Starting phenix.real_space_refine on Tue May 27 03:36:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v4y_42977/05_2025/8v4y_42977.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v4y_42977/05_2025/8v4y_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_42977/05_2025/8v4y_42977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v4y_42977/05_2025/8v4y_42977.map" model { file = "/net/cci-nas-00/data/ceres_data/8v4y_42977/05_2025/8v4y_42977.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v4y_42977/05_2025/8v4y_42977.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 14.24, per 1000 atoms: 0.48 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: 7.22 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 13.00 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: 12.12 Time building geometry restraints manager: 8.55 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: 51305 2.71 - 5.41: 3028 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: 2320 0.103 - 0.205: 318 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: 4.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.390 Extract box with map and model: 1.060 Check model and map are aligned: 0.190 Set scattering table: 0.280 Process input model: 70.190 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 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 : 0.011 0.285 16768 Z= 0.741 Angle : 1.331 13.529 23904 Z= 0.893 Chirality : 0.077 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (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 TRP 0.078 0.008 TRP W 348 HIS 0.011 0.003 HIS H 106 PHE 0.043 0.008 PHE W 297 TYR 0.116 0.011 TYR G 57 ARG 0.009 0.001 ARG C 35 Details of bonding type rmsd hydrogen bonds : bond 0.25185 ( 631) hydrogen bonds : angle 7.83905 ( 1767) covalent geometry : bond 0.01100 (16768) covalent geometry : angle 1.33100 (23904) *********************** 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 : 1.661 Fit side-chains 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: 4.3764 time to fit residues: 1081.7885 Evaluate side-chains 136 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 1.741 ------------------------------------------------------------------------------- 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 121 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3747 r_free = 0.3747 target = 0.097187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.077314 restraints weight = 90697.822| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.45 r_work: 0.3213 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3120 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= 0.181 Angle : 0.662 6.105 23904 Z= 0.391 Chirality : 0.042 0.149 2704 Planarity : 0.006 0.063 1995 Dihedral : 23.053 166.130 4579 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.34 % Favored : 97.58 % Rotamer: Outliers : 1.52 % Allowed : 12.84 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.23), residues: 1199 helix: 1.48 (0.19), residues: 730 sheet: 0.76 (0.58), residues: 72 loop : -1.35 (0.27), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP W 280 HIS 0.023 0.001 HIS W 477 PHE 0.009 0.001 PHE E 78 TYR 0.014 0.001 TYR W 195 ARG 0.008 0.001 ARG E 42 Details of bonding type rmsd hydrogen bonds : bond 0.06661 ( 631) hydrogen bonds : angle 4.11844 ( 1767) covalent geometry : bond 0.00381 (16768) covalent geometry : angle 0.66161 (23904) *********************** 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 164 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 1.819 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 outliers start: 16 outliers final: 2 residues processed: 155 average time/residue: 3.3944 time to fit residues: 568.5194 Evaluate side-chains 133 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 13 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN W 341 GLN W 598 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.087193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.066318 restraints weight = 89093.853| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.46 r_work: 0.2949 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 16768 Z= 0.224 Angle : 0.660 7.257 23904 Z= 0.391 Chirality : 0.043 0.155 2704 Planarity : 0.005 0.047 1995 Dihedral : 24.659 168.298 4578 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.17 % Favored : 96.66 % Rotamer: Outliers : 2.00 % Allowed : 13.32 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.24), residues: 1199 helix: 2.13 (0.20), residues: 725 sheet: 0.46 (0.61), residues: 74 loop : -1.34 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 280 HIS 0.009 0.001 HIS W 477 PHE 0.010 0.001 PHE E 84 TYR 0.011 0.001 TYR G 57 ARG 0.005 0.001 ARG E 83 Details of bonding type rmsd hydrogen bonds : bond 0.06650 ( 631) hydrogen bonds : angle 3.93645 ( 1767) covalent geometry : bond 0.00492 (16768) covalent geometry : angle 0.65993 (23904) *********************** 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 158 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.948 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: G 74 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8503 (mmmt) REVERT: H 31 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.7958 (mptt) REVERT: W 620 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7549 (mmm160) outliers start: 21 outliers final: 6 residues processed: 148 average time/residue: 3.8179 time to fit residues: 606.3833 Evaluate side-chains 136 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain W residue 367 SER Chi-restraints excluded: chain W residue 429 MET Chi-restraints excluded: chain W residue 620 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 85 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.087367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.066779 restraints weight = 88710.919| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.44 r_work: 0.2985 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.4566 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= 0.191 Angle : 0.607 6.015 23904 Z= 0.363 Chirality : 0.042 0.144 2704 Planarity : 0.004 0.048 1995 Dihedral : 24.942 163.708 4576 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.34 % Favored : 96.50 % Rotamer: Outliers : 1.24 % Allowed : 14.65 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.25), residues: 1199 helix: 2.36 (0.20), residues: 726 sheet: 0.51 (0.62), residues: 76 loop : -1.37 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 348 HIS 0.003 0.001 HIS W 535 PHE 0.008 0.001 PHE B 61 TYR 0.010 0.001 TYR W 195 ARG 0.008 0.000 ARG E 42 Details of bonding type rmsd hydrogen bonds : bond 0.05637 ( 631) hydrogen bonds : angle 3.74999 ( 1767) covalent geometry : bond 0.00418 (16768) covalent geometry : angle 0.60729 (23904) *********************** 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: 13 poor density : 139 time to evaluate : 1.788 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: 0.8808 (t0) cc_final: 0.8596 (t0) REVERT: H 31 LYS cc_start: 0.8569 (mppt) cc_final: 0.8090 (mptt) REVERT: W 620 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7548 (mmm160) outliers start: 13 outliers final: 4 residues processed: 148 average time/residue: 3.5729 time to fit residues: 573.1890 Evaluate side-chains 132 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASN 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 620 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 101 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.085323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.064840 restraints weight = 87564.581| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.42 r_work: 0.2939 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16768 Z= 0.227 Angle : 0.612 7.933 23904 Z= 0.364 Chirality : 0.043 0.156 2704 Planarity : 0.005 0.053 1995 Dihedral : 25.553 159.503 4576 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.09 % Favored : 95.75 % Rotamer: Outliers : 1.05 % Allowed : 14.75 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.25), residues: 1199 helix: 2.35 (0.20), residues: 726 sheet: 0.49 (0.61), residues: 76 loop : -1.40 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 348 HIS 0.003 0.001 HIS G 31 PHE 0.026 0.001 PHE W 391 TYR 0.012 0.001 TYR W 195 ARG 0.009 0.001 ARG E 42 Details of bonding type rmsd hydrogen bonds : bond 0.06072 ( 631) hydrogen bonds : angle 3.77444 ( 1767) covalent geometry : bond 0.00503 (16768) covalent geometry : angle 0.61217 (23904) *********************** 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 147 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 ASP cc_start: 0.8839 (t0) cc_final: 0.8587 (t0) REVERT: W 368 TRP cc_start: 0.6584 (m-10) cc_final: 0.6361 (m-10) REVERT: W 620 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7531 (mmm160) outliers start: 11 outliers final: 5 residues processed: 143 average time/residue: 3.7209 time to fit residues: 571.3464 Evaluate side-chains 133 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 56 LYS 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 620 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 12 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 126 optimal weight: 0.4980 chunk 136 optimal weight: 0.0970 chunk 121 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 overall best weight: 1.0580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.086608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.066172 restraints weight = 87646.122| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.43 r_work: 0.2969 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16768 Z= 0.162 Angle : 0.583 6.056 23904 Z= 0.347 Chirality : 0.040 0.147 2704 Planarity : 0.004 0.051 1995 Dihedral : 25.723 159.115 4576 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.00 % Favored : 96.83 % Rotamer: Outliers : 0.48 % Allowed : 16.18 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.25), residues: 1199 helix: 2.58 (0.20), residues: 726 sheet: 0.44 (0.61), residues: 76 loop : -1.35 (0.28), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 348 HIS 0.003 0.001 HIS W 535 PHE 0.007 0.001 PHE B 61 TYR 0.011 0.001 TYR W 195 ARG 0.006 0.000 ARG E 42 Details of bonding type rmsd hydrogen bonds : bond 0.05021 ( 631) hydrogen bonds : angle 3.58062 ( 1767) covalent geometry : bond 0.00351 (16768) covalent geometry : angle 0.58313 (23904) *********************** 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 137 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 65 ASP cc_start: 0.8784 (t0) cc_final: 0.8551 (t0) REVERT: E 42 ARG cc_start: 0.8189 (mtp85) cc_final: 0.7676 (mtp180) REVERT: W 368 TRP cc_start: 0.6433 (m-10) cc_final: 0.6229 (m-10) REVERT: W 620 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7446 (mmm160) outliers start: 5 outliers final: 3 residues processed: 135 average time/residue: 3.6571 time to fit residues: 531.7859 Evaluate side-chains 132 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 128 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain W residue 388 LEU Chi-restraints excluded: chain W residue 429 MET 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 124 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 29 optimal weight: 0.0670 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 7 optimal weight: 0.0270 chunk 142 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.088636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.068441 restraints weight = 88844.342| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.46 r_work: 0.3016 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16768 Z= 0.129 Angle : 0.568 7.210 23904 Z= 0.337 Chirality : 0.038 0.153 2704 Planarity : 0.004 0.052 1995 Dihedral : 25.778 159.294 4576 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.17 % Favored : 96.66 % Rotamer: Outliers : 0.76 % Allowed : 15.89 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.25), residues: 1199 helix: 2.85 (0.20), residues: 733 sheet: 0.82 (0.62), residues: 66 loop : -1.24 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 348 HIS 0.003 0.001 HIS W 477 PHE 0.024 0.001 PHE W 391 TYR 0.011 0.001 TYR W 195 ARG 0.006 0.000 ARG E 42 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 631) hydrogen bonds : angle 3.33278 ( 1767) covalent geometry : bond 0.00282 (16768) covalent geometry : angle 0.56806 (23904) *********************** 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 143 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 42 ARG cc_start: 0.8125 (mtp85) cc_final: 0.7738 (ttm110) REVERT: W 620 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7445 (mmm160) REVERT: W 623 MET cc_start: 0.8618 (mmm) cc_final: 0.8308 (mmm) outliers start: 8 outliers final: 3 residues processed: 141 average time/residue: 3.6744 time to fit residues: 563.1937 Evaluate side-chains 131 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 304 TYR Chi-restraints excluded: chain W residue 429 MET Chi-restraints excluded: chain W residue 535 HIS 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 143 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.083409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.062389 restraints weight = 89023.168| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.50 r_work: 0.2863 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 16768 Z= 0.261 Angle : 0.602 7.218 23904 Z= 0.356 Chirality : 0.044 0.167 2704 Planarity : 0.005 0.052 1995 Dihedral : 25.997 158.357 4576 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.25 % Favored : 95.58 % Rotamer: Outliers : 0.86 % Allowed : 15.89 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.25), residues: 1199 helix: 2.57 (0.20), residues: 726 sheet: 0.69 (0.63), residues: 67 loop : -1.33 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 280 HIS 0.003 0.001 HIS H 106 PHE 0.012 0.001 PHE B 61 TYR 0.009 0.001 TYR W 183 ARG 0.004 0.001 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.06101 ( 631) hydrogen bonds : angle 3.67253 ( 1767) covalent geometry : bond 0.00584 (16768) covalent geometry : angle 0.60168 (23904) *********************** 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: 9 poor density : 131 time to evaluate : 1.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 28 LYS cc_start: 0.6765 (tttt) cc_final: 0.6511 (pmmt) REVERT: D 65 ASP cc_start: 0.8797 (t0) cc_final: 0.8569 (t0) REVERT: E 42 ARG cc_start: 0.8185 (mtp85) cc_final: 0.7794 (ttm110) REVERT: W 620 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7473 (mmm160) outliers start: 9 outliers final: 3 residues processed: 137 average time/residue: 3.7527 time to fit residues: 553.2455 Evaluate side-chains 132 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 128 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 429 MET 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 75 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.084034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.063152 restraints weight = 88367.845| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.50 r_work: 0.2882 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16768 Z= 0.199 Angle : 0.587 6.845 23904 Z= 0.346 Chirality : 0.041 0.152 2704 Planarity : 0.004 0.051 1995 Dihedral : 26.143 159.389 4576 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.09 % Favored : 95.75 % Rotamer: Outliers : 0.76 % Allowed : 15.89 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.25), residues: 1199 helix: 2.57 (0.20), residues: 730 sheet: 0.87 (0.63), residues: 66 loop : -1.38 (0.28), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 368 HIS 0.002 0.001 HIS W 535 PHE 0.030 0.001 PHE W 391 TYR 0.010 0.001 TYR W 195 ARG 0.005 0.000 ARG E 42 Details of bonding type rmsd hydrogen bonds : bond 0.05397 ( 631) hydrogen bonds : angle 3.59653 ( 1767) covalent geometry : bond 0.00438 (16768) covalent geometry : angle 0.58741 (23904) *********************** 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 138 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 1.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 28 LYS cc_start: 0.6807 (tttt) cc_final: 0.6522 (pmmt) REVERT: D 65 ASP cc_start: 0.8768 (t0) cc_final: 0.8540 (t0) REVERT: E 42 ARG cc_start: 0.8166 (mtp85) cc_final: 0.7742 (ttm110) REVERT: H 31 LYS cc_start: 0.8588 (mppt) cc_final: 0.8290 (mptm) REVERT: W 620 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7442 (mmm160) outliers start: 8 outliers final: 5 residues processed: 136 average time/residue: 3.5726 time to fit residues: 523.3265 Evaluate side-chains 136 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain F residue 22 LEU 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 620 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 127 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.084655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.063875 restraints weight = 88711.033| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.49 r_work: 0.2901 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.5555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16768 Z= 0.164 Angle : 0.579 8.675 23904 Z= 0.342 Chirality : 0.040 0.152 2704 Planarity : 0.004 0.052 1995 Dihedral : 26.176 159.570 4576 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.67 % Favored : 96.16 % Rotamer: Outliers : 0.86 % Allowed : 15.98 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.25), residues: 1199 helix: 2.64 (0.20), residues: 730 sheet: 0.86 (0.63), residues: 66 loop : -1.35 (0.28), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP W 348 HIS 0.002 0.001 HIS W 535 PHE 0.009 0.001 PHE W 391 TYR 0.008 0.001 TYR W 195 ARG 0.005 0.000 ARG E 42 Details of bonding type rmsd hydrogen bonds : bond 0.04982 ( 631) hydrogen bonds : angle 3.54319 ( 1767) covalent geometry : bond 0.00357 (16768) covalent geometry : angle 0.57946 (23904) ********************** 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 142 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 28 LYS cc_start: 0.6795 (tttt) cc_final: 0.6539 (pmmt) REVERT: D 65 ASP cc_start: 0.8744 (t0) cc_final: 0.8521 (t0) REVERT: E 42 ARG cc_start: 0.8141 (mtp85) cc_final: 0.7708 (ttm110) REVERT: H 31 LYS cc_start: 0.8591 (mppt) cc_final: 0.8298 (mptm) REVERT: W 233 MET cc_start: 0.8465 (tpp) cc_final: 0.7947 (tpp) REVERT: W 620 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7451 (mmm160) outliers start: 9 outliers final: 6 residues processed: 139 average time/residue: 3.5488 time to fit residues: 533.2484 Evaluate side-chains 137 residues out of total 1051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain F residue 22 LEU 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 535 HIS 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 5 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.082070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.061182 restraints weight = 89003.896| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.49 r_work: 0.2832 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.5626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 16768 Z= 0.283 Angle : 0.617 6.612 23904 Z= 0.364 Chirality : 0.045 0.177 2704 Planarity : 0.005 0.047 1995 Dihedral : 26.431 159.557 4576 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.42 % Favored : 95.41 % Rotamer: Outliers : 0.76 % Allowed : 16.08 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.25), residues: 1199 helix: 2.26 (0.19), residues: 731 sheet: 0.16 (0.59), residues: 76 loop : -1.42 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 368 HIS 0.003 0.001 HIS W 535 PHE 0.030 0.002 PHE W 391 TYR 0.008 0.001 TYR A 54 ARG 0.004 0.001 ARG E 42 Details of bonding type rmsd hydrogen bonds : bond 0.06614 ( 631) hydrogen bonds : angle 3.82010 ( 1767) covalent geometry : bond 0.00632 (16768) covalent geometry : angle 0.61705 (23904) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21189.58 seconds wall clock time: 361 minutes 58.78 seconds (21718.78 seconds total)