Starting phenix.real_space_refine on Fri Apr 12 10:54:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v7l_43003/04_2024/8v7l_43003_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v7l_43003/04_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_43003/04_2024/8v7l_43003.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v7l_43003/04_2024/8v7l_43003.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v7l_43003/04_2024/8v7l_43003_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v7l_43003/04_2024/8v7l_43003_updated.pdb" } 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-5288/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: 11.63, per 1000 atoms: 0.46 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: 20.34 Conformation dependent library (CDL) restraints added in 1.9 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... running ksdssp... Secondary structure from input PDB file: 57 helices and 3 sheets defined 57.4% alpha, 3.3% beta 44 base pairs and 185 stacking pairs defined. Time for finding SS restraints: 12.82 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 removed outlier: 3.581A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 78 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 86 through 112 removed outlier: 3.748A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 31 through 40 removed outlier: 3.666A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 75 removed outlier: 3.843A pdb=" N TYR B 51 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU B 52 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 55 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU B 63 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B 66 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG B 67 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 74 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 35 Processing helix chain 'C' and resid 47 through 72 removed outlier: 3.868A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 removed outlier: 3.654A pdb=" N GLN C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'D' and resid 35 through 45 removed outlier: 3.732A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 80 removed outlier: 3.634A pdb=" N ALA D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 101 through 119 removed outlier: 3.518A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.599A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.194A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 48 through 75 removed outlier: 3.924A pdb=" N TYR F 51 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU F 52 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG F 55 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU F 58 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU F 63 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE F 66 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG F 67 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU F 74 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 47 through 72 removed outlier: 3.611A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 88 Processing helix chain 'G' and resid 93 through 96 No H-bonds generated for 'chain 'G' and resid 93 through 96' Processing helix chain 'H' and resid 35 through 45 removed outlier: 3.789A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 119 Processing helix chain 'W' and resid 182 through 197 removed outlier: 3.627A pdb=" N TYR W 195 " --> pdb=" O LEU W 191 " (cutoff:3.500A) Processing helix chain 'W' and resid 211 through 224 removed outlier: 3.608A pdb=" N LYS W 223 " --> pdb=" O LEU W 219 " (cutoff:3.500A) Processing helix chain 'W' and resid 238 through 251 removed outlier: 3.645A pdb=" N LEU W 241 " --> pdb=" O LYS W 238 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N HIS W 242 " --> pdb=" O SER W 239 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP W 244 " --> pdb=" O LEU W 241 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET W 245 " --> pdb=" O HIS W 242 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TRP W 251 " --> pdb=" O PHE W 248 " (cutoff:3.500A) Processing helix chain 'W' and resid 264 through 273 Processing helix chain 'W' and resid 287 through 299 removed outlier: 3.923A pdb=" N ILE W 291 " --> pdb=" O TYR W 287 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N SER W 295 " --> pdb=" O ILE W 291 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL W 296 " --> pdb=" O LYS W 292 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE W 297 " --> pdb=" O GLU W 293 " (cutoff:3.500A) Processing helix chain 'W' and resid 310 through 313 removed outlier: 3.680A pdb=" N ILE W 313 " --> pdb=" O ALA W 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 310 through 313' Processing helix chain 'W' and resid 319 through 326 Processing helix chain 'W' and resid 344 through 354 Processing helix chain 'W' and resid 356 through 358 No H-bonds generated for 'chain 'W' and resid 356 through 358' Processing helix chain 'W' and resid 362 through 368 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 386 through 389 No H-bonds generated for 'chain 'W' and resid 386 through 389' Processing helix chain 'W' and resid 397 through 400 No H-bonds generated for 'chain 'W' and resid 397 through 400' Processing helix chain 'W' and resid 418 through 429 Processing helix chain 'W' and resid 439 through 441 No H-bonds generated for 'chain 'W' and resid 439 through 441' Processing helix chain 'W' and resid 449 through 458 Processing helix chain 'W' and resid 477 through 481 Processing helix chain 'W' and resid 483 through 496 removed outlier: 3.828A pdb=" N ASP W 489 " --> pdb=" O MET W 485 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LYS W 490 " --> pdb=" O VAL W 486 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU W 491 " --> pdb=" O VAL W 487 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LEU W 492 " --> pdb=" O LEU W 488 " (cutoff:3.500A) Proline residue: W 493 - end of helix Processing helix chain 'W' and resid 509 through 522 Processing helix chain 'W' and resid 535 through 546 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 559 through 562 No H-bonds generated for 'chain 'W' and resid 559 through 562' Processing helix chain 'W' and resid 583 through 591 removed outlier: 3.603A pdb=" N ALA W 589 " --> pdb=" O VAL W 585 " (cutoff:3.500A) Processing helix chain 'W' and resid 613 through 628 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= A, first strand: chain 'W' and resid 331 through 335 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: 6.627A pdb=" N VAL W 258 " --> pdb=" O VAL W 284 " (cutoff:3.500A) Processing sheet with id= B, 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) Processing sheet with id= C, first strand: chain 'W' and resid 526 through 529 removed outlier: 6.902A pdb=" N VAL W 554 " --> pdb=" O CYS W 527 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N LEU W 529 " --> pdb=" O VAL W 554 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N MET W 556 " --> pdb=" O LEU W 529 " (cutoff:3.500A) No H-bonds generated for sheet with id= C 432 hydrogen bonds defined for protein. 1170 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: 10.45 Time building geometry restraints manager: 20.81 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: 220 2.10 - 2.72: 33773 2.72 - 3.35: 62911 3.35 - 3.97: 85915 3.97 - 4.60: 133053 Nonbonded interactions: 315872 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 1.850 nonbonded pdb=" H VAL E 117 " pdb=" OP1 DA I 131 " model vdw 1.788 1.850 nonbonded pdb=" HH TYR G 57 " pdb=" OE2 GLU G 61 " model vdw 1.799 1.850 nonbonded pdb=" HH TYR H 37 " pdb=" OP1 DG J 122 " model vdw 1.804 1.850 ... (remaining 315867 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain '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: 0.010 Normalize map: mean=0, sd=1: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.350 Extract box with map and model: 12.750 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 88.560 Find NCS groups from input model: 0.750 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: 0.010 Load rotamer database and sin/cos tables:13.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.780 ------------------------------------------------------------------------------- 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= 0.660 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 : 1.823 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: 3.5801 time to fit residues: 1019.9358 Evaluate side-chains 126 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 120 time to evaluate : 1.825 ------------------------------------------------------------------------------- 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: 9.9990 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 84 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN C 104 GLN F 25 ASN H 44 GLN W 342 ASN W 345 HIS W 352 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5844 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16305 Z= 0.207 Angle : 0.621 5.774 23222 Z= 0.364 Chirality : 0.036 0.137 2629 Planarity : 0.005 0.047 1958 Dihedral : 25.380 170.588 4409 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.94 % Favored : 97.97 % Rotamer: Outliers : 1.45 % Allowed : 16.41 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.23), residues: 1183 helix: 0.99 (0.19), residues: 724 sheet: -0.53 (0.58), residues: 78 loop : -1.66 (0.28), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP W 348 HIS 0.005 0.001 HIS W 535 PHE 0.011 0.001 PHE E 78 TYR 0.013 0.001 TYR W 524 ARG 0.009 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: 15 poor density : 129 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8035 (t70) cc_final: 0.7759 (t0) REVERT: E 120 MET cc_start: 0.6227 (OUTLIER) cc_final: 0.5948 (mmt) REVERT: G 73 ASN cc_start: 0.7857 (t0) cc_final: 0.7656 (t0) REVERT: G 99 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7148 (mtt180) REVERT: W 222 MET cc_start: 0.6004 (OUTLIER) cc_final: 0.5691 (mtt) REVERT: W 451 MET cc_start: 0.6868 (tpt) cc_final: 0.6545 (tpt) REVERT: W 508 MET cc_start: 0.7157 (mtt) cc_final: 0.6592 (ttm) outliers start: 15 outliers final: 5 residues processed: 138 average time/residue: 3.1595 time to fit residues: 475.8513 Evaluate side-chains 125 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain D residue 120 SER 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: 0.8980 chunk 89 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 chunk 44 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN F 93 GLN W 311 HIS ** W 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 532 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16305 Z= 0.299 Angle : 0.604 6.378 23222 Z= 0.351 Chirality : 0.036 0.158 2629 Planarity : 0.005 0.044 1958 Dihedral : 26.845 162.834 4404 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.13 % Favored : 96.79 % Rotamer: Outliers : 2.22 % Allowed : 16.12 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.24), residues: 1183 helix: 1.23 (0.19), residues: 718 sheet: -0.42 (0.59), residues: 78 loop : -1.65 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 348 HIS 0.014 0.001 HIS W 477 PHE 0.011 0.001 PHE W 353 TYR 0.013 0.001 TYR W 424 ARG 0.005 0.001 ARG B 67 *********************** 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 150 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 LYS cc_start: 0.8967 (mtmt) cc_final: 0.8766 (mtpm) REVERT: D 109 SER cc_start: 0.8292 (m) cc_final: 0.7982 (p) REVERT: F 53 GLU cc_start: 0.7505 (tt0) cc_final: 0.7139 (tt0) REVERT: F 84 MET cc_start: 0.7668 (mmm) cc_final: 0.7432 (mmt) REVERT: G 73 ASN cc_start: 0.8085 (t0) cc_final: 0.7867 (t0) REVERT: G 99 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7001 (mtt90) REVERT: W 451 MET cc_start: 0.6948 (tpt) cc_final: 0.6513 (tpt) REVERT: W 508 MET cc_start: 0.7217 (mtt) cc_final: 0.6639 (ttm) outliers start: 23 outliers final: 6 residues processed: 141 average time/residue: 2.9903 time to fit residues: 456.8455 Evaluate side-chains 128 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 121 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain W residue 304 TYR 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: 6.9990 chunk 98 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 62 optimal weight: 0.0470 chunk 87 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 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: 0.6249 moved from start: 0.5422 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= 0.231 Angle : 0.538 6.154 23222 Z= 0.313 Chirality : 0.034 0.140 2629 Planarity : 0.004 0.048 1958 Dihedral : 27.107 165.523 4403 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.54 % Favored : 97.38 % Rotamer: Outliers : 1.64 % Allowed : 16.80 % 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: 0.47 (0.24), residues: 1183 helix: 1.40 (0.19), residues: 718 sheet: -0.47 (0.61), residues: 73 loop : -1.61 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP W 348 HIS 0.003 0.001 HIS W 477 PHE 0.008 0.001 PHE W 353 TYR 0.011 0.001 TYR W 304 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 142 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 LYS cc_start: 0.9027 (mtmt) cc_final: 0.8759 (mtpm) REVERT: C 99 ARG cc_start: 0.7705 (mtp180) cc_final: 0.7479 (mtp85) REVERT: D 109 SER cc_start: 0.8306 (m) cc_final: 0.8070 (p) REVERT: F 53 GLU cc_start: 0.7492 (tt0) cc_final: 0.7222 (tt0) REVERT: W 451 MET cc_start: 0.7027 (tpt) cc_final: 0.6620 (tpt) REVERT: W 508 MET cc_start: 0.7273 (mtt) cc_final: 0.6670 (ttm) outliers start: 17 outliers final: 7 residues processed: 134 average time/residue: 2.8476 time to fit residues: 414.8497 Evaluate side-chains 127 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain W residue 245 MET Chi-restraints excluded: chain W residue 324 VAL Chi-restraints excluded: chain W residue 456 CYS Chi-restraints excluded: chain W residue 535 HIS 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: 4.9990 chunk 79 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 chunk 103 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.6317 moved from start: 0.5856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16305 Z= 0.308 Angle : 0.557 6.236 23222 Z= 0.323 Chirality : 0.035 0.138 2629 Planarity : 0.005 0.066 1958 Dihedral : 27.623 161.601 4403 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.80 % Favored : 96.11 % Rotamer: Outliers : 2.61 % Allowed : 16.51 % Favored : 80.89 % 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: 0.31 (0.24), residues: 1183 helix: 1.26 (0.19), residues: 721 sheet: -0.34 (0.62), residues: 70 loop : -1.71 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP W 348 HIS 0.004 0.001 HIS W 477 PHE 0.016 0.001 PHE W 353 TYR 0.012 0.001 TYR H 34 ARG 0.014 0.001 ARG E 42 *********************** 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 153 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7380 (tp30) REVERT: C 75 LYS cc_start: 0.9007 (mtmt) cc_final: 0.8741 (mtpm) REVERT: C 99 ARG cc_start: 0.7761 (mtp180) cc_final: 0.7536 (mtp85) REVERT: F 53 GLU cc_start: 0.7573 (tt0) cc_final: 0.7313 (tt0) REVERT: H 73 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7694 (tp30) REVERT: W 451 MET cc_start: 0.7022 (tpt) cc_final: 0.6649 (tpt) outliers start: 27 outliers final: 11 residues processed: 143 average time/residue: 3.0218 time to fit residues: 474.2282 Evaluate side-chains 131 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 283 CYS Chi-restraints excluded: chain W residue 324 VAL Chi-restraints excluded: chain W residue 456 CYS Chi-restraints excluded: chain W residue 535 HIS 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: 1.9990 chunk 125 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 139 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 moved from start: 0.6058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16305 Z= 0.217 Angle : 0.515 5.937 23222 Z= 0.296 Chirality : 0.032 0.137 2629 Planarity : 0.004 0.072 1958 Dihedral : 27.483 164.436 4403 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.13 % Favored : 96.79 % Rotamer: Outliers : 1.35 % Allowed : 19.11 % Favored : 79.54 % 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: 0.55 (0.24), residues: 1183 helix: 1.47 (0.20), residues: 723 sheet: -0.46 (0.62), residues: 70 loop : -1.60 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP W 348 HIS 0.003 0.001 HIS W 477 PHE 0.006 0.001 PHE B 61 TYR 0.010 0.001 TYR W 424 ARG 0.015 0.000 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 6 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 136 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7318 (tp30) REVERT: C 75 LYS cc_start: 0.9041 (mtmt) cc_final: 0.8679 (mtpp) REVERT: C 99 ARG cc_start: 0.7740 (mtp180) cc_final: 0.7530 (mtp85) REVERT: D 98 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8407 (mm) REVERT: F 53 GLU cc_start: 0.7512 (tt0) cc_final: 0.7276 (tt0) REVERT: G 99 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.6963 (mtt90) REVERT: H 32 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7524 (mm-30) REVERT: H 73 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7722 (tp30) REVERT: W 451 MET cc_start: 0.6869 (tpt) cc_final: 0.6522 (tpt) outliers start: 14 outliers final: 7 residues processed: 131 average time/residue: 2.9885 time to fit residues: 425.4609 Evaluate side-chains 131 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain G residue 99 ARG 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 535 HIS Chi-restraints excluded: chain W residue 550 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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: