Starting phenix.real_space_refine on Fri Aug 9 06:25:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v7l_43003/08_2024/8v7l_43003.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v7l_43003/08_2024/8v7l_43003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v7l_43003/08_2024/8v7l_43003.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v7l_43003/08_2024/8v7l_43003.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v7l_43003/08_2024/8v7l_43003.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v7l_43003/08_2024/8v7l_43003.cif" } resolution = 2.9 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= 0.005 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 27 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 282 5.49 5 Mg 1 5.21 5 S 34 5.16 5 C 8872 2.51 5 N 2861 2.21 5 O 3399 1.98 5 H 10096 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 74": "OE1" <-> "OE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "W TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W GLU 279": "OE1" <-> "OE2" Residue "W ASP 281": "OD1" <-> "OD2" Residue "W PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W GLU 422": "OE1" <-> "OE2" Residue "W TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W ASP 442": "OD1" <-> "OD2" Residue "W PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W ASP 530": "OD1" <-> "OD2" Residue "W TYR 545": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W GLU 619": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25545 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1563 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "B" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1468 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1730 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1542 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1604 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1349 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 1629 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "H" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1486 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2885 Classifications: {'DNA': 140} Link IDs: {'rna3p': 139} Chain: "J" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2855 Classifications: {'DNA': 140} Link IDs: {'rna3p': 139} Chain: "W" Number of atoms: 7406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 7406 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain breaks: 1 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.05, per 1000 atoms: 0.55 Number of scatterers: 25545 At special positions: 0 Unit cell: (147.343, 130.407, 116.012, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 34 16.00 P 282 15.00 Mg 1 11.99 O 3399 8.00 N 2861 7.00 C 8872 6.00 H 10096 1.00 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: 19.42 Conformation dependent library (CDL) restraints added in 2.5 seconds 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2266 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 12 sheets defined 65.7% alpha, 5.7% beta 44 base pairs and 185 stacking pairs defined. Time for finding SS restraints: 12.30 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.581A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.502A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 removed outlier: 3.646A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.653A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 removed outlier: 3.666A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.503A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.600A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.868A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.691A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.732A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.634A pdb=" N ALA D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 120 removed outlier: 3.518A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.534A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.636A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.570A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.689A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.532A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.513A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.611A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.569A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.789A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 120 Processing helix chain 'W' and resid 181 through 198 removed outlier: 3.627A pdb=" N TYR W 195 " --> pdb=" O LEU W 191 " (cutoff:3.500A) Processing helix chain 'W' and resid 210 through 225 removed outlier: 3.801A pdb=" N GLN W 214 " --> pdb=" O GLY W 210 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS W 223 " --> pdb=" O LEU W 219 " (cutoff:3.500A) Processing helix chain 'W' and resid 237 through 239 No H-bonds generated for 'chain 'W' and resid 237 through 239' Processing helix chain 'W' and resid 240 through 252 Processing helix chain 'W' and resid 263 through 274 Processing helix chain 'W' and resid 286 through 293 removed outlier: 3.521A pdb=" N LEU W 290 " --> pdb=" O SER W 286 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE W 291 " --> pdb=" O TYR W 287 " (cutoff:3.500A) Processing helix chain 'W' and resid 293 through 300 removed outlier: 3.818A pdb=" N PHE W 297 " --> pdb=" O GLU W 293 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE W 300 " --> pdb=" O VAL W 296 " (cutoff:3.500A) Processing helix chain 'W' and resid 310 through 314 removed outlier: 3.680A pdb=" N ILE W 313 " --> pdb=" O ALA W 310 " (cutoff:3.500A) Processing helix chain 'W' and resid 318 through 327 removed outlier: 3.805A pdb=" N PHE W 327 " --> pdb=" O ILE W 323 " (cutoff:3.500A) Processing helix chain 'W' and resid 343 through 355 removed outlier: 3.852A pdb=" N LEU W 347 " --> pdb=" O ASN W 343 " (cutoff:3.500A) Processing helix chain 'W' and resid 361 through 369 removed outlier: 4.396A pdb=" N SER W 367 " --> pdb=" O ASP W 363 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TRP W 368 " --> pdb=" O ASP W 364 " (cutoff:3.500A) Processing helix chain 'W' and resid 387 through 391 removed outlier: 4.584A pdb=" N PHE W 391 " --> pdb=" O VAL W 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 387 through 391' Processing helix chain 'W' and resid 396 through 401 Processing helix chain 'W' and resid 417 through 430 Processing helix chain 'W' and resid 438 through 442 Processing helix chain 'W' and resid 448 through 459 removed outlier: 3.989A pdb=" N GLN W 452 " --> pdb=" O ASN W 448 " (cutoff:3.500A) Processing helix chain 'W' and resid 476 through 482 removed outlier: 3.761A pdb=" N THR W 480 " --> pdb=" O MET W 476 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER W 482 " --> pdb=" O LEU W 478 " (cutoff:3.500A) Processing helix chain 'W' and resid 482 through 487 Processing helix chain 'W' and resid 490 through 497 Processing helix chain 'W' and resid 508 through 523 removed outlier: 3.506A pdb=" N LEU W 512 " --> pdb=" O MET W 508 " (cutoff:3.500A) Processing helix chain 'W' and resid 534 through 547 removed outlier: 3.919A pdb=" N GLN W 539 " --> pdb=" O HIS W 535 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP W 540 " --> pdb=" O ASP W 536 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR W 545 " --> pdb=" O SER W 541 " (cutoff:3.500A) Processing helix chain 'W' and resid 558 through 563 Processing helix chain 'W' and resid 582 through 592 removed outlier: 3.989A pdb=" N ASP W 586 " --> pdb=" O ASN W 582 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA W 589 " --> pdb=" O VAL W 585 " (cutoff:3.500A) Processing helix chain 'W' and resid 612 through 629 removed outlier: 3.859A pdb=" N ARG W 616 " --> pdb=" O THR W 612 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU W 627 " --> pdb=" O MET W 623 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP W 628 " --> pdb=" O LYS W 624 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.781A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.837A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.892A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.822A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.956A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'W' and resid 258 through 260 removed outlier: 6.248A pdb=" N HIS W 232 " --> pdb=" O CYS W 283 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N THR W 285 " --> pdb=" O HIS W 232 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL W 234 " --> pdb=" O THR W 285 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N MET W 233 " --> pdb=" O VAL W 306 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASP W 308 " --> pdb=" O MET W 233 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU W 235 " --> pdb=" O ASP W 308 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG W 303 " --> pdb=" O ASN W 331 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LEU W 333 " --> pdb=" O ARG W 303 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU W 305 " --> pdb=" O LEU W 333 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU W 335 " --> pdb=" O LEU W 305 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE W 307 " --> pdb=" O LEU W 335 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ILE W 202 " --> pdb=" O LEU W 393 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'W' and resid 408 through 414 removed outlier: 3.506A pdb=" N ARG W 606 " --> pdb=" O VAL W 410 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL W 574 " --> pdb=" O PHE W 605 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N PHE W 607 " --> pdb=" O VAL W 574 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU W 576 " --> pdb=" O PHE W 607 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N THR W 609 " --> pdb=" O LEU W 576 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU W 503 " --> pdb=" O ILE W 575 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU W 557 " --> pdb=" O ILE W 504 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N CYS W 527 " --> pdb=" O MET W 556 " (cutoff:3.500A) 521 hydrogen bonds defined for protein. 1530 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 100 hydrogen bonds 200 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 185 stacking parallelities Total time for adding SS restraints: 11.73 Time building geometry restraints manager: 20.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 10090 1.01 - 1.21: 224 1.21 - 1.41: 6465 1.41 - 1.61: 9550 1.61 - 1.82: 72 Bond restraints: 26401 Sorted by residual: bond pdb=" SG CYS W 527 " pdb=" HG CYS W 527 " ideal model delta sigma weight residual 1.200 1.341 -0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" SG CYS W 259 " pdb=" HG CYS W 259 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" SG CYS W 283 " pdb=" HG CYS W 283 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" SG CYS W 457 " pdb=" HG CYS W 457 " ideal model delta sigma weight residual 1.200 1.339 -0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" SG CYS W 456 " pdb=" HG CYS W 456 " ideal model delta sigma weight residual 1.200 1.339 -0.139 2.00e-02 2.50e+03 4.82e+01 ... (remaining 26396 not shown) Histogram of bond angle deviations from ideal: 98.07 - 105.65: 1648 105.65 - 113.23: 27169 113.23 - 120.82: 11212 120.82 - 128.40: 5680 128.40 - 135.98: 357 Bond angle restraints: 46066 Sorted by residual: angle pdb=" N HIS B 18 " pdb=" CA HIS B 18 " pdb=" C HIS B 18 " ideal model delta sigma weight residual 111.30 123.82 -12.52 1.43e+00 4.89e-01 7.66e+01 angle pdb=" N GLY D 101 " pdb=" CA GLY D 101 " pdb=" C GLY D 101 " ideal model delta sigma weight residual 112.73 122.49 -9.76 1.20e+00 6.94e-01 6.62e+01 angle pdb=" N ARG E 83 " pdb=" CA ARG E 83 " pdb=" C ARG E 83 " ideal model delta sigma weight residual 109.95 98.72 11.23 1.44e+00 4.82e-01 6.09e+01 angle pdb=" N GLY W 565 " pdb=" CA GLY W 565 " pdb=" C GLY W 565 " ideal model delta sigma weight residual 115.42 125.03 -9.61 1.27e+00 6.20e-01 5.73e+01 angle pdb=" N ASP W 610 " pdb=" CA ASP W 610 " pdb=" C ASP W 610 " ideal model delta sigma weight residual 111.28 119.04 -7.76 1.09e+00 8.42e-01 5.07e+01 ... (remaining 46061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.65: 10959 29.65 - 59.30: 1195 59.30 - 88.95: 66 88.95 - 118.59: 4 118.59 - 148.24: 2 Dihedral angle restraints: 12226 sinusoidal: 8223 harmonic: 4003 Sorted by residual: dihedral pdb=" O1B ADP W1101 " pdb=" O3A ADP W1101 " pdb=" PB ADP W1101 " pdb=" PA ADP W1101 " ideal model delta sinusoidal sigma weight residual 300.00 170.38 129.61 1 2.00e+01 2.50e-03 3.93e+01 dihedral pdb=" C5' ADP W1101 " pdb=" O5' ADP W1101 " pdb=" PA ADP W1101 " pdb=" O2A ADP W1101 " ideal model delta sinusoidal sigma weight residual -60.00 -156.68 96.69 1 2.00e+01 2.50e-03 2.68e+01 dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual -180.00 -158.73 -21.27 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 12223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2216 0.104 - 0.207: 336 0.207 - 0.311: 70 0.311 - 0.414: 6 0.414 - 0.518: 1 Chirality restraints: 2629 Sorted by residual: chirality pdb=" CA ARG E 40 " pdb=" N ARG E 40 " pdb=" C ARG E 40 " pdb=" CB ARG E 40 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.70e+00 chirality pdb=" CA LYS D 82 " pdb=" N LYS D 82 " pdb=" C LYS D 82 " pdb=" CB LYS D 82 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" CA LYS H 82 " pdb=" N LYS H 82 " pdb=" C LYS H 82 " pdb=" CB LYS H 82 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.55e+00 ... (remaining 2626 not shown) Planarity restraints: 3112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN W 481 " 0.211 2.00e-02 2.50e+03 4.71e-01 3.33e+03 pdb=" CG ASN W 481 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN W 481 " -0.208 2.00e-02 2.50e+03 pdb=" ND2 ASN W 481 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN W 481 " -0.786 2.00e-02 2.50e+03 pdb="HD22 ASN W 481 " 0.792 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN W 352 " 0.226 2.00e-02 2.50e+03 4.69e-01 3.30e+03 pdb=" CG ASN W 352 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN W 352 " -0.220 2.00e-02 2.50e+03 pdb=" ND2 ASN W 352 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN W 352 " 0.788 2.00e-02 2.50e+03 pdb="HD22 ASN W 352 " -0.774 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 38 " -0.055 2.00e-02 2.50e+03 4.29e-01 2.76e+03 pdb=" CG ASN C 38 " -0.000 2.00e-02 2.50e+03 pdb=" OD1 ASN C 38 " 0.054 2.00e-02 2.50e+03 pdb=" ND2 ASN C 38 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN C 38 " -0.740 2.00e-02 2.50e+03 pdb="HD22 ASN C 38 " 0.741 2.00e-02 2.50e+03 ... (remaining 3109 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 197 2.10 - 2.72: 33674 2.72 - 3.35: 62847 3.35 - 3.97: 85843 3.97 - 4.60: 132869 Nonbonded interactions: 315430 Sorted by model distance: nonbonded pdb=" HE2 LYS E 64 " pdb=" HE1 MET E 90 " model vdw 1.469 2.440 nonbonded pdb="HH11 ARG G 11 " pdb=" O4' DG I 92 " model vdw 1.768 2.450 nonbonded pdb=" H VAL E 117 " pdb=" OP1 DA I 131 " model vdw 1.788 2.450 nonbonded pdb=" HH TYR G 57 " pdb=" OE2 GLU G 61 " model vdw 1.799 2.450 nonbonded pdb=" HH TYR H 37 " pdb=" OP1 DG J 122 " model vdw 1.804 2.450 ... (remaining 315425 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' selection = (chain 'E' and resid 41 through 133) } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 11 through 112) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 120) selection = chain 'H' } 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: 2.870 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: 0.000 Extract box with map and model: 0.950 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 92.610 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5572 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 : 0.010 0.067 16305 Z= 0.659 Angle : 1.361 12.516 23222 Z= 0.911 Chirality : 0.080 0.518 2629 Planarity : 0.010 0.111 1958 Dihedral : 21.509 148.243 6838 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.55 % Favored : 96.20 % Rotamer: Outliers : 2.32 % Allowed : 3.57 % Favored : 94.11 % 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 (0.21), residues: 1183 helix: -0.48 (0.17), residues: 727 sheet: -0.72 (0.59), residues: 68 loop : -1.79 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP W 190 HIS 0.011 0.003 HIS H 106 PHE 0.041 0.006 PHE H 67 TYR 0.116 0.008 TYR G 57 ARG 0.010 0.001 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 248 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.7835 (t70) cc_final: 0.7438 (t0) REVERT: W 348 TRP cc_start: 0.7678 (t60) cc_final: 0.7305 (t60) REVERT: W 508 MET cc_start: 0.7289 (mtt) cc_final: 0.6772 (ttm) outliers start: 24 outliers final: 6 residues processed: 267 average time/residue: 3.4375 time to fit residues: 980.3021 Evaluate side-chains 126 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 120 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 283 CYS Chi-restraints excluded: chain W residue 456 CYS Chi-restraints excluded: chain W residue 459 HIS Chi-restraints excluded: chain W residue 558 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN F 25 ASN H 92 GLN W 342 ASN W 345 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5859 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16305 Z= 0.219 Angle : 0.643 5.711 23222 Z= 0.375 Chirality : 0.037 0.184 2629 Planarity : 0.005 0.050 1958 Dihedral : 25.478 167.478 4409 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.37 % Favored : 97.55 % Rotamer: Outliers : 1.64 % Allowed : 15.93 % Favored : 82.43 % 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: 0.40 (0.23), residues: 1183 helix: 1.44 (0.19), residues: 723 sheet: -0.71 (0.57), residues: 78 loop : -1.84 (0.26), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP W 348 HIS 0.008 0.001 HIS W 535 PHE 0.010 0.001 PHE E 78 TYR 0.015 0.001 TYR W 524 ARG 0.007 0.001 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 120 MET cc_start: 0.6525 (OUTLIER) cc_final: 0.6204 (mmt) REVERT: G 99 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7173 (mtt180) REVERT: W 207 MET cc_start: 0.7681 (mtm) cc_final: 0.7235 (mtm) REVERT: W 222 MET cc_start: 0.6005 (OUTLIER) cc_final: 0.5702 (mtt) REVERT: W 451 MET cc_start: 0.6790 (tpt) cc_final: 0.6409 (tpt) REVERT: W 508 MET cc_start: 0.7156 (mtt) cc_final: 0.6583 (ttm) outliers start: 17 outliers final: 3 residues processed: 135 average time/residue: 3.1058 time to fit residues: 452.6686 Evaluate side-chains 123 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 117 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain W residue 222 MET Chi-restraints excluded: chain W residue 224 HIS Chi-restraints excluded: chain W residue 283 CYS Chi-restraints excluded: chain W residue 456 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 108 optimal weight: 0.1980 chunk 89 optimal weight: 3.9990 chunk 36 optimal weight: 0.0070 chunk 131 optimal weight: 8.9990 chunk 141 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN F 75 HIS ** W 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6090 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16305 Z= 0.209 Angle : 0.568 6.278 23222 Z= 0.331 Chirality : 0.034 0.145 2629 Planarity : 0.004 0.045 1958 Dihedral : 26.291 160.426 4404 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.54 % Favored : 97.38 % Rotamer: Outliers : 1.83 % Allowed : 16.60 % Favored : 81.56 % 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: 1.11 (0.24), residues: 1183 helix: 2.06 (0.19), residues: 728 sheet: -0.67 (0.57), residues: 78 loop : -1.70 (0.27), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP W 348 HIS 0.011 0.001 HIS W 477 PHE 0.011 0.001 PHE W 391 TYR 0.011 0.001 TYR W 424 ARG 0.009 0.001 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 LYS cc_start: 0.8891 (mtmt) cc_final: 0.8674 (mtpm) REVERT: G 99 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7091 (mtt180) REVERT: W 207 MET cc_start: 0.7643 (mtm) cc_final: 0.7195 (mtm) REVERT: W 451 MET cc_start: 0.6872 (tpt) cc_final: 0.6331 (tpt) REVERT: W 508 MET cc_start: 0.7180 (mtt) cc_final: 0.6651 (ttm) outliers start: 19 outliers final: 4 residues processed: 138 average time/residue: 2.8182 time to fit residues: 422.8822 Evaluate side-chains 125 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 120 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain W residue 456 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 0.0020 chunk 87 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16305 Z= 0.261 Angle : 0.561 5.599 23222 Z= 0.326 Chirality : 0.035 0.210 2629 Planarity : 0.004 0.043 1958 Dihedral : 26.896 162.177 4403 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.62 % Favored : 97.30 % Rotamer: Outliers : 1.74 % Allowed : 16.99 % Favored : 81.27 % 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: 1.20 (0.25), residues: 1183 helix: 2.15 (0.19), residues: 729 sheet: -0.56 (0.59), residues: 78 loop : -1.74 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 244 HIS 0.005 0.001 HIS H 106 PHE 0.013 0.001 PHE W 248 TYR 0.015 0.002 TYR E 41 ARG 0.011 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7445 (tp30) REVERT: C 75 LYS cc_start: 0.8940 (mtmt) cc_final: 0.8700 (mtpm) REVERT: D 109 SER cc_start: 0.8293 (m) cc_final: 0.8055 (p) REVERT: H 73 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7432 (tp30) REVERT: W 207 MET cc_start: 0.7636 (mtm) cc_final: 0.7181 (mtm) REVERT: W 451 MET cc_start: 0.6939 (tpt) cc_final: 0.6424 (tpt) REVERT: W 508 MET cc_start: 0.7200 (mtt) cc_final: 0.6686 (ttm) outliers start: 18 outliers final: 5 residues processed: 138 average time/residue: 2.6444 time to fit residues: 397.5485 Evaluate side-chains 126 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 456 CYS Chi-restraints excluded: chain W residue 550 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 103 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 71 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 420 GLN ** W 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 moved from start: 0.5818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 16305 Z= 0.304 Angle : 0.566 6.134 23222 Z= 0.329 Chirality : 0.035 0.154 2629 Planarity : 0.004 0.046 1958 Dihedral : 27.443 160.505 4403 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.06 % Favored : 95.86 % Rotamer: Outliers : 1.83 % Allowed : 17.57 % Favored : 80.60 % 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: 1.03 (0.25), residues: 1183 helix: 2.02 (0.19), residues: 729 sheet: -0.63 (0.59), residues: 78 loop : -1.82 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 348 HIS 0.006 0.001 HIS H 106 PHE 0.013 0.001 PHE W 248 TYR 0.013 0.001 TYR W 526 ARG 0.004 0.000 ARG E 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 1.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7575 (mtpp) REVERT: C 61 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7534 (tp30) REVERT: C 75 LYS cc_start: 0.8948 (mtmt) cc_final: 0.8674 (mtpm) REVERT: C 99 ARG cc_start: 0.7767 (mtp180) cc_final: 0.7540 (mtp85) REVERT: D 109 SER cc_start: 0.8316 (m) cc_final: 0.8089 (p) REVERT: H 32 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7506 (mm-30) REVERT: H 73 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7466 (tp30) REVERT: W 451 MET cc_start: 0.6943 (tpt) cc_final: 0.6463 (tpt) REVERT: W 508 MET cc_start: 0.7230 (mtt) cc_final: 0.6721 (ttm) outliers start: 19 outliers final: 7 residues processed: 139 average time/residue: 2.5006 time to fit residues: 376.0570 Evaluate side-chains 129 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain W residue 304 TYR Chi-restraints excluded: chain W residue 456 CYS Chi-restraints excluded: chain W residue 550 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 0.0170 chunk 139 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 overall best weight: 1.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: