Starting phenix.real_space_refine on Sat Aug 8 15:36:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v4y_42977/08_2026/8v4y_42977.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v4y_42977/08_2026/8v4y_42977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v4y_42977/08_2026/8v4y_42977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v4y_42977/08_2026/8v4y_42977.map" model { file = "/net/cci-nas-00/data/ceres_data/8v4y_42977/08_2026/8v4y_42977.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v4y_42977/08_2026/8v4y_42977.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.006 sd= 0.039 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 32 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: 9 Type Number sf(0) Gaussians P 296 5.49 5 Mg 1 5.21 5 S 34 5.16 5 Be 1 3.05 5 C 9094 2.51 5 N 2943 2.21 5 O 3504 1.98 5 F 3 1.80 5 H 13550 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29426 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" 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: "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: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1371 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1752 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" 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: "I" Number of atoms: 4680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 4680 Classifications: {'DNA': 147} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 4646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 4646 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "W" Number of atoms: 7455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 7455 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 18, 'TRANS': 430} Chain breaks: 1 Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.29, per 1000 atoms: 0.18 Number of scatterers: 29426 At special positions: 0 Unit cell: (148.19, 128.714, 116.858, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) S 34 16.00 P 296 15.00 Mg 1 11.99 F 3 9.00 O 3504 8.00 N 2943 7.00 C 9094 6.00 Be 1 4.00 H 13550 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: 2.78 Conformation dependent library (CDL) restraints added in 757.7 milliseconds 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2298 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 12 sheets defined 65.3% alpha, 5.6% beta 38 base pairs and 190 stacking pairs defined. Time for finding SS restraints: 4.88 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: 3.835A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 removed outlier: 3.645A 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 15 through 19 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: 3.554A 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: 3.741A 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: 3.612A 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 122 Processing helix chain 'W' and resid 181 through 198 Processing helix chain 'W' and resid 210 through 225 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 removed outlier: 3.523A pdb=" N MET W 245 " --> pdb=" O LEU W 241 " (cutoff:3.500A) Processing helix chain 'W' and resid 263 through 274 Processing helix chain 'W' and resid 287 through 293 Processing helix chain 'W' and resid 293 through 298 Processing helix chain 'W' and resid 310 through 314 Processing helix chain 'W' and resid 318 through 325 removed outlier: 3.575A pdb=" N ARG W 325 " --> pdb=" O SER W 321 " (cutoff:3.500A) Processing helix chain 'W' and resid 344 through 355 removed outlier: 4.375A pdb=" N LEU W 350 " --> pdb=" O GLU W 346 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE W 353 " --> pdb=" O SER W 349 " (cutoff:3.500A) Processing helix chain 'W' and resid 361 through 369 removed outlier: 5.177A pdb=" N SER W 367 " --> pdb=" O ASP W 363 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TRP W 368 " --> pdb=" O ASP W 364 " (cutoff:3.500A) Processing helix chain 'W' and resid 387 through 391 removed outlier: 4.443A 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: 4.059A pdb=" N GLN W 452 " --> pdb=" O ASN W 448 " (cutoff:3.500A) Processing helix chain 'W' and resid 460 through 463 Processing helix chain 'W' and resid 475 through 481 removed outlier: 3.662A pdb=" N VAL W 479 " --> pdb=" O ASP W 475 " (cutoff:3.500A) Processing helix chain 'W' and resid 482 through 489 removed outlier: 3.613A pdb=" N ASP W 489 " --> pdb=" O MET W 485 " (cutoff:3.500A) Processing helix chain 'W' and resid 490 through 497 Processing helix chain 'W' and resid 508 through 523 removed outlier: 3.724A pdb=" N LEU W 512 " --> pdb=" O MET W 508 " (cutoff:3.500A) Processing helix chain 'W' and resid 534 through 547 removed outlier: 3.744A pdb=" N GLN W 539 " --> pdb=" O HIS W 535 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP W 540 " --> pdb=" O ASP W 536 " (cutoff:3.500A) Processing helix chain 'W' and resid 559 through 563 Processing helix chain 'W' and resid 582 through 592 removed outlier: 4.084A pdb=" N ASP W 586 " --> pdb=" O ASN W 582 " (cutoff:3.500A) Processing helix chain 'W' and resid 612 through 629 removed outlier: 4.182A pdb=" N ARG W 616 " --> pdb=" O THR W 612 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU W 627 " --> pdb=" O MET W 623 " (cutoff:3.500A) removed outlier: 3.768A 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: 6.643A 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: 6.893A 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 257 through 260 removed outlier: 6.614A pdb=" N VAL W 258 " --> pdb=" O VAL W 284 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N SER W 286 " --> pdb=" O VAL W 258 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N LEU W 260 " --> pdb=" O SER W 286 " (cutoff:3.500A) removed outlier: 6.912A 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: 6.570A pdb=" N CYS W 527 " --> pdb=" O MET W 556 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N SER W 558 " --> pdb=" O CYS W 527 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LEU W 529 " --> pdb=" O SER W 558 " (cutoff:3.500A) 547 hydrogen bonds defined for protein. 1599 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 84 hydrogen bonds 168 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 190 stacking parallelities Total time for adding SS restraints: 7.14 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 13544 1.02 - 1.22: 290 1.22 - 1.42: 6691 1.42 - 1.62: 9728 1.62 - 1.82: 65 Bond restraints: 30318 Sorted by residual: bond pdb=" F1 BEF W1103 " pdb="BE BEF W1103 " ideal model delta sigma weight residual 1.476 1.761 -0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" F2 BEF W1103 " pdb="BE BEF W1103 " ideal model delta sigma weight residual 1.476 1.760 -0.284 2.00e-02 2.50e+03 2.02e+02 bond pdb=" F3 BEF W1103 " pdb="BE BEF W1103 " ideal model delta sigma weight residual 1.476 1.759 -0.283 2.00e-02 2.50e+03 2.01e+02 bond pdb=" ND2 ASN W 567 " pdb="HD22 ASN W 567 " ideal model delta sigma weight residual 0.860 0.982 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" ND2 ASN W 436 " pdb="HD21 ASN W 436 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.67e+01 ... (remaining 30313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 51068 2.71 - 5.41: 3265 5.41 - 8.12: 581 8.12 - 10.82: 22 10.82 - 13.53: 6 Bond angle restraints: 54942 Sorted by residual: angle pdb=" N VAL W 502 " pdb=" CA VAL W 502 " pdb=" C VAL W 502 " ideal model delta sigma weight residual 108.48 122.01 -13.53 1.44e+00 4.82e-01 8.83e+01 angle pdb=" N TRP W 177 " pdb=" CA TRP W 177 " pdb=" C TRP W 177 " ideal model delta sigma weight residual 111.71 121.63 -9.92 1.15e+00 7.56e-01 7.44e+01 angle pdb=" N GLY D 101 " pdb=" CA GLY D 101 " pdb=" C GLY D 101 " ideal model delta sigma weight residual 112.73 122.47 -9.74 1.20e+00 6.94e-01 6.59e+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 98.74 11.21 1.44e+00 4.82e-01 6.06e+01 angle pdb=" N GLY W 201 " pdb=" CA GLY W 201 " pdb=" C GLY W 201 " ideal model delta sigma weight residual 112.61 124.64 -12.03 1.60e+00 3.91e-01 5.65e+01 ... (remaining 54937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.81: 11691 29.81 - 59.62: 1199 59.62 - 89.44: 44 89.44 - 119.25: 1 119.25 - 149.06: 1 Dihedral angle restraints: 12936 sinusoidal: 8882 harmonic: 4054 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 -60.00 -164.12 104.11 1 2.00e+01 2.50e-03 2.99e+01 dihedral pdb=" CA THR W 609 " pdb=" C THR W 609 " pdb=" N ASP W 610 " pdb=" CA ASP W 610 " ideal model delta harmonic sigma weight residual -180.00 -155.56 -24.44 0 5.00e+00 4.00e-02 2.39e+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 -158.71 -21.29 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 12933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2026 0.103 - 0.205: 612 0.205 - 0.308: 59 0.308 - 0.411: 5 0.411 - 0.514: 2 Chirality restraints: 2704 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 2.00 0.51 2.00e-01 2.50e+01 6.59e+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 4.25e+00 chirality pdb=" CA ASP W 281 " pdb=" N ASP W 281 " pdb=" C ASP W 281 " pdb=" CB ASP W 281 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.02e+00 ... (remaining 2701 not shown) Planarity restraints: 3394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 38 " -0.087 2.00e-02 2.50e+03 4.88e-01 3.58e+03 pdb=" CG ASN C 38 " 0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN C 38 " 0.085 2.00e-02 2.50e+03 pdb=" ND2 ASN C 38 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN C 38 " -0.842 2.00e-02 2.50e+03 pdb="HD22 ASN C 38 " 0.841 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN W 342 " 0.292 2.00e-02 2.50e+03 4.39e-01 2.89e+03 pdb=" CG ASN W 342 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN W 342 " -0.287 2.00e-02 2.50e+03 pdb=" ND2 ASN W 342 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN W 342 " 0.709 2.00e-02 2.50e+03 pdb="HD22 ASN W 342 " -0.695 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN W 360 " -0.301 2.00e-02 2.50e+03 4.29e-01 2.76e+03 pdb=" CG ASN W 360 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN W 360 " 0.291 2.00e-02 2.50e+03 pdb=" ND2 ASN W 360 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN W 360 " -0.692 2.00e-02 2.50e+03 pdb="HD22 ASN W 360 " 0.670 2.00e-02 2.50e+03 ... (remaining 3391 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.73: 14 1.73 - 2.44: 13051 2.44 - 3.16: 83161 3.16 - 3.88: 111052 3.88 - 4.60: 180703 Nonbonded interactions: 387981 Sorted by model distance: nonbonded pdb=" HB THR W 474 " pdb=" HE1 HIS W 477 " model vdw 1.007 2.270 nonbonded pdb=" HH TYR W 461 " pdb=" HD2 HIS W 477 " model vdw 1.154 2.100 nonbonded pdb="HH22 ARG A 72 " pdb=" OP1 DC J 51 " model vdw 1.161 2.450 nonbonded pdb="HH12 ARG C 11 " pdb=" H1' DT I 178 " model vdw 1.192 2.270 nonbonded pdb=" HB THR W 474 " pdb=" CE1 HIS W 477 " model vdw 1.283 2.970 ... (remaining 387976 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' } ncs_group { reference = (chain 'B' and resid 20 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = chain 'D' 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: 5.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.160 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 32.220 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 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:6.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 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 : 0.012 0.285 16768 Z= 0.840 Angle : 1.398 13.529 23904 Z= 1.010 Chirality : 0.087 0.514 2704 Planarity : 0.011 0.111 1995 Dihedral : 20.030 149.062 7056 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.67 % Favored : 96.16 % Rotamer: Outliers : 0.67 % Allowed : 2.85 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.22), residues: 1199 helix: -0.52 (0.17), residues: 721 sheet: 0.43 (0.57), residues: 73 loop : -1.05 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 35 TYR 0.116 0.011 TYR G 57 PHE 0.043 0.008 PHE W 297 TRP 0.078 0.008 TRP W 348 HIS 0.011 0.003 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.01164 / 0.84 (16768) covalent geometry : angle 1.39802 / 1.01 (23904) hydrogen bonds : bond 0.25185 / 16.63 ( 631) hydrogen bonds : angle 7.83905 / 5.72 ( 1767) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 226 time to evaluate : 0.691 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: C 95 LYS cc_start: 0.8842 (ttmt) cc_final: 0.8636 (tmtt) REVERT: E 79 LYS cc_start: 0.8754 (tttt) cc_final: 0.8507 (tttp) REVERT: E 105 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7521 (mt-10) REVERT: E 115 LYS cc_start: 0.8840 (mttt) cc_final: 0.8520 (mtmp) REVERT: F 68 ASP cc_start: 0.8292 (m-30) cc_final: 0.8015 (m-30) REVERT: H 117 LYS cc_start: 0.9076 (tttt) cc_final: 0.8864 (tttm) outliers start: 7 outliers final: 2 residues processed: 233 average time/residue: 2.0869 time to fit residues: 518.3431 Evaluate side-chains 139 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 137 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 432 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 93 GLN W 477 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.099602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.079862 restraints weight = 92114.900| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.46 r_work: 0.3268 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16768 Z= 0.205 Angle : 0.702 8.226 23904 Z= 0.436 Chirality : 0.044 0.171 2704 Planarity : 0.006 0.089 1995 Dihedral : 22.714 157.878 4579 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.50 % Favored : 97.33 % Rotamer: Outliers : 1.43 % Allowed : 13.61 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.23), residues: 1199 helix: 1.16 (0.19), residues: 726 sheet: 0.70 (0.60), residues: 74 loop : -1.47 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 99 TYR 0.016 0.002 TYR W 195 PHE 0.010 0.001 PHE F 100 TRP 0.014 0.001 TRP W 348 HIS 0.021 0.002 HIS W 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.20 (16768) covalent geometry : angle 0.70227 / 0.44 (23904) hydrogen bonds : bond 0.08679 / 5.70 ( 631) hydrogen bonds : angle 4.61630 / 3.28 ( 1767) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.707 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 outliers start: 15 outliers final: 4 residues processed: 157 average time/residue: 1.5911 time to fit residues: 270.5330 Evaluate side-chains 138 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 134 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain W residue 367 SER Chi-restraints excluded: chain W residue 429 MET Chi-restraints excluded: chain W residue 432 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 77 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.091464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.070966 restraints weight = 88657.034| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.46 r_work: 0.3082 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16768 Z= 0.220 Angle : 0.664 6.290 23904 Z= 0.418 Chirality : 0.041 0.239 2704 Planarity : 0.005 0.056 1995 Dihedral : 23.788 173.820 4578 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.17 % Favored : 96.75 % Rotamer: Outliers : 1.24 % Allowed : 13.99 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.24), residues: 1199 helix: 1.81 (0.19), residues: 723 sheet: 0.37 (0.59), residues: 74 loop : -1.55 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 83 TYR 0.012 0.002 TYR B 51 PHE 0.016 0.002 PHE W 391 TRP 0.014 0.001 TRP W 348 HIS 0.008 0.001 HIS W 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.22 (16768) covalent geometry : angle 0.66396 / 0.42 (23904) hydrogen bonds : bond 0.07492 / 4.84 ( 631) hydrogen bonds : angle 4.14040 / 2.93 ( 1767) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.709 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: E 94 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.7918 (mp0) REVERT: W 233 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7710 (ttm) REVERT: W 444 MET cc_start: 0.8783 (ttp) cc_final: 0.8419 (ttm) outliers start: 13 outliers final: 3 residues processed: 144 average time/residue: 1.5821 time to fit residues: 247.1225 Evaluate side-chains 136 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 131 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain W residue 233 MET Chi-restraints excluded: chain W residue 388 LEU Chi-restraints excluded: chain W residue 429 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 49 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... W 342 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.088054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.067478 restraints weight = 88381.127| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.43 r_work: 0.2996 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16768 Z= 0.241 Angle : 0.648 6.708 23904 Z= 0.410 Chirality : 0.040 0.288 2704 Planarity : 0.005 0.053 1995 Dihedral : 24.612 168.365 4576 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.75 % Favored : 96.16 % Rotamer: Outliers : 1.71 % Allowed : 13.51 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.24), residues: 1199 helix: 1.96 (0.19), residues: 725 sheet: 0.24 (0.61), residues: 74 loop : -1.64 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 67 TYR 0.013 0.001 TYR W 195 PHE 0.010 0.001 PHE E 84 TRP 0.011 0.001 TRP W 348 HIS 0.005 0.001 HIS W 385 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.24 (16768) covalent geometry : angle 0.64833 / 0.41 (23904) hydrogen bonds : bond 0.07084 / 4.59 ( 631) hydrogen bonds : angle 4.05986 / 2.86 ( 1767) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.677 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: E 94 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.7984 (mp0) REVERT: H 27 ARG cc_start: 0.7363 (tpp-160) cc_final: 0.7138 (tpp-160) outliers start: 18 outliers final: 9 residues processed: 146 average time/residue: 1.6059 time to fit residues: 253.7263 Evaluate side-chains 139 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 429 MET Chi-restraints excluded: chain W residue 442 ASP Chi-restraints excluded: chain W residue 519 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 39 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.088540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.068039 restraints weight = 88722.915| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.44 r_work: 0.3013 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16768 Z= 0.155 Angle : 0.582 5.958 23904 Z= 0.381 Chirality : 0.037 0.241 2704 Planarity : 0.004 0.048 1995 Dihedral : 24.789 166.793 4576 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.34 % Favored : 96.50 % Rotamer: Outliers : 1.05 % Allowed : 14.94 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.25), residues: 1199 helix: 2.19 (0.20), residues: 726 sheet: 0.38 (0.62), residues: 76 loop : -1.53 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 42 TYR 0.010 0.001 TYR W 195 PHE 0.017 0.001 PHE W 391 TRP 0.010 0.001 TRP W 348 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.16 (16768) covalent geometry : angle 0.58242 / 0.38 (23904) hydrogen bonds : bond 0.05932 / 3.81 ( 631) hydrogen bonds : angle 3.86956 / 2.72 ( 1767) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 42 ARG cc_start: 0.8232 (mtp85) cc_final: 0.7783 (mtp180) REVERT: E 94 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.7936 (mp0) REVERT: H 27 ARG cc_start: 0.7314 (tpp-160) cc_final: 0.7085 (tpp-160) REVERT: W 284 VAL cc_start: 0.9240 (t) cc_final: 0.9036 (m) outliers start: 11 outliers final: 4 residues processed: 145 average time/residue: 1.5811 time to fit residues: 247.9940 Evaluate side-chains 135 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 429 MET Chi-restraints excluded: chain W residue 442 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 60 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.086680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.066183 restraints weight = 88268.278| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.43 r_work: 0.2969 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16768 Z= 0.205 Angle : 0.610 7.731 23904 Z= 0.388 Chirality : 0.038 0.272 2704 Planarity : 0.005 0.061 1995 Dihedral : 25.190 164.700 4576 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.25 % Favored : 95.58 % Rotamer: Outliers : 1.33 % Allowed : 14.94 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.25), residues: 1199 helix: 2.23 (0.19), residues: 726 sheet: 0.34 (0.62), residues: 76 loop : -1.55 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 129 TYR 0.014 0.001 TYR W 195 PHE 0.009 0.001 PHE F 100 TRP 0.010 0.001 TRP W 348 HIS 0.003 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.20 (16768) covalent geometry : angle 0.60962 / 0.39 (23904) hydrogen bonds : bond 0.06206 / 4.00 ( 631) hydrogen bonds : angle 3.84062 / 2.70 ( 1767) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 42 ARG cc_start: 0.8165 (mtp85) cc_final: 0.7850 (mtp180) REVERT: E 94 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: W 620 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7449 (mmm160) outliers start: 14 outliers final: 7 residues processed: 138 average time/residue: 1.6302 time to fit residues: 244.0056 Evaluate side-chains 135 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 367 SER Chi-restraints excluded: chain W residue 429 MET Chi-restraints excluded: chain W residue 442 ASP Chi-restraints excluded: chain W residue 620 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 138 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.086375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.065783 restraints weight = 88088.280| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.45 r_work: 0.2962 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16768 Z= 0.184 Angle : 0.587 8.248 23904 Z= 0.377 Chirality : 0.037 0.253 2704 Planarity : 0.004 0.051 1995 Dihedral : 25.486 161.759 4576 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.84 % Favored : 96.00 % Rotamer: Outliers : 1.14 % Allowed : 15.03 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.25), residues: 1199 helix: 2.22 (0.19), residues: 732 sheet: 0.38 (0.62), residues: 76 loop : -1.59 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 67 TYR 0.011 0.001 TYR W 195 PHE 0.028 0.001 PHE W 391 TRP 0.009 0.001 TRP W 348 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.18 (16768) covalent geometry : angle 0.58706 / 0.38 (23904) hydrogen bonds : bond 0.06016 / 3.84 ( 631) hydrogen bonds : angle 3.78629 / 2.66 ( 1767) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.708 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: D 65 ASP cc_start: 0.8878 (t0) cc_final: 0.8664 (t0) REVERT: E 42 ARG cc_start: 0.8160 (mtp85) cc_final: 0.7756 (mtp180) REVERT: E 94 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.7937 (mp0) REVERT: W 620 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7464 (mmm160) outliers start: 12 outliers final: 7 residues processed: 138 average time/residue: 1.6430 time to fit residues: 244.7170 Evaluate side-chains 137 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 388 LEU Chi-restraints excluded: chain W residue 429 MET Chi-restraints excluded: chain W residue 442 ASP Chi-restraints excluded: chain W residue 620 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 107 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.084438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.063460 restraints weight = 88971.214| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.49 r_work: 0.2878 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16768 Z= 0.215 Angle : 0.611 7.953 23904 Z= 0.383 Chirality : 0.038 0.290 2704 Planarity : 0.004 0.050 1995 Dihedral : 25.815 160.543 4576 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.00 % Favored : 95.83 % Rotamer: Outliers : 1.24 % Allowed : 14.94 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.25), residues: 1199 helix: 2.20 (0.19), residues: 732 sheet: 0.75 (0.65), residues: 66 loop : -1.63 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 83 TYR 0.011 0.001 TYR W 195 PHE 0.013 0.001 PHE W 391 TRP 0.014 0.002 TRP W 368 HIS 0.003 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.22 (16768) covalent geometry : angle 0.61073 / 0.38 (23904) hydrogen bonds : bond 0.06237 / 4.01 ( 631) hydrogen bonds : angle 3.80116 / 2.67 ( 1767) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 VAL cc_start: 0.8376 (t) cc_final: 0.8088 (p) REVERT: D 65 ASP cc_start: 0.8850 (t0) cc_final: 0.8603 (t0) REVERT: E 42 ARG cc_start: 0.8131 (mtp85) cc_final: 0.7789 (mtp180) REVERT: E 94 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.7989 (mp0) REVERT: W 620 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7457 (mmm160) outliers start: 13 outliers final: 8 residues processed: 140 average time/residue: 1.7642 time to fit residues: 266.3221 Evaluate side-chains 137 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 388 LEU Chi-restraints excluded: chain W residue 429 MET Chi-restraints excluded: chain W residue 442 ASP Chi-restraints excluded: chain W residue 620 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 85 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 133 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.084350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.063447 restraints weight = 89024.190| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.49 r_work: 0.2882 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16768 Z= 0.191 Angle : 0.589 9.098 23904 Z= 0.374 Chirality : 0.038 0.278 2704 Planarity : 0.004 0.049 1995 Dihedral : 25.995 160.853 4576 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.59 % Favored : 96.25 % Rotamer: Outliers : 1.14 % Allowed : 14.94 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.25), residues: 1199 helix: 2.26 (0.19), residues: 732 sheet: 0.43 (0.62), residues: 76 loop : -1.58 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 42 TYR 0.010 0.001 TYR W 195 PHE 0.033 0.001 PHE W 391 TRP 0.015 0.001 TRP W 368 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.19 (16768) covalent geometry : angle 0.58854 / 0.37 (23904) hydrogen bonds : bond 0.06036 / 3.85 ( 631) hydrogen bonds : angle 3.76797 / 2.65 ( 1767) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 VAL cc_start: 0.8342 (t) cc_final: 0.8073 (p) REVERT: D 65 ASP cc_start: 0.8839 (t0) cc_final: 0.8583 (t0) REVERT: E 42 ARG cc_start: 0.8201 (mtp85) cc_final: 0.7865 (mtp180) REVERT: E 94 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.7963 (mp0) REVERT: W 620 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7425 (mmm160) REVERT: W 623 MET cc_start: 0.8374 (mpm) cc_final: 0.8159 (mpm) outliers start: 12 outliers final: 7 residues processed: 137 average time/residue: 1.6964 time to fit residues: 251.6723 Evaluate side-chains 135 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 388 LEU Chi-restraints excluded: chain W residue 429 MET Chi-restraints excluded: chain W residue 442 ASP Chi-restraints excluded: chain W residue 620 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 12 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.083915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.063013 restraints weight = 89165.525| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.49 r_work: 0.2870 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16768 Z= 0.209 Angle : 0.600 8.346 23904 Z= 0.377 Chirality : 0.038 0.293 2704 Planarity : 0.004 0.051 1995 Dihedral : 26.162 161.136 4576 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.17 % Favored : 95.66 % Rotamer: Outliers : 1.14 % Allowed : 15.22 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.25), residues: 1199 helix: 2.21 (0.19), residues: 732 sheet: 0.67 (0.65), residues: 67 loop : -1.60 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 42 TYR 0.011 0.001 TYR E 41 PHE 0.010 0.001 PHE W 391 TRP 0.022 0.002 TRP W 368 HIS 0.002 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.21 (16768) covalent geometry : angle 0.59965 / 0.38 (23904) hydrogen bonds : bond 0.06156 / 3.94 ( 631) hydrogen bonds : angle 3.78743 / 2.66 ( 1767) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2398 Ramachandran restraints generated. 1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 VAL cc_start: 0.8354 (t) cc_final: 0.8076 (p) REVERT: D 65 ASP cc_start: 0.8840 (t0) cc_final: 0.8584 (t0) REVERT: E 42 ARG cc_start: 0.8162 (mtp85) cc_final: 0.7822 (mtp180) REVERT: E 94 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.7975 (mp0) REVERT: W 620 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7437 (mmm160) REVERT: W 623 MET cc_start: 0.8373 (mpm) cc_final: 0.8159 (mpm) outliers start: 12 outliers final: 7 residues processed: 134 average time/residue: 1.7128 time to fit residues: 248.5432 Evaluate side-chains 135 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 388 LEU Chi-restraints excluded: chain W residue 429 MET Chi-restraints excluded: chain W residue 442 ASP Chi-restraints excluded: chain W residue 620 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 125 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 70 optimal weight: 0.0030 chunk 51 optimal weight: 1.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.084510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.063578 restraints weight = 89252.095| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.53 r_work: 0.2899 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16768 Z= 0.150 Angle : 0.570 8.390 23904 Z= 0.364 Chirality : 0.037 0.276 2704 Planarity : 0.004 0.051 1995 Dihedral : 26.248 161.743 4576 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.50 % Favored : 96.33 % Rotamer: Outliers : 0.95 % Allowed : 15.51 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.25), residues: 1199 helix: 2.37 (0.20), residues: 732 sheet: 0.73 (0.65), residues: 67 loop : -1.52 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG W 383 TYR 0.010 0.001 TYR W 195 PHE 0.033 0.001 PHE W 391 TRP 0.013 0.001 TRP W 368 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.15 (16768) covalent geometry : angle 0.57003 / 0.36 (23904) hydrogen bonds : bond 0.05438 / 3.45 ( 631) hydrogen bonds : angle 3.69563 / 2.59 ( 1767) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9977.60 seconds wall clock time: 169 minutes 2.69 seconds (10142.69 seconds total)