Starting phenix.real_space_refine on Wed Feb 14 20:24:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk1_32555/02_2024/7wk1_32555.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk1_32555/02_2024/7wk1_32555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk1_32555/02_2024/7wk1_32555.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk1_32555/02_2024/7wk1_32555.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk1_32555/02_2024/7wk1_32555.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk1_32555/02_2024/7wk1_32555.pdb" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians S 42 5.16 5 Cl 2 4.86 5 C 6656 2.51 5 N 1684 2.21 5 O 1816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 39": "NH1" <-> "NH2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 586": "NH1" <-> "NH2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 79": "NH1" <-> "NH2" Residue "B PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 586": "NH1" <-> "NH2" Residue "B ARG 587": "NH1" <-> "NH2" Residue "B PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10200 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5099 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 638} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5099 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 638} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.90, per 1000 atoms: 0.58 Number of scatterers: 10200 At special positions: 0 Unit cell: (86.818, 126.566, 117.152, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 42 16.00 O 1816 8.00 N 1684 7.00 C 6656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.76 Conformation dependent library (CDL) restraints added in 1.8 seconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 7 sheets defined 66.8% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.602A pdb=" N CYS A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 69 removed outlier: 3.882A pdb=" N ALA A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 removed outlier: 4.054A pdb=" N TRP A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 75' Processing helix chain 'A' and resid 79 through 106 removed outlier: 4.909A pdb=" N LEU A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 120 removed outlier: 3.851A pdb=" N GLY A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 141 through 156 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.804A pdb=" N HIS A 160 " --> pdb=" O PRO A 157 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 161 " --> pdb=" O ASP A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 161' Processing helix chain 'A' and resid 179 through 206 removed outlier: 3.883A pdb=" N ALA A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 removed outlier: 3.563A pdb=" N VAL A 212 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR A 214 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 241 Processing helix chain 'A' and resid 251 through 263 Processing helix chain 'A' and resid 268 through 292 Processing helix chain 'A' and resid 301 through 317 removed outlier: 3.621A pdb=" N ALA A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 374 Processing helix chain 'A' and resid 380 through 397 removed outlier: 3.758A pdb=" N GLU A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 417 removed outlier: 3.716A pdb=" N VAL A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 437 removed outlier: 3.662A pdb=" N VAL A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 458 removed outlier: 3.784A pdb=" N LEU A 450 " --> pdb=" O GLN A 446 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 464 through 466 No H-bonds generated for 'chain 'A' and resid 464 through 466' Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 475 through 492 removed outlier: 3.515A pdb=" N ALA A 479 " --> pdb=" O ASN A 475 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 490 " --> pdb=" O CYS A 486 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 515 removed outlier: 3.569A pdb=" N LEU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 571 Processing helix chain 'A' and resid 573 through 595 removed outlier: 3.782A pdb=" N TYR A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARG A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 591 " --> pdb=" O ARG A 587 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 686 removed outlier: 3.754A pdb=" N SER A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 706 removed outlier: 3.562A pdb=" N GLN A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 718 removed outlier: 3.529A pdb=" N ARG A 717 " --> pdb=" O ARG A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 736 removed outlier: 3.857A pdb=" N ALA A 725 " --> pdb=" O THR A 721 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 726 " --> pdb=" O VAL A 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.552A pdb=" N LEU B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 69 removed outlier: 3.752A pdb=" N ALA B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 removed outlier: 4.080A pdb=" N TRP B 74 " --> pdb=" O PRO B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 105 removed outlier: 3.729A pdb=" N SER B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 92 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 110 Processing helix chain 'B' and resid 113 through 119 removed outlier: 3.978A pdb=" N LEU B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 119 " --> pdb=" O PHE B 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 113 through 119' Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 141 through 156 removed outlier: 3.659A pdb=" N VAL B 151 " --> pdb=" O MET B 147 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.571A pdb=" N HIS B 160 " --> pdb=" O PRO B 157 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE B 161 " --> pdb=" O ASP B 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 157 through 161' Processing helix chain 'B' and resid 180 through 206 removed outlier: 3.981A pdb=" N ALA B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 215 removed outlier: 3.590A pdb=" N VAL B 212 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR B 214 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 241 removed outlier: 3.569A pdb=" N PHE B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 268 through 292 removed outlier: 3.641A pdb=" N THR B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 317 removed outlier: 3.514A pdb=" N ALA B 317 " --> pdb=" O ILE B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 376 removed outlier: 3.795A pdb=" N SER B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B 361 " --> pdb=" O ALA B 357 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS B 375 " --> pdb=" O TYR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 397 removed outlier: 3.963A pdb=" N GLU B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 416 removed outlier: 3.740A pdb=" N VAL B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 437 removed outlier: 3.611A pdb=" N VAL B 436 " --> pdb=" O MET B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 458 removed outlier: 3.779A pdb=" N LEU B 450 " --> pdb=" O GLN B 446 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 467 through 474 Processing helix chain 'B' and resid 475 through 492 removed outlier: 3.550A pdb=" N ALA B 479 " --> pdb=" O ASN B 475 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE B 490 " --> pdb=" O CYS B 486 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 492 " --> pdb=" O MET B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 515 removed outlier: 3.544A pdb=" N LEU B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 571 Processing helix chain 'B' and resid 573 through 595 removed outlier: 3.845A pdb=" N TYR B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ARG B 587 " --> pdb=" O LYS B 583 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS B 593 " --> pdb=" O GLN B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 685 removed outlier: 4.733A pdb=" N SER B 675 " --> pdb=" O VAL B 671 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU B 676 " --> pdb=" O GLY B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 706 removed outlier: 3.828A pdb=" N LYS B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 718 removed outlier: 3.551A pdb=" N ARG B 717 " --> pdb=" O ARG B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 736 removed outlier: 3.803A pdb=" N ALA B 725 " --> pdb=" O THR B 721 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 726 " --> pdb=" O VAL B 722 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 25 removed outlier: 3.607A pdb=" N VAL A 22 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 22 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA3, first strand: chain 'A' and resid 522 through 523 Processing sheet with id=AA4, first strand: chain 'A' and resid 545 through 549 removed outlier: 6.670A pdb=" N LYS A 546 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ASP A 661 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU A 548 " --> pdb=" O ASP A 661 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AA6, first strand: chain 'B' and resid 522 through 523 Processing sheet with id=AA7, first strand: chain 'B' and resid 545 through 549 removed outlier: 6.675A pdb=" N LYS B 546 " --> pdb=" O VAL B 659 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ASP B 661 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU B 548 " --> pdb=" O ASP B 661 " (cutoff:3.500A) 570 hydrogen bonds defined for protein. 1674 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: 2.94 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3212 1.34 - 1.46: 2260 1.46 - 1.58: 4864 1.58 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 10400 Sorted by residual: bond pdb=" CA VAL A 163 " pdb=" CB VAL A 163 " ideal model delta sigma weight residual 1.540 1.527 0.014 1.23e-02 6.61e+03 1.21e+00 bond pdb=" C VAL B 653 " pdb=" N PRO B 654 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.04e-01 bond pdb=" C VAL A 653 " pdb=" N PRO A 654 " ideal model delta sigma weight residual 1.334 1.353 -0.020 2.34e-02 1.83e+03 6.95e-01 bond pdb=" CA ASP A 669 " pdb=" C ASP A 669 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.34e-02 5.57e+03 5.79e-01 bond pdb=" C GLY B 166 " pdb=" N ASN B 167 " ideal model delta sigma weight residual 1.328 1.338 -0.010 1.30e-02 5.92e+03 5.79e-01 ... (remaining 10395 not shown) Histogram of bond angle deviations from ideal: 100.81 - 107.44: 299 107.44 - 114.07: 6166 114.07 - 120.70: 4403 120.70 - 127.33: 3194 127.33 - 133.97: 74 Bond angle restraints: 14136 Sorted by residual: angle pdb=" C ASP B 467 " pdb=" N VAL B 468 " pdb=" CA VAL B 468 " ideal model delta sigma weight residual 120.33 122.69 -2.36 8.00e-01 1.56e+00 8.69e+00 angle pdb=" C ASP A 669 " pdb=" N VAL A 670 " pdb=" CA VAL A 670 " ideal model delta sigma weight residual 121.97 126.24 -4.27 1.80e+00 3.09e-01 5.62e+00 angle pdb=" N VAL A 80 " pdb=" CA VAL A 80 " pdb=" C VAL A 80 " ideal model delta sigma weight residual 109.34 113.75 -4.41 2.08e+00 2.31e-01 4.49e+00 angle pdb=" C ARG A 79 " pdb=" N VAL A 80 " pdb=" CA VAL A 80 " ideal model delta sigma weight residual 121.97 125.66 -3.69 1.80e+00 3.09e-01 4.20e+00 angle pdb=" C ASP B 669 " pdb=" N VAL B 670 " pdb=" CA VAL B 670 " ideal model delta sigma weight residual 121.97 125.56 -3.59 1.80e+00 3.09e-01 3.99e+00 ... (remaining 14131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 5999 17.18 - 34.36: 150 34.36 - 51.53: 22 51.53 - 68.71: 6 68.71 - 85.89: 5 Dihedral angle restraints: 6182 sinusoidal: 2346 harmonic: 3836 Sorted by residual: dihedral pdb=" CA ASP A 669 " pdb=" C ASP A 669 " pdb=" N VAL A 670 " pdb=" CA VAL A 670 " ideal model delta harmonic sigma weight residual -180.00 -164.27 -15.73 0 5.00e+00 4.00e-02 9.90e+00 dihedral pdb=" N LYS A 681 " pdb=" CA LYS A 681 " pdb=" CB LYS A 681 " pdb=" CG LYS A 681 " ideal model delta sinusoidal sigma weight residual -180.00 -121.99 -58.01 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N LEU A 496 " pdb=" CA LEU A 496 " pdb=" CB LEU A 496 " pdb=" CG LEU A 496 " ideal model delta sinusoidal sigma weight residual -60.00 -113.85 53.85 3 1.50e+01 4.44e-03 9.24e+00 ... (remaining 6179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 985 0.026 - 0.053: 479 0.053 - 0.079: 171 0.079 - 0.105: 65 0.105 - 0.131: 18 Chirality restraints: 1718 Sorted by residual: chirality pdb=" CA PRO A 553 " pdb=" N PRO A 553 " pdb=" C PRO A 553 " pdb=" CB PRO A 553 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA PRO B 553 " pdb=" N PRO B 553 " pdb=" C PRO B 553 " pdb=" CB PRO B 553 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ILE A 331 " pdb=" N ILE A 331 " pdb=" C ILE A 331 " pdb=" CB ILE A 331 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 1715 not shown) Planarity restraints: 1758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 552 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO B 553 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 553 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 553 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 552 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO A 553 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 553 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 553 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 111 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.76e+00 pdb=" N PRO A 112 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " 0.018 5.00e-02 4.00e+02 ... (remaining 1755 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1226 2.75 - 3.29: 10788 3.29 - 3.82: 16684 3.82 - 4.36: 19765 4.36 - 4.90: 33560 Nonbonded interactions: 82023 Sorted by model distance: nonbonded pdb=" OH TYR A 78 " pdb=" OD2 ASP A 87 " model vdw 2.212 2.440 nonbonded pdb=" OH TYR A 118 " pdb=" O GLY A 334 " model vdw 2.225 2.440 nonbonded pdb=" O ASP A 669 " pdb=" N GLY A 672 " model vdw 2.238 2.520 nonbonded pdb=" OD1 ASN A 475 " pdb=" OG1 THR A 477 " model vdw 2.244 2.440 nonbonded pdb=" OD1 ASN B 475 " pdb=" OG1 THR B 477 " model vdw 2.248 2.440 ... (remaining 82018 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' 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 individual isotropic 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: 3.110 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: 15.500 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 27.740 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 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 : 0.002 0.025 10400 Z= 0.111 Angle : 0.443 6.082 14136 Z= 0.251 Chirality : 0.037 0.131 1718 Planarity : 0.003 0.035 1758 Dihedral : 8.422 85.889 3710 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.70 % Rotamer: Outliers : 2.94 % Allowed : 4.72 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.19), residues: 1322 helix: -2.20 (0.14), residues: 860 sheet: -3.22 (0.77), residues: 36 loop : -3.28 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 83 HIS 0.002 0.000 HIS A 656 PHE 0.009 0.001 PHE B 555 TYR 0.008 0.001 TYR A 127 ARG 0.001 0.000 ARG B 512 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 314 time to evaluate : 1.156 Fit side-chains REVERT: A 73 ASP cc_start: 0.7646 (t0) cc_final: 0.7313 (m-30) REVERT: A 119 SER cc_start: 0.8633 (t) cc_final: 0.8415 (p) REVERT: A 269 ILE cc_start: 0.8302 (pt) cc_final: 0.7931 (pt) REVERT: A 273 ILE cc_start: 0.8837 (mt) cc_final: 0.8585 (mt) REVERT: A 345 LEU cc_start: 0.6245 (mt) cc_final: 0.5738 (mt) REVERT: A 350 LEU cc_start: 0.5830 (OUTLIER) cc_final: 0.5410 (pt) REVERT: A 369 LYS cc_start: 0.8083 (mmtt) cc_final: 0.7580 (mttm) REVERT: A 385 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.7073 (t80) REVERT: A 560 ASP cc_start: 0.7912 (m-30) cc_final: 0.7648 (m-30) REVERT: A 580 LYS cc_start: 0.8180 (mmtt) cc_final: 0.7786 (mtpt) REVERT: B 66 LYS cc_start: 0.8607 (tppt) cc_final: 0.8018 (mttm) REVERT: B 73 ASP cc_start: 0.7799 (t0) cc_final: 0.7562 (t0) REVERT: B 77 LYS cc_start: 0.7489 (pttm) cc_final: 0.7013 (tptt) REVERT: B 134 ARG cc_start: 0.7776 (mtt90) cc_final: 0.7362 (mtp180) REVERT: B 350 LEU cc_start: 0.6233 (OUTLIER) cc_final: 0.5900 (tm) REVERT: B 355 SER cc_start: 0.8950 (m) cc_final: 0.8617 (t) REVERT: B 366 SER cc_start: 0.8939 (t) cc_final: 0.8231 (m) REVERT: B 560 ASP cc_start: 0.7781 (m-30) cc_final: 0.7536 (m-30) REVERT: B 580 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7937 (mtpt) outliers start: 33 outliers final: 6 residues processed: 336 average time/residue: 0.2290 time to fit residues: 106.1236 Evaluate side-chains 184 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 175 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 496 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 119 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 230 GLN A 656 HIS A 728 HIS A 730 GLN A 731 ASN B 160 HIS B 421 GLN B 656 HIS B 728 HIS B 730 GLN B 731 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10400 Z= 0.227 Angle : 0.572 6.246 14136 Z= 0.298 Chirality : 0.043 0.204 1718 Planarity : 0.005 0.049 1758 Dihedral : 4.678 54.590 1431 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 4.37 % Allowed : 11.32 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.22), residues: 1322 helix: -0.27 (0.17), residues: 862 sheet: -3.57 (0.64), residues: 50 loop : -2.84 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 518 HIS 0.009 0.001 HIS A 656 PHE 0.024 0.002 PHE A 130 TYR 0.027 0.001 TYR A 371 ARG 0.006 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 184 time to evaluate : 1.165 Fit side-chains REVERT: A 73 ASP cc_start: 0.7645 (t0) cc_final: 0.7238 (t0) REVERT: A 119 SER cc_start: 0.8851 (t) cc_final: 0.8537 (p) REVERT: A 269 ILE cc_start: 0.8331 (pt) cc_final: 0.7951 (pt) REVERT: A 273 ILE cc_start: 0.8895 (mt) cc_final: 0.8676 (mt) REVERT: A 309 ILE cc_start: 0.9495 (OUTLIER) cc_final: 0.9287 (mp) REVERT: A 345 LEU cc_start: 0.6466 (mt) cc_final: 0.6203 (mt) REVERT: A 350 LEU cc_start: 0.5919 (OUTLIER) cc_final: 0.5454 (pt) REVERT: A 369 LYS cc_start: 0.7999 (mmtt) cc_final: 0.7636 (mttm) REVERT: A 385 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.7235 (t80) REVERT: A 560 ASP cc_start: 0.7979 (m-30) cc_final: 0.7704 (m-30) REVERT: A 580 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7755 (mtpt) REVERT: B 66 LYS cc_start: 0.8827 (tppt) cc_final: 0.8122 (mttm) REVERT: B 73 ASP cc_start: 0.7984 (t0) cc_final: 0.7747 (t0) REVERT: B 96 LEU cc_start: 0.8668 (mt) cc_final: 0.8467 (mt) REVERT: B 134 ARG cc_start: 0.7835 (mtt90) cc_final: 0.7553 (mtm-85) REVERT: B 350 LEU cc_start: 0.6343 (OUTLIER) cc_final: 0.6004 (tp) REVERT: B 366 SER cc_start: 0.8691 (t) cc_final: 0.7896 (m) REVERT: B 580 LYS cc_start: 0.8186 (mmtt) cc_final: 0.7971 (mtpt) REVERT: B 590 LYS cc_start: 0.5754 (OUTLIER) cc_final: 0.5522 (pttp) outliers start: 49 outliers final: 22 residues processed: 217 average time/residue: 0.2201 time to fit residues: 67.5277 Evaluate side-chains 182 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 155 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 695 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 120 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 119 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 421 GLN A 656 HIS B 135 HIS B 160 HIS B 656 HIS B 732 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10400 Z= 0.354 Angle : 0.627 10.363 14136 Z= 0.328 Chirality : 0.045 0.183 1718 Planarity : 0.005 0.072 1758 Dihedral : 4.810 55.850 1426 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.73 % Favored : 93.19 % Rotamer: Outliers : 4.46 % Allowed : 12.75 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.23), residues: 1322 helix: 0.23 (0.17), residues: 868 sheet: -3.28 (0.65), residues: 50 loop : -2.75 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 518 HIS 0.012 0.002 HIS A 656 PHE 0.022 0.002 PHE A 122 TYR 0.022 0.002 TYR A 247 ARG 0.006 0.001 ARG B 677 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 162 time to evaluate : 1.209 Fit side-chains REVERT: A 77 LYS cc_start: 0.7787 (pttm) cc_final: 0.6952 (tptt) REVERT: A 78 TYR cc_start: 0.6208 (t80) cc_final: 0.5911 (t80) REVERT: A 269 ILE cc_start: 0.8304 (pt) cc_final: 0.7798 (pt) REVERT: A 273 ILE cc_start: 0.8903 (mt) cc_final: 0.8671 (mp) REVERT: A 350 LEU cc_start: 0.6210 (OUTLIER) cc_final: 0.5662 (tp) REVERT: A 369 LYS cc_start: 0.8087 (mmtt) cc_final: 0.7681 (mttm) REVERT: A 385 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7767 (t80) REVERT: A 432 MET cc_start: 0.8170 (tpp) cc_final: 0.7920 (tpp) REVERT: A 560 ASP cc_start: 0.8118 (m-30) cc_final: 0.7846 (m-30) REVERT: A 580 LYS cc_start: 0.8200 (mmtt) cc_final: 0.7835 (mtpt) REVERT: B 66 LYS cc_start: 0.8831 (tppt) cc_final: 0.8133 (mttm) REVERT: B 73 ASP cc_start: 0.8195 (t0) cc_final: 0.7855 (t0) REVERT: B 134 ARG cc_start: 0.7929 (mtt90) cc_final: 0.7481 (mtp180) REVERT: B 350 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6312 (tp) REVERT: B 369 LYS cc_start: 0.8183 (mmtt) cc_final: 0.7732 (mttm) REVERT: B 398 PHE cc_start: 0.7418 (m-80) cc_final: 0.6970 (m-80) REVERT: B 414 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7192 (tm-30) REVERT: B 580 LYS cc_start: 0.8253 (mmtt) cc_final: 0.8001 (mtpt) outliers start: 50 outliers final: 30 residues processed: 199 average time/residue: 0.2234 time to fit residues: 62.9666 Evaluate side-chains 170 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 590 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 62 optimal weight: 0.3980 chunk 13 optimal weight: 0.5980 chunk 57 optimal weight: 0.0470 chunk 80 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 127 optimal weight: 0.2980 chunk 114 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 656 HIS B 160 HIS B 464 GLN B 656 HIS ** B 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10400 Z= 0.167 Angle : 0.531 8.690 14136 Z= 0.277 Chirality : 0.041 0.172 1718 Planarity : 0.004 0.060 1758 Dihedral : 4.626 53.943 1426 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.82 % Favored : 94.10 % Rotamer: Outliers : 3.39 % Allowed : 14.88 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.24), residues: 1322 helix: 0.72 (0.18), residues: 862 sheet: -3.18 (0.70), residues: 50 loop : -2.57 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 482 HIS 0.011 0.001 HIS A 656 PHE 0.014 0.001 PHE B 667 TYR 0.016 0.001 TYR B 247 ARG 0.005 0.000 ARG B 576 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 146 time to evaluate : 1.161 Fit side-chains revert: symmetry clash REVERT: A 77 LYS cc_start: 0.7589 (pttm) cc_final: 0.6984 (tptt) REVERT: A 78 TYR cc_start: 0.6309 (t80) cc_final: 0.5955 (t80) REVERT: A 119 SER cc_start: 0.8930 (t) cc_final: 0.8407 (p) REVERT: A 269 ILE cc_start: 0.8283 (pt) cc_final: 0.7750 (pt) REVERT: A 273 ILE cc_start: 0.8871 (mt) cc_final: 0.8640 (mp) REVERT: A 313 ILE cc_start: 0.9061 (mm) cc_final: 0.8835 (mm) REVERT: A 350 LEU cc_start: 0.6053 (OUTLIER) cc_final: 0.5557 (tp) REVERT: A 369 LYS cc_start: 0.8060 (mmtt) cc_final: 0.7714 (mttm) REVERT: A 385 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7657 (t80) REVERT: A 560 ASP cc_start: 0.8060 (m-30) cc_final: 0.7815 (m-30) REVERT: A 580 LYS cc_start: 0.8233 (mmtt) cc_final: 0.7878 (mtpt) REVERT: B 66 LYS cc_start: 0.8804 (tppt) cc_final: 0.8121 (mttm) REVERT: B 73 ASP cc_start: 0.8120 (t0) cc_final: 0.7840 (t0) REVERT: B 134 ARG cc_start: 0.7929 (mtt90) cc_final: 0.7463 (mtp180) REVERT: B 350 LEU cc_start: 0.6625 (OUTLIER) cc_final: 0.6230 (tp) REVERT: B 369 LYS cc_start: 0.8164 (mmtt) cc_final: 0.7730 (mttm) REVERT: B 580 LYS cc_start: 0.8277 (mmtt) cc_final: 0.7967 (mtpt) REVERT: B 590 LYS cc_start: 0.5527 (OUTLIER) cc_final: 0.5311 (pttp) outliers start: 38 outliers final: 22 residues processed: 173 average time/residue: 0.2257 time to fit residues: 54.7384 Evaluate side-chains 164 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 666 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 0.0170 chunk 108 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 32 optimal weight: 0.1980 chunk 42 optimal weight: 1.9990 overall best weight: 0.5822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 656 HIS B 160 HIS B 656 HIS ** B 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10400 Z= 0.211 Angle : 0.532 7.691 14136 Z= 0.275 Chirality : 0.041 0.163 1718 Planarity : 0.004 0.065 1758 Dihedral : 4.612 53.884 1426 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.43 % Favored : 93.49 % Rotamer: Outliers : 4.19 % Allowed : 15.15 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.24), residues: 1322 helix: 0.88 (0.18), residues: 870 sheet: -3.06 (0.71), residues: 50 loop : -2.51 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 482 HIS 0.011 0.002 HIS B 656 PHE 0.013 0.001 PHE A 115 TYR 0.014 0.001 TYR B 247 ARG 0.006 0.000 ARG B 576 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 144 time to evaluate : 1.233 Fit side-chains REVERT: A 77 LYS cc_start: 0.7905 (pttm) cc_final: 0.7183 (tptt) REVERT: A 78 TYR cc_start: 0.6442 (t80) cc_final: 0.6061 (t80) REVERT: A 119 SER cc_start: 0.8965 (t) cc_final: 0.8420 (p) REVERT: A 155 MET cc_start: 0.7582 (mtt) cc_final: 0.7369 (mtp) REVERT: A 269 ILE cc_start: 0.8183 (pt) cc_final: 0.7640 (pt) REVERT: A 273 ILE cc_start: 0.8889 (mt) cc_final: 0.8643 (mp) REVERT: A 313 ILE cc_start: 0.9053 (mm) cc_final: 0.8824 (mm) REVERT: A 348 ASP cc_start: 0.4970 (OUTLIER) cc_final: 0.4244 (t0) REVERT: A 350 LEU cc_start: 0.6048 (OUTLIER) cc_final: 0.5533 (tp) REVERT: A 369 LYS cc_start: 0.8033 (mmtt) cc_final: 0.7695 (mttm) REVERT: A 385 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.7709 (t80) REVERT: A 560 ASP cc_start: 0.8090 (m-30) cc_final: 0.7825 (m-30) REVERT: A 580 LYS cc_start: 0.8249 (mmtt) cc_final: 0.7886 (mtpt) REVERT: B 66 LYS cc_start: 0.8767 (tppt) cc_final: 0.8104 (mttm) REVERT: B 73 ASP cc_start: 0.8147 (t0) cc_final: 0.7827 (t0) REVERT: B 134 ARG cc_start: 0.7934 (mtt90) cc_final: 0.7419 (mtp180) REVERT: B 350 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.6209 (tp) REVERT: B 369 LYS cc_start: 0.8122 (mmtt) cc_final: 0.7666 (mttm) REVERT: B 580 LYS cc_start: 0.8302 (mmtt) cc_final: 0.8004 (mtpt) REVERT: B 590 LYS cc_start: 0.5568 (OUTLIER) cc_final: 0.5367 (pttp) outliers start: 47 outliers final: 31 residues processed: 175 average time/residue: 0.2134 time to fit residues: 53.2362 Evaluate side-chains 175 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 139 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 590 LYS Chi-restraints excluded: chain B residue 666 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 31 optimal weight: 0.0020 chunk 127 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 59 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 656 HIS B 656 HIS ** B 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10400 Z= 0.203 Angle : 0.527 6.984 14136 Z= 0.276 Chirality : 0.041 0.178 1718 Planarity : 0.004 0.063 1758 Dihedral : 4.624 54.684 1426 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.20 % Favored : 93.72 % Rotamer: Outliers : 4.72 % Allowed : 14.80 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.24), residues: 1322 helix: 0.99 (0.18), residues: 870 sheet: -2.89 (0.73), residues: 50 loop : -2.42 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 482 HIS 0.011 0.001 HIS A 656 PHE 0.014 0.001 PHE B 667 TYR 0.016 0.001 TYR A 247 ARG 0.006 0.000 ARG B 576 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 141 time to evaluate : 1.223 Fit side-chains REVERT: A 77 LYS cc_start: 0.7883 (pttm) cc_final: 0.7175 (tptt) REVERT: A 78 TYR cc_start: 0.6482 (t80) cc_final: 0.6129 (t80) REVERT: A 119 SER cc_start: 0.8910 (t) cc_final: 0.8348 (p) REVERT: A 155 MET cc_start: 0.7619 (mtt) cc_final: 0.7403 (mtp) REVERT: A 269 ILE cc_start: 0.8176 (pt) cc_final: 0.7634 (pt) REVERT: A 273 ILE cc_start: 0.8887 (mt) cc_final: 0.8640 (mp) REVERT: A 313 ILE cc_start: 0.9061 (mm) cc_final: 0.8828 (mm) REVERT: A 350 LEU cc_start: 0.5829 (OUTLIER) cc_final: 0.5494 (tp) REVERT: A 369 LYS cc_start: 0.8027 (mmtt) cc_final: 0.7704 (mttm) REVERT: A 385 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7759 (t80) REVERT: A 560 ASP cc_start: 0.8088 (m-30) cc_final: 0.7826 (m-30) REVERT: A 580 LYS cc_start: 0.8286 (mmtt) cc_final: 0.7918 (mtpt) REVERT: B 66 LYS cc_start: 0.8723 (tppt) cc_final: 0.8261 (mttm) REVERT: B 73 ASP cc_start: 0.8145 (t0) cc_final: 0.7451 (m-30) REVERT: B 100 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8182 (mm) REVERT: B 134 ARG cc_start: 0.7964 (mtt90) cc_final: 0.7496 (mtp180) REVERT: B 350 LEU cc_start: 0.6625 (OUTLIER) cc_final: 0.6240 (tp) REVERT: B 369 LYS cc_start: 0.8143 (mmtt) cc_final: 0.7715 (mttm) REVERT: B 580 LYS cc_start: 0.8317 (mmtt) cc_final: 0.8003 (mtpt) outliers start: 53 outliers final: 34 residues processed: 180 average time/residue: 0.2148 time to fit residues: 55.4488 Evaluate side-chains 173 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 135 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 93 optimal weight: 0.0980 chunk 107 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 127 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 58 optimal weight: 0.2980 chunk 78 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 656 HIS B 160 HIS B 464 GLN B 656 HIS ** B 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10400 Z= 0.193 Angle : 0.526 9.138 14136 Z= 0.275 Chirality : 0.041 0.162 1718 Planarity : 0.004 0.063 1758 Dihedral : 4.612 55.182 1426 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.51 % Favored : 93.42 % Rotamer: Outliers : 4.37 % Allowed : 16.04 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.24), residues: 1322 helix: 1.11 (0.18), residues: 864 sheet: -2.75 (0.74), residues: 50 loop : -2.37 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 482 HIS 0.011 0.001 HIS A 656 PHE 0.013 0.001 PHE B 667 TYR 0.018 0.001 TYR A 247 ARG 0.007 0.000 ARG B 576 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 138 time to evaluate : 1.023 Fit side-chains REVERT: A 77 LYS cc_start: 0.7851 (pttm) cc_final: 0.7203 (tptt) REVERT: A 78 TYR cc_start: 0.6571 (t80) cc_final: 0.6225 (t80) REVERT: A 119 SER cc_start: 0.8910 (t) cc_final: 0.8331 (p) REVERT: A 155 MET cc_start: 0.7689 (mtt) cc_final: 0.7461 (mtp) REVERT: A 269 ILE cc_start: 0.8168 (pt) cc_final: 0.7547 (pt) REVERT: A 273 ILE cc_start: 0.8866 (mt) cc_final: 0.8616 (mp) REVERT: A 313 ILE cc_start: 0.9045 (mm) cc_final: 0.8828 (mm) REVERT: A 350 LEU cc_start: 0.5518 (OUTLIER) cc_final: 0.5285 (tp) REVERT: A 369 LYS cc_start: 0.7963 (mmtt) cc_final: 0.7614 (mttm) REVERT: A 385 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7859 (t80) REVERT: A 560 ASP cc_start: 0.8067 (m-30) cc_final: 0.7801 (m-30) REVERT: A 580 LYS cc_start: 0.8291 (mmtt) cc_final: 0.7924 (mtpt) REVERT: B 66 LYS cc_start: 0.8742 (tppt) cc_final: 0.8202 (mttm) REVERT: B 73 ASP cc_start: 0.8102 (t0) cc_final: 0.7452 (m-30) REVERT: B 100 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8167 (mm) REVERT: B 134 ARG cc_start: 0.7960 (mtt90) cc_final: 0.7509 (mtp180) REVERT: B 350 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.6168 (tp) REVERT: B 369 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7689 (mttm) REVERT: B 580 LYS cc_start: 0.8321 (mmtt) cc_final: 0.8003 (mtpt) outliers start: 49 outliers final: 37 residues processed: 174 average time/residue: 0.2078 time to fit residues: 52.0351 Evaluate side-chains 175 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 134 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 115 optimal weight: 0.2980 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 656 HIS B 160 HIS B 656 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10400 Z= 0.224 Angle : 0.537 8.865 14136 Z= 0.282 Chirality : 0.041 0.157 1718 Planarity : 0.004 0.067 1758 Dihedral : 4.687 56.891 1426 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.43 % Favored : 93.49 % Rotamer: Outliers : 4.46 % Allowed : 16.67 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.25), residues: 1322 helix: 1.15 (0.18), residues: 864 sheet: -2.69 (0.73), residues: 50 loop : -2.32 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 482 HIS 0.011 0.002 HIS A 656 PHE 0.015 0.001 PHE B 667 TYR 0.022 0.001 TYR A 371 ARG 0.008 0.000 ARG B 576 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 141 time to evaluate : 1.143 Fit side-chains REVERT: A 77 LYS cc_start: 0.7770 (pttm) cc_final: 0.7164 (tptt) REVERT: A 78 TYR cc_start: 0.6591 (t80) cc_final: 0.6244 (t80) REVERT: A 119 SER cc_start: 0.8938 (t) cc_final: 0.8348 (p) REVERT: A 155 MET cc_start: 0.7682 (mtt) cc_final: 0.7436 (mtp) REVERT: A 269 ILE cc_start: 0.8225 (pt) cc_final: 0.7708 (pt) REVERT: A 273 ILE cc_start: 0.8872 (mt) cc_final: 0.8626 (mp) REVERT: A 313 ILE cc_start: 0.9058 (mm) cc_final: 0.8845 (mm) REVERT: A 350 LEU cc_start: 0.5543 (OUTLIER) cc_final: 0.5343 (tp) REVERT: A 369 LYS cc_start: 0.7879 (mmtt) cc_final: 0.7508 (mttm) REVERT: A 560 ASP cc_start: 0.8068 (m-30) cc_final: 0.7813 (m-30) REVERT: A 580 LYS cc_start: 0.8279 (mmtt) cc_final: 0.7917 (mtpt) REVERT: B 66 LYS cc_start: 0.8779 (tppt) cc_final: 0.8227 (mttm) REVERT: B 73 ASP cc_start: 0.8059 (t0) cc_final: 0.7371 (m-30) REVERT: B 100 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8181 (mm) REVERT: B 134 ARG cc_start: 0.7939 (mtt90) cc_final: 0.7464 (mtp180) REVERT: B 350 LEU cc_start: 0.6522 (OUTLIER) cc_final: 0.6083 (tp) REVERT: B 369 LYS cc_start: 0.8089 (mmtt) cc_final: 0.7678 (mttm) REVERT: B 580 LYS cc_start: 0.8328 (mmtt) cc_final: 0.8004 (mtpt) outliers start: 50 outliers final: 41 residues processed: 178 average time/residue: 0.2187 time to fit residues: 55.8329 Evaluate side-chains 181 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 137 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 463 MET Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 541 GLU Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.0970 chunk 121 optimal weight: 0.0870 chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 77 optimal weight: 0.0570 chunk 125 optimal weight: 0.4980 chunk 76 optimal weight: 0.5980 overall best weight: 0.2274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 656 HIS B 160 HIS B 656 HIS ** B 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10400 Z= 0.151 Angle : 0.523 9.611 14136 Z= 0.274 Chirality : 0.040 0.170 1718 Planarity : 0.004 0.058 1758 Dihedral : 4.594 55.615 1426 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.20 % Favored : 93.72 % Rotamer: Outliers : 3.83 % Allowed : 17.74 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.25), residues: 1322 helix: 1.23 (0.18), residues: 862 sheet: -2.59 (0.76), residues: 50 loop : -2.28 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 482 HIS 0.011 0.001 HIS A 656 PHE 0.024 0.001 PHE A 130 TYR 0.019 0.001 TYR A 247 ARG 0.008 0.000 ARG B 576 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 142 time to evaluate : 1.225 Fit side-chains REVERT: A 77 LYS cc_start: 0.7836 (pttm) cc_final: 0.7196 (tptt) REVERT: A 78 TYR cc_start: 0.6569 (t80) cc_final: 0.6213 (t80) REVERT: A 119 SER cc_start: 0.8817 (t) cc_final: 0.8250 (p) REVERT: A 155 MET cc_start: 0.7691 (mtt) cc_final: 0.7486 (mtp) REVERT: A 269 ILE cc_start: 0.8127 (pt) cc_final: 0.7604 (pt) REVERT: A 273 ILE cc_start: 0.8865 (mt) cc_final: 0.8624 (mt) REVERT: A 313 ILE cc_start: 0.9043 (mm) cc_final: 0.8839 (mm) REVERT: A 369 LYS cc_start: 0.7907 (mmtt) cc_final: 0.7595 (mttm) REVERT: A 560 ASP cc_start: 0.8036 (m-30) cc_final: 0.7784 (m-30) REVERT: A 580 LYS cc_start: 0.8265 (mmtt) cc_final: 0.7898 (mtpt) REVERT: B 66 LYS cc_start: 0.8735 (tppt) cc_final: 0.8198 (mttm) REVERT: B 73 ASP cc_start: 0.7945 (t0) cc_final: 0.7307 (m-30) REVERT: B 100 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8011 (mm) REVERT: B 134 ARG cc_start: 0.7920 (mtt90) cc_final: 0.7441 (mtp180) REVERT: B 350 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.6120 (tp) REVERT: B 369 LYS cc_start: 0.8039 (mmtt) cc_final: 0.7640 (mttm) REVERT: B 580 LYS cc_start: 0.8304 (mmtt) cc_final: 0.8002 (mtpt) outliers start: 43 outliers final: 32 residues processed: 171 average time/residue: 0.2102 time to fit residues: 51.4273 Evaluate side-chains 171 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 137 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 111 optimal weight: 0.0870 chunk 32 optimal weight: 3.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 656 HIS B 160 HIS B 656 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10400 Z= 0.231 Angle : 0.549 8.825 14136 Z= 0.288 Chirality : 0.042 0.197 1718 Planarity : 0.004 0.067 1758 Dihedral : 4.575 57.148 1424 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.88 % Favored : 93.04 % Rotamer: Outliers : 3.21 % Allowed : 18.45 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.25), residues: 1322 helix: 1.21 (0.18), residues: 864 sheet: -2.56 (0.75), residues: 50 loop : -2.23 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 482 HIS 0.011 0.002 HIS A 656 PHE 0.019 0.001 PHE A 130 TYR 0.017 0.001 TYR A 371 ARG 0.008 0.000 ARG B 576 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 137 time to evaluate : 1.265 Fit side-chains REVERT: A 77 LYS cc_start: 0.7801 (pttm) cc_final: 0.7189 (tptt) REVERT: A 78 TYR cc_start: 0.6583 (t80) cc_final: 0.6250 (t80) REVERT: A 119 SER cc_start: 0.8951 (t) cc_final: 0.8351 (p) REVERT: A 155 MET cc_start: 0.7512 (mtt) cc_final: 0.7290 (mtp) REVERT: A 269 ILE cc_start: 0.8247 (pt) cc_final: 0.7744 (pt) REVERT: A 273 ILE cc_start: 0.8876 (mt) cc_final: 0.8635 (mt) REVERT: A 369 LYS cc_start: 0.7943 (mmtt) cc_final: 0.7606 (mttm) REVERT: A 398 PHE cc_start: 0.7187 (m-80) cc_final: 0.6837 (m-80) REVERT: A 560 ASP cc_start: 0.8074 (m-30) cc_final: 0.7837 (m-30) REVERT: A 580 LYS cc_start: 0.8267 (mmtt) cc_final: 0.7910 (mtpt) REVERT: B 66 LYS cc_start: 0.8775 (tppt) cc_final: 0.8232 (mttm) REVERT: B 73 ASP cc_start: 0.7960 (t0) cc_final: 0.7322 (m-30) REVERT: B 134 ARG cc_start: 0.7962 (mtt90) cc_final: 0.7465 (mtp180) REVERT: B 229 PHE cc_start: 0.7759 (m-80) cc_final: 0.7555 (m-80) REVERT: B 350 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6185 (tp) REVERT: B 369 LYS cc_start: 0.8147 (mmtt) cc_final: 0.7760 (mttm) REVERT: B 580 LYS cc_start: 0.8328 (mmtt) cc_final: 0.8008 (mtpt) outliers start: 36 outliers final: 32 residues processed: 165 average time/residue: 0.2152 time to fit residues: 50.8046 Evaluate side-chains 169 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 136 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.0170 chunk 15 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 92 optimal weight: 0.8980 chunk 5 optimal weight: 0.0770 chunk 75 optimal weight: 0.6980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 656 HIS B 160 HIS B 656 HIS ** B 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.147788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.116909 restraints weight = 14477.955| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.26 r_work: 0.3224 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10400 Z= 0.178 Angle : 0.542 11.924 14136 Z= 0.282 Chirality : 0.041 0.168 1718 Planarity : 0.004 0.060 1758 Dihedral : 4.550 56.574 1424 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.20 % Favored : 93.72 % Rotamer: Outliers : 3.12 % Allowed : 18.81 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.25), residues: 1322 helix: 1.25 (0.18), residues: 864 sheet: -2.52 (0.76), residues: 50 loop : -2.16 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 482 HIS 0.012 0.002 HIS A 656 PHE 0.020 0.001 PHE A 130 TYR 0.019 0.001 TYR A 247 ARG 0.008 0.000 ARG B 576 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2547.66 seconds wall clock time: 47 minutes 6.80 seconds (2826.80 seconds total)