Starting phenix.real_space_refine on Mon Aug 5 13:29:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tjp_41307/08_2024/8tjp_41307.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tjp_41307/08_2024/8tjp_41307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tjp_41307/08_2024/8tjp_41307.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tjp_41307/08_2024/8tjp_41307.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tjp_41307/08_2024/8tjp_41307.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tjp_41307/08_2024/8tjp_41307.cif" } resolution = 3.71 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= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 8340 2.51 5 N 2484 2.21 5 O 2604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 99": "OD1" <-> "OD2" Residue "A ASP 162": "OD1" <-> "OD2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A GLU 530": "OE1" <-> "OE2" Residue "A GLU 537": "OE1" <-> "OE2" Residue "A GLU 550": "OE1" <-> "OE2" Residue "A ASP 556": "OD1" <-> "OD2" Residue "A ASP 606": "OD1" <-> "OD2" Residue "A GLU 668": "OE1" <-> "OE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A GLU 765": "OE1" <-> "OE2" Residue "A GLU 844": "OE1" <-> "OE2" Residue "A GLU 850": "OE1" <-> "OE2" Residue "A TYR 899": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B ASP 162": "OD1" <-> "OD2" Residue "B ASP 200": "OD1" <-> "OD2" Residue "B GLU 221": "OE1" <-> "OE2" Residue "B ASP 241": "OD1" <-> "OD2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B GLU 287": "OE1" <-> "OE2" Residue "B GLU 323": "OE1" <-> "OE2" Residue "B GLU 336": "OE1" <-> "OE2" Residue "B ASP 360": "OD1" <-> "OD2" Residue "B GLU 537": "OE1" <-> "OE2" Residue "B GLU 550": "OE1" <-> "OE2" Residue "B GLU 636": "OE1" <-> "OE2" Residue "B GLU 655": "OE1" <-> "OE2" Residue "B ASP 669": "OD1" <-> "OD2" Residue "B ASP 749": "OD1" <-> "OD2" Residue "B ASP 751": "OD1" <-> "OD2" Residue "B GLU 760": "OE1" <-> "OE2" Residue "B GLU 765": "OE1" <-> "OE2" Residue "B GLU 795": "OE1" <-> "OE2" Residue "B GLU 820": "OE1" <-> "OE2" Residue "B GLU 828": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 13464 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6732 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 896, 6671 Classifications: {'peptide': 896} Link IDs: {'PTRANS': 46, 'TRANS': 849} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 896, 6671 Classifications: {'peptide': 896} Link IDs: {'PTRANS': 46, 'TRANS': 849} Chain breaks: 3 bond proxies already assigned to first conformer: 6728 Chain: "B" Number of atoms: 6732 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 896, 6671 Classifications: {'peptide': 896} Link IDs: {'PTRANS': 46, 'TRANS': 849} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 896, 6671 Classifications: {'peptide': 896} Link IDs: {'PTRANS': 46, 'TRANS': 849} Chain breaks: 3 bond proxies already assigned to first conformer: 6728 Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N AARG A 13 " occ=0.48 ... (20 atoms not shown) pdb=" NH2BARG A 13 " occ=0.52 residue: pdb=" N AARG A 27 " occ=0.61 ... (20 atoms not shown) pdb=" NH2BARG A 27 " occ=0.39 residue: pdb=" N AASN A 48 " occ=0.47 ... (14 atoms not shown) pdb=" ND2BASN A 48 " occ=0.53 residue: pdb=" N AARG A 58 " occ=0.29 ... (20 atoms not shown) pdb=" NH2BARG A 58 " occ=0.71 residue: pdb=" N AGLU A 161 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU A 161 " occ=0.54 residue: pdb=" N AARG A 486 " occ=0.45 ... (20 atoms not shown) pdb=" NH2BARG A 486 " occ=0.55 residue: pdb=" N AARG B 13 " occ=0.58 ... (20 atoms not shown) pdb=" NH2BARG B 13 " occ=0.42 residue: pdb=" N AARG B 27 " occ=0.42 ... (20 atoms not shown) pdb=" NH2BARG B 27 " occ=0.58 residue: pdb=" N AASN B 48 " occ=0.51 ... (14 atoms not shown) pdb=" ND2BASN B 48 " occ=0.49 residue: pdb=" N AARG B 58 " occ=0.44 ... (20 atoms not shown) pdb=" NH2BARG B 58 " occ=0.56 residue: pdb=" N AGLU B 161 " occ=0.70 ... (16 atoms not shown) pdb=" OE2BGLU B 161 " occ=0.30 residue: pdb=" N AARG B 486 " occ=0.57 ... (20 atoms not shown) pdb=" NH2BARG B 486 " occ=0.43 Time building chain proxies: 15.00, per 1000 atoms: 1.11 Number of scatterers: 13464 At special positions: 0 Unit cell: (114.466, 96.492, 199.606, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 2604 8.00 N 2484 7.00 C 8340 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: 5.46 Conformation dependent library (CDL) restraints added in 4.9 seconds 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3244 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 12 sheets defined 48.4% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 3 through 32 removed outlier: 3.723A pdb=" N ASP A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 60 Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 111 through 118 Processing helix chain 'A' and resid 119 through 136 Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 171 through 178 removed outlier: 4.221A pdb=" N VAL A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 191 removed outlier: 3.807A pdb=" N SER A 183 " --> pdb=" O PRO A 179 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 204 through 219 Processing helix chain 'A' and resid 236 through 246 removed outlier: 3.550A pdb=" N VAL A 240 " --> pdb=" O PRO A 236 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'A' and resid 310 through 326 removed outlier: 3.889A pdb=" N CYS A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 332 removed outlier: 3.525A pdb=" N VAL A 332 " --> pdb=" O PRO A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 357 removed outlier: 3.869A pdb=" N ILE A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 Processing helix chain 'A' and resid 379 through 381 No H-bonds generated for 'chain 'A' and resid 379 through 381' Processing helix chain 'A' and resid 382 through 398 Processing helix chain 'A' and resid 481 through 498 removed outlier: 3.877A pdb=" N ARG A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 527 through 541 Processing helix chain 'A' and resid 575 through 582 removed outlier: 4.067A pdb=" N SER A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 596 Processing helix chain 'A' and resid 597 through 600 Processing helix chain 'A' and resid 603 through 610 removed outlier: 3.505A pdb=" N VAL A 607 " --> pdb=" O LYS A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 641 removed outlier: 3.844A pdb=" N GLN A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Proline residue: A 625 - end of helix removed outlier: 3.648A pdb=" N TYR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 663 removed outlier: 3.749A pdb=" N ALA A 657 " --> pdb=" O GLN A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 684 removed outlier: 3.718A pdb=" N LEU A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 705 removed outlier: 3.543A pdb=" N ARG A 705 " --> pdb=" O ARG A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 740 Processing helix chain 'A' and resid 756 through 761 Processing helix chain 'A' and resid 762 through 770 Processing helix chain 'A' and resid 792 through 796 Processing helix chain 'A' and resid 797 through 807 Processing helix chain 'A' and resid 810 through 821 Processing helix chain 'A' and resid 835 through 845 Processing helix chain 'A' and resid 864 through 877 Processing helix chain 'A' and resid 883 through 887 Processing helix chain 'B' and resid 3 through 32 removed outlier: 3.776A pdb=" N ASP B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 60 Processing helix chain 'B' and resid 74 through 79 Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 111 through 118 Processing helix chain 'B' and resid 119 through 137 removed outlier: 3.539A pdb=" N ARG B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 144 Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 178 through 191 removed outlier: 4.000A pdb=" N SER B 183 " --> pdb=" O PRO B 179 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'B' and resid 204 through 219 Processing helix chain 'B' and resid 236 through 245 removed outlier: 3.521A pdb=" N GLN B 245 " --> pdb=" O ASP B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 285 Processing helix chain 'B' and resid 310 through 325 removed outlier: 3.662A pdb=" N CYS B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 332 removed outlier: 3.512A pdb=" N VAL B 332 " --> pdb=" O PRO B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 357 removed outlier: 4.443A pdb=" N ILE B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 Processing helix chain 'B' and resid 379 through 382 removed outlier: 3.578A pdb=" N ALA B 382 " --> pdb=" O THR B 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 379 through 382' Processing helix chain 'B' and resid 383 through 398 Processing helix chain 'B' and resid 414 through 418 Processing helix chain 'B' and resid 481 through 497 Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 527 through 541 Processing helix chain 'B' and resid 575 through 582 removed outlier: 3.801A pdb=" N SER B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 597 Processing helix chain 'B' and resid 598 through 600 No H-bonds generated for 'chain 'B' and resid 598 through 600' Processing helix chain 'B' and resid 603 through 610 Processing helix chain 'B' and resid 619 through 641 Proline residue: B 625 - end of helix Processing helix chain 'B' and resid 653 through 662 removed outlier: 3.774A pdb=" N ALA B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 683 Processing helix chain 'B' and resid 697 through 705 Processing helix chain 'B' and resid 727 through 740 Processing helix chain 'B' and resid 756 through 761 removed outlier: 3.723A pdb=" N ARG B 761 " --> pdb=" O GLN B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 771 Processing helix chain 'B' and resid 792 through 796 Processing helix chain 'B' and resid 797 through 807 Processing helix chain 'B' and resid 811 through 821 Processing helix chain 'B' and resid 835 through 846 Processing helix chain 'B' and resid 864 through 877 Processing helix chain 'B' and resid 883 through 888 Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 199 removed outlier: 8.454A pdb=" N ILE A 197 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL A 150 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL A 199 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU A 152 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 230 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER A 38 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLU A 276 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ILE A 36 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA A 290 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 293 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE A 453 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER A 295 " --> pdb=" O HIS A 451 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N HIS A 451 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU A 297 " --> pdb=" O ASN A 449 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASN A 449 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA A 334 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU A 367 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 102 through 103 Processing sheet with id=AA3, first strand: chain 'A' and resid 399 through 400 removed outlier: 3.521A pdb=" N GLN A 427 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 479 Processing sheet with id=AA5, first strand: chain 'A' and resid 789 through 790 removed outlier: 5.172A pdb=" N GLY A 650 " --> pdb=" O HIS A 783 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 647 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL A 561 " --> pdb=" O ILE A 827 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 689 through 692 Processing sheet with id=AA7, first strand: chain 'B' and resid 196 through 199 removed outlier: 8.319A pdb=" N ILE B 197 " --> pdb=" O THR B 148 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL B 150 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL B 199 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU B 152 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 230 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 274 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER B 38 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLU B 276 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ILE B 36 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA B 290 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE B 453 " --> pdb=" O ARG B 293 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER B 295 " --> pdb=" O HIS B 451 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N HIS B 451 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU B 297 " --> pdb=" O ASN B 449 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASN B 449 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 334 " --> pdb=" O ARG B 437 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER B 441 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 102 through 103 Processing sheet with id=AA9, first strand: chain 'B' and resid 399 through 400 Processing sheet with id=AB1, first strand: chain 'B' and resid 473 through 479 Processing sheet with id=AB2, first strand: chain 'B' and resid 789 through 790 removed outlier: 3.761A pdb=" N ARG B 789 " --> pdb=" O SER B 784 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY B 650 " --> pdb=" O HIS B 783 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL B 560 " --> pdb=" O ALA B 647 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N VAL B 649 " --> pdb=" O VAL B 560 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N PHE B 562 " --> pdb=" O VAL B 649 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL B 561 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 689 through 692 681 hydrogen bonds defined for protein. 1922 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: 4.90 Time building geometry restraints manager: 5.97 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: 4808 1.34 - 1.46: 2821 1.46 - 1.58: 6033 1.58 - 1.70: 0 1.70 - 1.81: 62 Bond restraints: 13724 Sorted by residual: bond pdb=" N VAL A 643 " pdb=" CA VAL A 643 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.23e+00 bond pdb=" C ILE B 376 " pdb=" O ILE B 376 " ideal model delta sigma weight residual 1.242 1.230 0.012 1.13e-02 7.83e+03 1.19e+00 bond pdb=" CB VAL B 174 " pdb=" CG2 VAL B 174 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.10e+00 bond pdb=" CB PRO A 86 " pdb=" CG PRO A 86 " ideal model delta sigma weight residual 1.492 1.544 -0.052 5.00e-02 4.00e+02 1.07e+00 bond pdb=" C GLY A 95 " pdb=" O GLY A 95 " ideal model delta sigma weight residual 1.231 1.242 -0.011 1.11e-02 8.12e+03 1.06e+00 ... (remaining 13719 not shown) Histogram of bond angle deviations from ideal: 100.04 - 106.83: 431 106.83 - 113.62: 7558 113.62 - 120.41: 5082 120.41 - 127.21: 5431 127.21 - 134.00: 170 Bond angle restraints: 18672 Sorted by residual: angle pdb=" CB AASN A 48 " pdb=" CG AASN A 48 " pdb=" ND2AASN A 48 " ideal model delta sigma weight residual 116.40 124.08 -7.68 1.50e+00 4.44e-01 2.62e+01 angle pdb=" CB BASN B 48 " pdb=" CG BASN B 48 " pdb=" ND2BASN B 48 " ideal model delta sigma weight residual 116.40 124.06 -7.66 1.50e+00 4.44e-01 2.61e+01 angle pdb=" CB BASN A 48 " pdb=" CG BASN A 48 " pdb=" ND2BASN A 48 " ideal model delta sigma weight residual 116.40 123.97 -7.57 1.50e+00 4.44e-01 2.54e+01 angle pdb=" CB AASN B 48 " pdb=" CG AASN B 48 " pdb=" ND2AASN B 48 " ideal model delta sigma weight residual 116.40 123.96 -7.56 1.50e+00 4.44e-01 2.54e+01 angle pdb=" N TYR A 752 " pdb=" CA TYR A 752 " pdb=" C TYR A 752 " ideal model delta sigma weight residual 107.88 112.91 -5.03 1.41e+00 5.03e-01 1.27e+01 ... (remaining 18667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 7541 16.87 - 33.75: 519 33.75 - 50.62: 122 50.62 - 67.50: 28 67.50 - 84.37: 18 Dihedral angle restraints: 8228 sinusoidal: 3150 harmonic: 5078 Sorted by residual: dihedral pdb=" CA CYS B 41 " pdb=" C CYS B 41 " pdb=" N ARG B 42 " pdb=" CA ARG B 42 " ideal model delta harmonic sigma weight residual 180.00 163.34 16.66 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA PHE B 264 " pdb=" C PHE B 264 " pdb=" N GLY B 265 " pdb=" CA GLY B 265 " ideal model delta harmonic sigma weight residual 180.00 163.49 16.51 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CG ARG A 430 " pdb=" CD ARG A 430 " pdb=" NE ARG A 430 " pdb=" CZ ARG A 430 " ideal model delta sinusoidal sigma weight residual 180.00 137.32 42.68 2 1.50e+01 4.44e-03 9.80e+00 ... (remaining 8225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1298 0.028 - 0.057: 517 0.057 - 0.085: 139 0.085 - 0.114: 99 0.114 - 0.142: 37 Chirality restraints: 2090 Sorted by residual: chirality pdb=" CA VAL A 548 " pdb=" N VAL A 548 " pdb=" C VAL A 548 " pdb=" CB VAL A 548 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CA VAL A 226 " pdb=" N VAL A 226 " pdb=" C VAL A 226 " pdb=" CB VAL A 226 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE A 36 " pdb=" N ILE A 36 " pdb=" C ILE A 36 " pdb=" CB ILE A 36 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 2087 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 582 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.97e+00 pdb=" N PRO B 583 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 583 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 583 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 85 " -0.036 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO A 86 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 86 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 86 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 328 " -0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO B 329 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 329 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 329 " -0.027 5.00e-02 4.00e+02 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 411 2.71 - 3.26: 13970 3.26 - 3.80: 21132 3.80 - 4.35: 26019 4.35 - 4.90: 45138 Nonbonded interactions: 106670 Sorted by model distance: nonbonded pdb=" N GLU B 820 " pdb=" OE1 GLU B 820 " model vdw 2.161 3.120 nonbonded pdb=" O ARG A 460 " pdb=" NH1 ARG A 460 " model vdw 2.170 3.120 nonbonded pdb=" NE2 GLN A 122 " pdb=" O GLY A 176 " model vdw 2.281 3.120 nonbonded pdb=" O ASP A 139 " pdb=" OG SER A 142 " model vdw 2.292 3.040 nonbonded pdb=" O ARG B 498 " pdb=" NH1 ARG B 528 " model vdw 2.300 3.120 ... (remaining 106665 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 12 or resid 14 through 26 or resid 28 through 47 \ or resid 49 through 57 or resid 59 through 160 or resid 162 through 485 or resi \ d 487 through 910)) selection = (chain 'B' and (resid 2 through 12 or resid 14 through 26 or resid 28 through 47 \ or resid 49 through 57 or resid 59 through 160 or resid 162 through 485 or resi \ d 487 through 910)) } 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=0.29 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.290 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: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 50.400 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.090 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 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 : 0.003 0.052 13724 Z= 0.200 Angle : 0.604 7.681 18672 Z= 0.347 Chirality : 0.040 0.142 2090 Planarity : 0.005 0.056 2520 Dihedral : 13.180 84.371 4984 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.04 % Favored : 96.90 % Rotamer: Outliers : 0.73 % Allowed : 7.04 % Favored : 92.23 % 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 (0.20), residues: 1812 helix: 2.05 (0.20), residues: 722 sheet: 0.10 (0.34), residues: 226 loop : -0.91 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 602 HIS 0.003 0.001 HIS B 338 PHE 0.011 0.001 PHE B 103 TYR 0.010 0.001 TYR B 823 ARG 0.005 0.000 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.596 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2417 time to fit residues: 18.2317 Evaluate side-chains 34 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 139 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13724 Z= 0.218 Angle : 0.588 8.516 18672 Z= 0.302 Chirality : 0.043 0.147 2090 Planarity : 0.005 0.048 2520 Dihedral : 3.828 19.645 1994 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.03 % Allowed : 6.82 % Favored : 92.16 % 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: 1.25 (0.20), residues: 1812 helix: 2.40 (0.19), residues: 742 sheet: 0.57 (0.34), residues: 228 loop : -0.55 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 801 HIS 0.004 0.001 HIS A 79 PHE 0.013 0.001 PHE A 242 TYR 0.011 0.001 TYR B 800 ARG 0.009 0.001 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 43 average time/residue: 0.2272 time to fit residues: 16.6262 Evaluate side-chains 33 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 0.6980 chunk 50 optimal weight: 0.0970 chunk 134 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 44 optimal weight: 0.1980 chunk 161 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 160 optimal weight: 0.3980 chunk 55 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13724 Z= 0.139 Angle : 0.541 7.481 18672 Z= 0.273 Chirality : 0.042 0.177 2090 Planarity : 0.004 0.048 2520 Dihedral : 3.603 19.805 1994 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.81 % Allowed : 7.04 % Favored : 92.16 % 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: 1.50 (0.20), residues: 1812 helix: 2.56 (0.19), residues: 742 sheet: 0.80 (0.34), residues: 228 loop : -0.38 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 801 HIS 0.004 0.001 HIS B 211 PHE 0.011 0.001 PHE A 585 TYR 0.009 0.001 TYR A 11 ARG 0.006 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 40 average time/residue: 0.2478 time to fit residues: 16.5223 Evaluate side-chains 35 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 5.9990 chunk 121 optimal weight: 0.0980 chunk 84 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 162 optimal weight: 0.9980 chunk 172 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 143 optimal weight: 0.5980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN B 902 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13724 Z= 0.205 Angle : 0.553 6.840 18672 Z= 0.279 Chirality : 0.041 0.152 2090 Planarity : 0.004 0.050 2520 Dihedral : 3.613 19.028 1994 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.95 % Allowed : 6.89 % Favored : 92.16 % 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: 1.57 (0.20), residues: 1812 helix: 2.58 (0.19), residues: 748 sheet: 0.67 (0.34), residues: 234 loop : -0.28 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 801 HIS 0.004 0.001 HIS A 660 PHE 0.010 0.001 PHE A 585 TYR 0.008 0.001 TYR A 802 ARG 0.004 0.000 ARG B 682 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 1.537 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 37 average time/residue: 0.2080 time to fit residues: 13.7722 Evaluate side-chains 33 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 423 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 87 optimal weight: 0.4980 chunk 154 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 57 optimal weight: 0.0570 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 HIS B 567 GLN B 804 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13724 Z= 0.140 Angle : 0.522 7.752 18672 Z= 0.260 Chirality : 0.041 0.202 2090 Planarity : 0.004 0.050 2520 Dihedral : 3.458 20.784 1994 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.73 % Allowed : 7.18 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.63 (0.20), residues: 1812 helix: 2.52 (0.19), residues: 764 sheet: 0.79 (0.35), residues: 230 loop : -0.22 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 801 HIS 0.003 0.001 HIS B 211 PHE 0.012 0.001 PHE A 585 TYR 0.007 0.001 TYR A 11 ARG 0.004 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 1.399 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.2317 time to fit residues: 14.6541 Evaluate side-chains 33 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN A 783 HIS A 902 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13724 Z= 0.274 Angle : 0.604 9.710 18672 Z= 0.302 Chirality : 0.041 0.162 2090 Planarity : 0.004 0.049 2520 Dihedral : 3.765 18.435 1994 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.81 % Allowed : 7.11 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.48 (0.20), residues: 1812 helix: 2.41 (0.19), residues: 764 sheet: 0.62 (0.34), residues: 236 loop : -0.29 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 801 HIS 0.006 0.001 HIS A 79 PHE 0.011 0.001 PHE A 585 TYR 0.015 0.002 TYR B 641 ARG 0.004 0.001 ARG B 705 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 1.407 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 33 average time/residue: 0.2190 time to fit residues: 13.2193 Evaluate side-chains 32 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 423 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 125 optimal weight: 0.2980 chunk 97 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 104 optimal weight: 0.4980 chunk 79 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13724 Z= 0.140 Angle : 0.518 7.637 18672 Z= 0.260 Chirality : 0.041 0.166 2090 Planarity : 0.004 0.047 2520 Dihedral : 3.480 18.948 1994 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.95 % Allowed : 6.96 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.65 (0.20), residues: 1812 helix: 2.62 (0.19), residues: 758 sheet: 0.70 (0.34), residues: 236 loop : -0.24 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 54 HIS 0.002 0.001 HIS A 660 PHE 0.017 0.001 PHE A 868 TYR 0.013 0.001 TYR B 641 ARG 0.003 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 1.521 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 34 average time/residue: 0.2172 time to fit residues: 13.4877 Evaluate side-chains 31 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 84 optimal weight: 0.0040 chunk 15 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13724 Z= 0.182 Angle : 0.536 9.796 18672 Z= 0.267 Chirality : 0.040 0.207 2090 Planarity : 0.004 0.046 2520 Dihedral : 3.493 17.784 1994 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.53 % Favored : 97.41 % Rotamer: Outliers : 0.88 % Allowed : 7.11 % Favored : 92.01 % 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: 1.67 (0.20), residues: 1812 helix: 2.61 (0.19), residues: 762 sheet: 0.70 (0.34), residues: 236 loop : -0.23 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 801 HIS 0.003 0.001 HIS A 660 PHE 0.014 0.001 PHE A 868 TYR 0.016 0.001 TYR B 641 ARG 0.003 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 31 time to evaluate : 1.509 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 32 average time/residue: 0.2112 time to fit residues: 12.4681 Evaluate side-chains 32 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 835 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 164 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 125 optimal weight: 0.0050 chunk 49 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 104 optimal weight: 0.0030 chunk 169 optimal weight: 1.9990 overall best weight: 0.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 405 HIS A 519 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13724 Z= 0.128 Angle : 0.530 11.396 18672 Z= 0.258 Chirality : 0.041 0.244 2090 Planarity : 0.004 0.047 2520 Dihedral : 3.348 18.983 1994 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.91 % Favored : 98.03 % Rotamer: Outliers : 0.81 % Allowed : 7.11 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.73 (0.20), residues: 1812 helix: 2.58 (0.19), residues: 768 sheet: 0.97 (0.35), residues: 226 loop : -0.19 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 54 HIS 0.003 0.000 HIS B 338 PHE 0.027 0.001 PHE A 868 TYR 0.012 0.001 TYR B 641 ARG 0.003 0.000 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 1.582 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 32 average time/residue: 0.2284 time to fit residues: 13.7986 Evaluate side-chains 32 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 423 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 163 optimal weight: 0.6980 chunk 141 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 chunk 86 optimal weight: 0.0270 chunk 112 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13724 Z= 0.138 Angle : 0.538 11.849 18672 Z= 0.262 Chirality : 0.040 0.235 2090 Planarity : 0.004 0.048 2520 Dihedral : 3.310 19.280 1994 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.20 % Favored : 97.75 % Rotamer: Outliers : 0.88 % Allowed : 7.18 % Favored : 91.94 % 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: 1.77 (0.20), residues: 1812 helix: 2.60 (0.19), residues: 768 sheet: 0.98 (0.35), residues: 226 loop : -0.14 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 801 HIS 0.002 0.001 HIS B 338 PHE 0.015 0.001 PHE A 868 TYR 0.013 0.001 TYR B 641 ARG 0.003 0.000 ARG A 359 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 1.466 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 34 average time/residue: 0.2133 time to fit residues: 13.2595 Evaluate side-chains 34 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 835 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 2.9990 chunk 130 optimal weight: 0.0270 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 141 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 17 optimal weight: 0.0370 chunk 26 optimal weight: 8.9990 chunk 124 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.027856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2412 r_free = 0.2412 target = 0.020262 restraints weight = 834485.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2459 r_free = 0.2459 target = 0.021485 restraints weight = 163439.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.022376 restraints weight = 81934.921| |-----------------------------------------------------------------------------| r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2488 r_free = 0.2488 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2487 r_free = 0.2487 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2487 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13724 Z= 0.129 Angle : 0.529 11.674 18672 Z= 0.258 Chirality : 0.040 0.235 2090 Planarity : 0.004 0.051 2520 Dihedral : 3.241 18.727 1994 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.14 % Favored : 97.80 % Rotamer: Outliers : 0.88 % Allowed : 7.26 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.20), residues: 1812 helix: 2.62 (0.19), residues: 768 sheet: 0.92 (0.34), residues: 228 loop : -0.08 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 801 HIS 0.003 0.000 HIS B 338 PHE 0.014 0.001 PHE A 868 TYR 0.012 0.001 TYR B 641 ARG 0.003 0.000 ARG A 732 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2448.78 seconds wall clock time: 44 minutes 34.25 seconds (2674.25 seconds total)