Starting phenix.real_space_refine on Sun Jul 5 16:08:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v4y_42977/07_2026/8v4y_42977.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v4y_42977/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8v4y_42977/07_2026/8v4y_42977.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v4y_42977/07_2026/8v4y_42977.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v4y_42977/07_2026/8v4y_42977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v4y_42977/07_2026/8v4y_42977.map" } 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-dev-6108/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: 5.09, per 1000 atoms: 0.17 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: 3.09 Conformation dependent library (CDL) restraints added in 900.4 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: 6.03 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: 8.11 Time building geometry restraints manager: 4.42 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: 5.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.180 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 36.230 Find NCS groups from input model: 0.260 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:9.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.290 ------------------------------------------------------------------------------- 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 : 1.397 13.529 23904 Z= 1.009 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 1.39669 / 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 : 0.728 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 95 LYS cc_start: 0.8842 (ttmt) cc_final: 0.8637 (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: 0.8866 (tttm) outliers start: 7 outliers final: 2 residues processed: 233 average time/residue: 2.1631 time to fit residues: 535.9323 Evaluate side-chains 137 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 135 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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: 4.9990 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 342 ASN W 477 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.099598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.079878 restraints weight = 92191.833| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.47 r_work: 0.3270 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16768 Z= 0.202 Angle : 0.691 7.338 23904 Z= 0.431 Chirality : 0.044 0.177 2704 Planarity : 0.006 0.087 1995 Dihedral : 22.641 157.290 4579 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.59 % Favored : 97.33 % Rotamer: Outliers : 1.24 % Allowed : 13.80 % 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: 1.13 (0.19), residues: 726 sheet: 0.73 (0.60), residues: 74 loop : -1.41 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 72 TYR 0.016 0.002 TYR W 195 PHE 0.008 0.001 PHE F 100 TRP 0.014 0.002 TRP W 348 HIS 0.021 0.002 HIS W 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.20 (16768) covalent geometry : angle 0.69053 / 0.43 (23904) hydrogen bonds : bond 0.09027 / 5.92 ( 631) hydrogen bonds : angle 4.59645 / 3.26 ( 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 159 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 153 average time/residue: 1.7189 time to fit residues: 284.3395 Evaluate side-chains 136 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 133 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 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: 1.9990 chunk 141 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... W 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.090309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.069753 restraints weight = 88679.080| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.47 r_work: 0.3051 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16768 Z= 0.258 Angle : 0.693 8.016 23904 Z= 0.430 Chirality : 0.042 0.238 2704 Planarity : 0.006 0.055 1995 Dihedral : 23.916 175.219 4578 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 1.62 % Allowed : 14.08 % Favored : 84.30 % 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: 0.77 (0.24), residues: 1199 helix: 1.64 (0.19), residues: 724 sheet: 0.33 (0.60), residues: 74 loop : -1.63 (0.27), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG W 603 TYR 0.013 0.002 TYR E 41 PHE 0.022 0.002 PHE W 391 TRP 0.014 0.002 TRP W 348 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.26 (16768) covalent geometry : angle 0.69346 / 0.43 (23904) hydrogen bonds : bond 0.07955 / 5.17 ( 631) hydrogen bonds : angle 4.19644 / 2.96 ( 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: 17 poor density : 134 time to evaluate : 0.764 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 112 THR cc_start: 0.9379 (t) cc_final: 0.9172 (m) REVERT: E 94 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.7951 (mp0) REVERT: H 31 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8202 (tppt) outliers start: 17 outliers final: 4 residues processed: 141 average time/residue: 1.7417 time to fit residues: 265.5841 Evaluate side-chains 134 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain W residue 429 MET Chi-restraints excluded: chain W residue 432 ILE Chi-restraints excluded: chain W residue 442 ASP 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: 10.0000 chunk 47 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 137 optimal weight: 0.5980 chunk 85 optimal weight: 10.0000 chunk 111 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.090861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.070614 restraints weight = 88754.016| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.44 r_work: 0.3072 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16768 Z= 0.157 Angle : 0.591 6.113 23904 Z= 0.387 Chirality : 0.038 0.240 2704 Planarity : 0.004 0.053 1995 Dihedral : 24.249 168.719 4578 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.92 % Favored : 97.00 % 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: 1.20 (0.24), residues: 1199 helix: 2.03 (0.20), residues: 724 sheet: 0.32 (0.61), residues: 76 loop : -1.52 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG W 603 TYR 0.010 0.001 TYR W 472 PHE 0.009 0.001 PHE W 248 TRP 0.010 0.001 TRP W 348 HIS 0.005 0.001 HIS W 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.16 (16768) covalent geometry : angle 0.59091 / 0.39 (23904) hydrogen bonds : bond 0.06089 / 3.89 ( 631) hydrogen bonds : angle 3.93489 / 2.77 ( 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 150 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 94 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.7903 (mp0) REVERT: W 444 MET cc_start: 0.8677 (ttp) cc_final: 0.8401 (ttm) outliers start: 13 outliers final: 7 residues processed: 143 average time/residue: 1.6579 time to fit residues: 257.3074 Evaluate side-chains 137 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain E residue 45 THR 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 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: 8.9990 chunk 108 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3564 r_free = 0.3564 target = 0.087133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.066579 restraints weight = 88755.097| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.43 r_work: 0.2977 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 16768 Z= 0.243 Angle : 0.644 7.635 23904 Z= 0.405 Chirality : 0.039 0.277 2704 Planarity : 0.005 0.049 1995 Dihedral : 24.833 169.428 4576 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.34 % Favored : 95.58 % Rotamer: Outliers : 1.43 % Allowed : 14.65 % 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: 1.27 (0.25), residues: 1199 helix: 2.10 (0.19), residues: 726 sheet: 0.33 (0.61), residues: 76 loop : -1.54 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 83 TYR 0.011 0.001 TYR W 195 PHE 0.010 0.001 PHE E 84 TRP 0.010 0.001 TRP W 348 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.24 (16768) covalent geometry : angle 0.64419 / 0.40 (23904) hydrogen bonds : bond 0.06822 / 4.41 ( 631) hydrogen bonds : angle 3.93546 / 2.77 ( 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 146 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 94 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: W 284 VAL cc_start: 0.9232 (t) cc_final: 0.9032 (m) outliers start: 15 outliers final: 8 residues processed: 139 average time/residue: 1.7034 time to fit residues: 255.9101 Evaluate side-chains 134 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 388 LEU Chi-restraints excluded: chain W residue 429 MET Chi-restraints excluded: chain W residue 432 ILE 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: 0.9980 chunk 107 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 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: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.087041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.066505 restraints weight = 87844.767| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.44 r_work: 0.2982 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16768 Z= 0.184 Angle : 0.597 8.074 23904 Z= 0.383 Chirality : 0.038 0.248 2704 Planarity : 0.004 0.048 1995 Dihedral : 25.180 164.724 4576 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.50 % Favored : 96.33 % Rotamer: Outliers : 1.43 % Allowed : 15.13 % Favored : 83.44 % 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: 2.21 (0.20), residues: 726 sheet: 0.34 (0.62), residues: 76 loop : -1.50 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 67 TYR 0.012 0.001 TYR W 195 PHE 0.019 0.001 PHE W 391 TRP 0.010 0.001 TRP W 348 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.18 (16768) covalent geometry : angle 0.59664 / 0.38 (23904) hydrogen bonds : bond 0.06118 / 3.92 ( 631) hydrogen bonds : angle 3.84474 / 2.71 ( 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 145 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 ASP cc_start: 0.8875 (t0) cc_final: 0.8626 (t0) REVERT: E 94 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: W 620 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7493 (mmm160) outliers start: 15 outliers final: 6 residues processed: 140 average time/residue: 1.7682 time to fit residues: 267.4442 Evaluate side-chains 133 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 30 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.086007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.065388 restraints weight = 87895.691| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.45 r_work: 0.2958 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16768 Z= 0.205 Angle : 0.600 6.420 23904 Z= 0.382 Chirality : 0.038 0.275 2704 Planarity : 0.004 0.050 1995 Dihedral : 25.508 161.754 4576 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.42 % Favored : 95.41 % Rotamer: Outliers : 1.14 % Allowed : 15.13 % 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: 1.38 (0.25), residues: 1199 helix: 2.19 (0.19), residues: 732 sheet: 0.38 (0.62), residues: 76 loop : -1.55 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 42 TYR 0.009 0.001 TYR W 195 PHE 0.011 0.001 PHE W 391 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 0.00405 / 0.20 (16768) covalent geometry : angle 0.59990 / 0.38 (23904) hydrogen bonds : bond 0.06157 / 3.95 ( 631) hydrogen bonds : angle 3.80442 / 2.68 ( 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 138 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 VAL cc_start: 0.8410 (t) cc_final: 0.8110 (p) REVERT: E 94 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.7941 (mp0) REVERT: W 620 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7369 (mmm160) outliers start: 12 outliers final: 7 residues processed: 135 average time/residue: 1.8227 time to fit residues: 265.6813 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 : 0.687 ------------------------------------------------------------------------------- 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 56 LYS 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 Chi-restraints excluded: chain W residue 620 ARG Chi-restraints excluded: chain W residue 628 ASP 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: 3.9990 chunk 112 optimal weight: 2.9990 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: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.085502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.065027 restraints weight = 87700.349| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.42 r_work: 0.2944 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16768 Z= 0.222 Angle : 0.602 6.837 23904 Z= 0.382 Chirality : 0.038 0.269 2704 Planarity : 0.004 0.049 1995 Dihedral : 25.697 161.767 4576 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.17 % Favored : 95.66 % Rotamer: Outliers : 1.14 % Allowed : 15.32 % 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: 1.33 (0.25), residues: 1199 helix: 2.16 (0.19), residues: 732 sheet: 0.36 (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 0.009 0.001 TYR W 195 PHE 0.021 0.001 PHE W 391 TRP 0.011 0.001 TRP W 368 HIS 0.002 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.22 (16768) covalent geometry : angle 0.60162 / 0.38 (23904) hydrogen bonds : bond 0.06314 / 4.05 ( 631) hydrogen bonds : angle 3.82198 / 2.69 ( 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 140 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 VAL cc_start: 0.8429 (t) cc_final: 0.8171 (p) REVERT: E 94 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.7948 (mp0) REVERT: W 620 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7380 (mmm160) outliers start: 12 outliers final: 7 residues processed: 138 average time/residue: 1.8093 time to fit residues: 269.3750 Evaluate side-chains 133 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 56 LYS 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 Chi-restraints excluded: chain W residue 620 ARG Chi-restraints excluded: chain W residue 630 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 85 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.084315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.063362 restraints weight = 88487.098| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.48 r_work: 0.2890 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16768 Z= 0.183 Angle : 0.583 6.427 23904 Z= 0.374 Chirality : 0.037 0.263 2704 Planarity : 0.004 0.050 1995 Dihedral : 25.823 161.934 4576 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.92 % Favored : 95.91 % Rotamer: Outliers : 0.95 % Allowed : 15.60 % Favored : 83.44 % 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: 1.41 (0.25), residues: 1199 helix: 2.23 (0.19), residues: 732 sheet: 0.78 (0.66), residues: 66 loop : -1.60 (0.27), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 42 TYR 0.009 0.001 TYR W 195 PHE 0.008 0.001 PHE B 61 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 0.00349 / 0.18 (16768) covalent geometry : angle 0.58283 / 0.37 (23904) hydrogen bonds : bond 0.05946 / 3.79 ( 631) hydrogen bonds : angle 3.77963 / 2.66 ( 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 135 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 VAL cc_start: 0.8281 (t) cc_final: 0.8008 (p) REVERT: E 94 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.7942 (mp0) REVERT: W 620 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7316 (mmm160) outliers start: 10 outliers final: 6 residues processed: 134 average time/residue: 1.8061 time to fit residues: 261.0304 Evaluate side-chains 133 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 56 LYS 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 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: 7.9990 chunk 27 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.083213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.062265 restraints weight = 89378.319| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.51 r_work: 0.2852 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16768 Z= 0.252 Angle : 0.640 12.479 23904 Z= 0.394 Chirality : 0.039 0.282 2704 Planarity : 0.005 0.052 1995 Dihedral : 26.137 162.023 4576 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.75 % Favored : 95.08 % Rotamer: Outliers : 1.05 % Allowed : 15.41 % 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: 1.19 (0.24), residues: 1199 helix: 2.04 (0.19), residues: 732 sheet: 0.63 (0.66), residues: 65 loop : -1.66 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 131 TYR 0.010 0.001 TYR E 41 PHE 0.043 0.002 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 0.00521 / 0.25 (16768) covalent geometry : angle 0.64045 / 0.39 (23904) hydrogen bonds : bond 0.06762 / 4.34 ( 631) hydrogen bonds : angle 3.89135 / 2.73 ( 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 137 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.727 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 114 VAL cc_start: 0.8386 (t) cc_final: 0.8116 (p) REVERT: E 94 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8016 (mp0) REVERT: W 620 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7397 (mmm160) outliers start: 11 outliers final: 7 residues processed: 135 average time/residue: 1.8147 time to fit residues: 264.1758 Evaluate side-chains 134 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 125 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.084931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.064153 restraints weight = 89432.093| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.50 r_work: 0.2898 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16768 Z= 0.146 Angle : 0.569 7.147 23904 Z= 0.366 Chirality : 0.037 0.248 2704 Planarity : 0.004 0.056 1995 Dihedral : 26.245 163.034 4576 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.59 % Favored : 96.25 % Rotamer: Outliers : 1.05 % Allowed : 15.03 % 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: 1.51 (0.25), residues: 1199 helix: 2.31 (0.20), residues: 732 sheet: 0.70 (0.67), residues: 67 loop : -1.54 (0.28), residues: 400 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 0.009 0.001 PHE W 391 TRP 0.019 0.001 TRP W 368 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.15 (16768) covalent geometry : angle 0.56899 / 0.37 (23904) hydrogen bonds : bond 0.05415 / 3.42 ( 631) hydrogen bonds : angle 3.70442 / 2.60 ( 1767) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10536.73 seconds wall clock time: 178 minutes 56.60 seconds (10736.60 seconds total)