cc_final: 0.5997 (mm) REVERT: B 291 CYS cc_start: 0.7723 (m) cc_final: 0.7444 (m) REVERT: B 594 ILE cc_start: 0.6945 (OUTLIER) cc_final: 0.6648 (mm) REVERT: B 614 PHE cc_start: 0.4436 (m-80) cc_final: 0.4110 (m-80) REVERT: B 718 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6646 (pp) outliers start: 59 outliers final: 42 residues processed: 133 average time/residue: 0.1924 time to fit residues: 41.2835 Evaluate side-chains 117 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 71 time to evaluate : 1.405 ------------------------------------------------------------------------------- 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 159 VAL Chi-restraints excluded: chain A residue 183 ILE 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 251 GLU Chi-restraints excluded: chain A residue 339 THR 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 556 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 159 VAL 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 202 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 281 LEU 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 413 VAL Chi-restraints excluded: chain B residue 420 MET 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 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 612 LEU Chi-restraints excluded: chain B residue 718 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 50.0000 chunk 90 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 143 optimal weight: 8.9990 chunk 123 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 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 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6045 moved from start: 0.6741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12658 Z= 0.244 Angle : 0.774 14.797 17171 Z= 0.387 Chirality : 0.045 0.193 1954 Planarity : 0.005 0.053 2163 Dihedral : 6.090 53.258 1723 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.44 % Favored : 91.50 % Rotamer: Outliers : 2.99 % Allowed : 20.89 % Favored : 76.11 % 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: -2.02 (0.20), residues: 1564 helix: -0.24 (0.20), residues: 690 sheet: -1.96 (0.42), residues: 128 loop : -2.32 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 570 HIS 0.004 0.001 HIS A 84 PHE 0.072 0.002 PHE B 639 TYR 0.029 0.001 TYR B 642 ARG 0.006 0.000 ARG B 203 ********************** REFINEMENT MACRO_CYCLE 10 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 120 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 79 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 SER cc_start: 0.7060 (OUTLIER) cc_final: 0.6368 (p) REVERT: A 82 MET cc_start: 0.6943 (mtm) cc_final: 0.6621 (mtm) REVERT: A 251 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7574 (mp0) REVERT: A 420 MET cc_start: 0.7363 (tpp) cc_final: 0.6187 (ttt) REVERT: A 514 MET cc_start: 0.3884 (ppp) cc_final: 0.3637 (tmm) REVERT: A 760 ASN cc_start: 0.6692 (m-40) cc_final: 0.6333 (m110) REVERT: B 241 MET cc_start: 0.6647 (tpp) cc_final: 0.6389 (tpp) REVERT: B 469 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7808 (m-80) REVERT: B 594 ILE cc_start: 0.6850 (OUTLIER) cc_final: 0.6565 (mm) REVERT: B 639 PHE cc_start: 0.6433 (m-80) cc_final: 0.6220 (m-80) outliers start: 41 outliers final: 34 residues processed: 116 average time/residue: 0.2010 time to fit residues: 37.6488 Evaluate side-chains 113 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 75 time to evaluate : 1.375 ------------------------------------------------------------------------------- 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 159 VAL Chi-restraints excluded: chain A residue 183 ILE 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 251 GLU Chi-restraints excluded: chain A residue 339 THR 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 556 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 111 HIS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 160 ILE 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 339 THR Chi-restraints excluded: chain B residue 344 SER 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 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 612 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 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 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 660 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 = 0.4535 r_free = 0.4535 target = 0.137556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.107558 restraints weight = 31303.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.105092 restraints weight = 33019.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.106664 restraints weight = 25416.471| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.6950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12658 Z= 0.314 Angle : 0.816 14.640 17171 Z= 0.410 Chirality : 0.046 0.190 1954 Planarity : 0.005 0.053 2163 Dihedral : 6.306 54.222 1723 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.61 % Favored : 89.32 % Rotamer: Outliers : 3.07 % Allowed : 21.18 % Favored : 75.75 % 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: -2.11 (0.20), residues: 1564 helix: -0.33 (0.19), residues: 694 sheet: -1.63 (0.44), residues: 122 loop : -2.44 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 500 HIS 0.005 0.001 HIS A 84 PHE 0.078 0.002 PHE B 639 TYR 0.022 0.002 TYR A 185 ARG 0.004 0.001 ARG B 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2149.13 seconds wall clock time: 41 minutes 14.78 seconds (2474.78 seconds total)