Starting phenix.real_space_refine on Mon Sep 30 11:54:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v7l_43003/09_2024/8v7l_43003.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v7l_43003/09_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_43003/09_2024/8v7l_43003.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v7l_43003/09_2024/8v7l_43003.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v7l_43003/09_2024/8v7l_43003.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v7l_43003/09_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. Time to flip 26 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 13.02, per 1000 atoms: 0.51 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.34 Conformation dependent library (CDL) restraints added in 1.6 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: 10.85 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: 10.00 Time building geometry restraints manager: 7.54 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: 0.00 - 2.50: 42309 2.50 - 5.01: 3189 5.01 - 7.51: 503 7.51 - 10.01: 58 10.01 - 12.52: 7 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: 3.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.420 Extract box with map and model: 1.040 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 60.940 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.080 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:11.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.230 ------------------------------------------------------------------------------- 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 : 1.656 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: 3.4737 time to fit residues: 990.6141 Evaluate side-chains 126 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 120 time to evaluate : 1.844 ------------------------------------------------------------------------------- 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 : 1.689 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: 3.0573 time to fit residues: 445.7377 Evaluate side-chains 123 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 117 time to evaluate : 1.996 ------------------------------------------------------------------------------- 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 : 1.807 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: 2.8175 time to fit residues: 422.8390 Evaluate side-chains 125 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 120 time to evaluate : 2.010 ------------------------------------------------------------------------------- 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 : 1.657 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: 2.6491 time to fit residues: 399.2953 Evaluate side-chains 126 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 1.722 ------------------------------------------------------------------------------- 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 : 1.640 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: 2.8977 time to fit residues: 436.4853 Evaluate side-chains 129 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 1.710 ------------------------------------------------------------------------------- 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... 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: 0.6265 moved from start: 0.6072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16305 Z= 0.223 Angle : 0.527 5.856 23222 Z= 0.304 Chirality : 0.032 0.140 2629 Planarity : 0.004 0.046 1958 Dihedral : 27.401 163.234 4403 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.53 % Rotamer: Outliers : 1.25 % Allowed : 18.92 % Favored : 79.83 % 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: 1.27 (0.25), residues: 1183 helix: 2.23 (0.19), residues: 728 sheet: -0.53 (0.59), residues: 78 loop : -1.76 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 348 HIS 0.004 0.001 HIS H 106 PHE 0.010 0.001 PHE W 353 TYR 0.010 0.001 TYR W 424 ARG 0.006 0.000 ARG W 272 *********************** 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 137 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 2.012 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: C 61 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7546 (tp30) REVERT: C 75 LYS cc_start: 0.8924 (mtmt) cc_final: 0.8647 (mtpm) REVERT: C 99 ARG cc_start: 0.7780 (mtp180) cc_final: 0.7574 (mtp85) REVERT: E 133 GLU cc_start: 0.6777 (mt-10) cc_final: 0.6509 (mt-10) REVERT: H 73 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7503 (tp30) REVERT: W 451 MET cc_start: 0.6845 (tpt) cc_final: 0.6367 (tpt) REVERT: W 508 MET cc_start: 0.7234 (mtt) cc_final: 0.6724 (ttm) outliers start: 13 outliers final: 7 residues processed: 135 average time/residue: 2.8268 time to fit residues: 418.9880 Evaluate side-chains 125 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain W residue 304 TYR Chi-restraints excluded: chain W residue 324 VAL Chi-restraints excluded: chain W residue 456 CYS 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: 2.9990 chunk 79 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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** ** 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: 0.6354 moved from start: 0.6299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 16305 Z= 0.415 Angle : 0.607 6.312 23222 Z= 0.351 Chirality : 0.038 0.148 2629 Planarity : 0.005 0.050 1958 Dihedral : 28.258 161.027 4403 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.82 % Favored : 95.10 % Rotamer: Outliers : 2.22 % Allowed : 18.82 % Favored : 78.96 % 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: 0.70 (0.25), residues: 1183 helix: 1.74 (0.19), residues: 733 sheet: -0.63 (0.60), residues: 78 loop : -1.96 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP W 348 HIS 0.006 0.001 HIS H 106 PHE 0.009 0.002 PHE B 61 TYR 0.013 0.002 TYR W 526 ARG 0.005 0.001 ARG F 55 *********************** REFINEMENT MACRO_CYCLE 7 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 143 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7559 (tp30) REVERT: C 75 LYS cc_start: 0.8960 (mtmt) cc_final: 0.8666 (mtpm) REVERT: C 99 ARG cc_start: 0.7820 (mtp180) cc_final: 0.7593 (mtp85) REVERT: D 98 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8425 (mm) REVERT: H 32 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7613 (mm-30) REVERT: H 73 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7606 (tp30) outliers start: 23 outliers final: 11 residues processed: 133 average time/residue: 2.7890 time to fit residues: 403.5075 Evaluate side-chains 128 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 98 LEU 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 283 CYS Chi-restraints excluded: chain W residue 304 TYR Chi-restraints excluded: chain W residue 324 VAL Chi-restraints excluded: chain W residue 360 ASN Chi-restraints excluded: chain W residue 456 CYS Chi-restraints excluded: chain W residue 550 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.6276 moved from start: 0.6399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16305 Z= 0.196 Angle : 0.528 6.047 23222 Z= 0.301 Chirality : 0.032 0.142 2629 Planarity : 0.004 0.097 1958 Dihedral : 27.782 164.061 4403 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.55 % Favored : 96.37 % Rotamer: Outliers : 1.06 % Allowed : 19.98 % Favored : 78.96 % 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: 1.29 (0.25), residues: 1183 helix: 2.26 (0.19), residues: 728 sheet: -0.57 (0.61), residues: 78 loop : -1.77 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 348 HIS 0.006 0.001 HIS W 535 PHE 0.007 0.001 PHE W 555 TYR 0.009 0.001 TYR W 424 ARG 0.017 0.000 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 8 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 133 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7537 (tp30) REVERT: C 75 LYS cc_start: 0.8912 (mtmt) cc_final: 0.8595 (mtpm) REVERT: C 99 ARG cc_start: 0.7785 (mtp180) cc_final: 0.7581 (mtp85) REVERT: H 73 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7547 (tp30) REVERT: W 451 MET cc_start: 0.6826 (tpt) cc_final: 0.6357 (tpt) REVERT: W 508 MET cc_start: 0.7264 (mtt) cc_final: 0.6733 (ttm) outliers start: 11 outliers final: 7 residues processed: 131 average time/residue: 2.9021 time to fit residues: 412.7269 Evaluate side-chains 122 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain W residue 222 MET Chi-restraints excluded: chain W residue 304 TYR Chi-restraints excluded: chain W residue 324 VAL Chi-restraints excluded: chain W residue 550 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.6501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 16305 Z= 0.370 Angle : 0.588 7.898 23222 Z= 0.336 Chirality : 0.036 0.151 2629 Planarity : 0.005 0.082 1958 Dihedral : 28.270 160.798 4402 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.73 % Favored : 95.18 % Rotamer: Outliers : 1.06 % Allowed : 20.46 % Favored : 78.47 % 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: 0.88 (0.25), residues: 1183 helix: 1.89 (0.19), residues: 734 sheet: -0.70 (0.61), residues: 78 loop : -1.88 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP W 348 HIS 0.006 0.001 HIS W 535 PHE 0.010 0.002 PHE B 61 TYR 0.013 0.001 TYR W 526 ARG 0.013 0.001 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 9 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 125 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: C 61 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7545 (tp30) REVERT: C 75 LYS cc_start: 0.8939 (mtmt) cc_final: 0.8616 (mtpm) REVERT: C 99 ARG cc_start: 0.7832 (mtp180) cc_final: 0.7610 (mtp85) REVERT: D 98 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8423 (mm) REVERT: H 73 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7568 (tp30) outliers start: 11 outliers final: 7 residues processed: 122 average time/residue: 2.8835 time to fit residues: 388.2760 Evaluate side-chains 121 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 283 CYS Chi-restraints excluded: chain W residue 304 TYR Chi-restraints excluded: chain W residue 324 VAL Chi-restraints excluded: chain W residue 550 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 132 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 70 optimal weight: 0.4980 chunk 90 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 242 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 moved from start: 0.6582 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= 0.275 Angle : 0.556 8.140 23222 Z= 0.316 Chirality : 0.033 0.141 2629 Planarity : 0.005 0.079 1958 Dihedral : 28.084 163.006 4402 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.56 % Favored : 95.35 % Rotamer: Outliers : 0.87 % Allowed : 20.66 % Favored : 78.47 % 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: 735 sheet: -0.67 (0.62), residues: 78 loop : -1.84 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP W 348 HIS 0.005 0.001 HIS W 535 PHE 0.008 0.001 PHE B 61 TYR 0.010 0.001 TYR W 424 ARG 0.014 0.000 ARG E 42 ********************** REFINEMENT MACRO_CYCLE 10 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 123 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 114 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: C 61 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7543 (tp30) REVERT: C 75 LYS cc_start: 0.8913 (mtmt) cc_final: 0.8598 (mtpm) REVERT: C 99 ARG cc_start: 0.7809 (mtp180) cc_final: 0.7604 (mtp85) REVERT: F 53 GLU cc_start: 0.7403 (tt0) cc_final: 0.7097 (tt0) REVERT: G 95 LYS cc_start: 0.9001 (ttmt) cc_final: 0.8706 (tmtt) REVERT: H 73 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7580 (tp30) outliers start: 9 outliers final: 7 residues processed: 122 average time/residue: 2.9357 time to fit residues: 390.2155 Evaluate side-chains 121 residues out of total 1036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 113 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain W residue 222 MET Chi-restraints excluded: chain W residue 283 CYS Chi-restraints excluded: chain W residue 304 TYR Chi-restraints excluded: chain W residue 324 VAL Chi-restraints excluded: chain W residue 550 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.100487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.075002 restraints weight = 97871.093| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.03 r_work: 0.3171 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.6600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16305 Z= 0.226 Angle : 0.547 11.713 23222 Z= 0.309 Chirality : 0.032 0.141 2629 Planarity : 0.004 0.076 1958 Dihedral : 28.055 163.417 4402 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.48 % Favored : 95.44 % Rotamer: Outliers : 0.97 % Allowed : 20.56 % Favored : 78.47 % 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: 1.17 (0.25), residues: 1183 helix: 2.13 (0.19), residues: 734 sheet: -0.69 (0.62), residues: 78 loop : -1.78 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP W 521 HIS 0.006 0.001 HIS W 535 PHE 0.015 0.001 PHE W 391 TYR 0.010 0.001 TYR W 424 ARG 0.013 0.000 ARG E 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8385.02 seconds wall clock time: 147 minutes 42.86 seconds (8862.86 seconds total)