Starting phenix.real_space_refine on Sat Mar 7 04:24:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i2g_52584/03_2026/9i2g_52584.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i2g_52584/03_2026/9i2g_52584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9i2g_52584/03_2026/9i2g_52584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i2g_52584/03_2026/9i2g_52584.map" model { file = "/net/cci-nas-00/data/ceres_data/9i2g_52584/03_2026/9i2g_52584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i2g_52584/03_2026/9i2g_52584.cif" } resolution = 3.0 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= 0.001 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 268 5.49 5 Mg 21 5.21 5 S 63 5.16 5 C 11537 2.51 5 N 3398 2.21 5 O 4363 1.98 5 H 17292 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36942 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 9460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 9460 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 19, 'TRANS': 558} Chain breaks: 1 Chain: "C" Number of atoms: 9460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 9460 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 19, 'TRANS': 558} Chain breaks: 1 Chain: "E" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1804 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 9, 'rna3p_pur': 22, 'rna3p_pyr': 15} Link IDs: {'rna2p': 18, 'rna3p': 37} Chain breaks: 1 Chain: "G" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 1034 Classifications: {'DNA': 33} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 32} Chain breaks: 2 Chain: "I" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 1001 Classifications: {'DNA': 32} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 31} Chain breaks: 2 Chain: "A" Number of atoms: 9460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 9460 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 19, 'TRANS': 558} Chain breaks: 1 Chain: "H" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 1034 Classifications: {'DNA': 33} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 32} Chain breaks: 2 Chain: "D" Number of atoms: 1834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1834 Classifications: {'RNA': 57} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 11, 'rna3p_pur': 22, 'rna3p_pyr': 14} Link IDs: {'rna2p': 20, 'rna3p': 36} Chain breaks: 1 Chain: "F" Number of atoms: 1834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1834 Classifications: {'RNA': 57} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 13, 'rna3p_pur': 21, 'rna3p_pyr': 12} Link IDs: {'rna2p': 23, 'rna3p': 33} Chain breaks: 1 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.20, per 1000 atoms: 0.17 Number of scatterers: 36942 At special positions: 0 Unit cell: (149.6, 161.7, 116.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 63 16.00 P 268 15.00 Mg 21 11.99 O 4363 8.00 N 3398 7.00 C 11537 6.00 H 17292 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 793.1 milliseconds 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3282 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 23 sheets defined 51.6% alpha, 11.8% beta 70 base pairs and 108 stacking pairs defined. Time for finding SS restraints: 5.64 Creating SS restraints... Processing helix chain 'B' and resid 5 through 13 Processing helix chain 'B' and resid 15 through 24 removed outlier: 3.533A pdb=" N LEU B 19 " --> pdb=" O SER B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 36 Processing helix chain 'B' and resid 62 through 88 Processing helix chain 'B' and resid 102 through 110 removed outlier: 3.868A pdb=" N HIS B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 128 removed outlier: 4.108A pdb=" N PHE B 128 " --> pdb=" O PHE B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 169 through 193 removed outlier: 4.631A pdb=" N ILE B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N MET B 181 " --> pdb=" O ILE B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 242 through 246 Processing helix chain 'B' and resid 269 through 287 Processing helix chain 'B' and resid 302 through 327 removed outlier: 3.860A pdb=" N LEU B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN B 327 " --> pdb=" O LYS B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 364 Processing helix chain 'B' and resid 377 through 389 Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 428 through 445 removed outlier: 4.446A pdb=" N LYS B 440 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASN B 441 " --> pdb=" O GLU B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 476 Processing helix chain 'B' and resid 483 through 488 removed outlier: 3.590A pdb=" N ARG B 487 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS B 488 " --> pdb=" O THR B 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 483 through 488' Processing helix chain 'B' and resid 526 through 530 removed outlier: 3.663A pdb=" N GLY B 529 " --> pdb=" O LYS B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 553 Processing helix chain 'B' and resid 566 through 586 Processing helix chain 'C' and resid 5 through 13 Processing helix chain 'C' and resid 15 through 24 removed outlier: 3.530A pdb=" N LEU C 19 " --> pdb=" O SER C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 38 through 41 Processing helix chain 'C' and resid 62 through 88 Processing helix chain 'C' and resid 102 through 110 removed outlier: 4.017A pdb=" N HIS C 110 " --> pdb=" O ASN C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 128 removed outlier: 4.095A pdb=" N PHE C 128 " --> pdb=" O PHE C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 146 through 158 Processing helix chain 'C' and resid 169 through 193 removed outlier: 4.508A pdb=" N ILE C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N MET C 181 " --> pdb=" O ILE C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 237 Processing helix chain 'C' and resid 243 through 246 removed outlier: 3.502A pdb=" N THR C 246 " --> pdb=" O ASP C 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 243 through 246' Processing helix chain 'C' and resid 269 through 287 Processing helix chain 'C' and resid 302 through 327 removed outlier: 3.833A pdb=" N LEU C 306 " --> pdb=" O GLY C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 364 Processing helix chain 'C' and resid 377 through 389 Processing helix chain 'C' and resid 416 through 423 Processing helix chain 'C' and resid 428 through 446 removed outlier: 4.403A pdb=" N LYS C 440 " --> pdb=" O VAL C 436 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASN C 441 " --> pdb=" O GLU C 437 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR C 446 " --> pdb=" O ASN C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 476 removed outlier: 3.641A pdb=" N VAL C 476 " --> pdb=" O LEU C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 488 removed outlier: 3.578A pdb=" N LYS C 488 " --> pdb=" O THR C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 518 Processing helix chain 'C' and resid 526 through 530 Processing helix chain 'C' and resid 545 through 553 Processing helix chain 'C' and resid 566 through 586 Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 15 through 24 removed outlier: 3.503A pdb=" N LEU A 19 " --> pdb=" O SER A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'A' and resid 38 through 41 Processing helix chain 'A' and resid 62 through 88 Processing helix chain 'A' and resid 102 through 110 removed outlier: 3.914A pdb=" N HIS A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 128 removed outlier: 4.096A pdb=" N PHE A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 169 through 193 removed outlier: 4.606A pdb=" N ILE A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N MET A 181 " --> pdb=" O ILE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 243 through 246 removed outlier: 3.521A pdb=" N THR A 246 " --> pdb=" O ASP A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 246' Processing helix chain 'A' and resid 269 through 287 Processing helix chain 'A' and resid 302 through 327 removed outlier: 3.821A pdb=" N LEU A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 364 Processing helix chain 'A' and resid 377 through 389 Processing helix chain 'A' and resid 393 through 395 No H-bonds generated for 'chain 'A' and resid 393 through 395' Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 428 through 445 removed outlier: 4.413A pdb=" N LYS A 440 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASN A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 476 Processing helix chain 'A' and resid 483 through 488 removed outlier: 3.629A pdb=" N LYS A 488 " --> pdb=" O THR A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 530 removed outlier: 3.672A pdb=" N GLY A 529 " --> pdb=" O LYS A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 553 Processing helix chain 'A' and resid 566 through 586 Processing sheet with id=AA1, first strand: chain 'B' and resid 43 through 48 Processing sheet with id=AA2, first strand: chain 'B' and resid 195 through 199 Processing sheet with id=AA3, first strand: chain 'B' and resid 217 through 219 Processing sheet with id=AA4, first strand: chain 'B' and resid 256 through 257 Processing sheet with id=AA5, first strand: chain 'B' and resid 289 through 292 removed outlier: 4.604A pdb=" N TYR B 289 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 411 through 412 removed outlier: 6.278A pdb=" N THR B 370 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL B 458 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 455 " --> pdb=" O TYR B 499 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL B 501 " --> pdb=" O VAL B 455 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N MET B 457 " --> pdb=" O VAL B 501 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE B 500 " --> pdb=" O HIS B 493 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N HIS B 493 " --> pdb=" O ILE B 500 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 397 through 399 Processing sheet with id=AA8, first strand: chain 'C' and resid 43 through 48 Processing sheet with id=AA9, first strand: chain 'C' and resid 195 through 199 removed outlier: 4.680A pdb=" N GLU C 240 " --> pdb=" O LYS C 122 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 195 through 199 Processing sheet with id=AB2, first strand: chain 'C' and resid 217 through 219 Processing sheet with id=AB3, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AB4, first strand: chain 'C' and resid 289 through 292 removed outlier: 4.589A pdb=" N TYR C 289 " --> pdb=" O GLY C 301 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 411 through 412 removed outlier: 6.316A pdb=" N THR C 370 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL C 458 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL C 455 " --> pdb=" O TYR C 499 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL C 501 " --> pdb=" O VAL C 455 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N MET C 457 " --> pdb=" O VAL C 501 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 495 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE C 500 " --> pdb=" O HIS C 493 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS C 493 " --> pdb=" O ILE C 500 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 397 through 399 Processing sheet with id=AB7, first strand: chain 'A' and resid 43 through 48 Processing sheet with id=AB8, first strand: chain 'A' and resid 195 through 199 removed outlier: 4.697A pdb=" N GLU A 240 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 195 through 199 Processing sheet with id=AC1, first strand: chain 'A' and resid 217 through 219 Processing sheet with id=AC2, first strand: chain 'A' and resid 256 through 257 Processing sheet with id=AC3, first strand: chain 'A' and resid 289 through 292 removed outlier: 4.711A pdb=" N TYR A 289 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 411 through 412 removed outlier: 6.262A pdb=" N THR A 370 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL A 458 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL A 455 " --> pdb=" O TYR A 499 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL A 501 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N MET A 457 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 495 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE A 500 " --> pdb=" O HIS A 493 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N HIS A 493 " --> pdb=" O ILE A 500 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 397 through 399 718 hydrogen bonds defined for protein. 2040 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 181 hydrogen bonds 338 hydrogen bond angles 0 basepair planarities 70 basepair parallelities 108 stacking parallelities Total time for adding SS restraints: 8.93 Time building geometry restraints manager: 4.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17259 1.03 - 1.23: 149 1.23 - 1.42: 9018 1.42 - 1.62: 11312 1.62 - 1.81: 93 Bond restraints: 37831 Sorted by residual: bond pdb=" N THR B 4 " pdb=" H THR B 4 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N THR C 4 " pdb=" H THR C 4 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N THR A 4 " pdb=" H THR A 4 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" C3' DA G 9 " pdb=" O3' DA G 9 " ideal model delta sigma weight residual 1.422 1.468 -0.046 3.00e-02 1.11e+03 2.34e+00 bond pdb=" C3' DC I 54 " pdb=" O3' DC I 54 " ideal model delta sigma weight residual 1.422 1.464 -0.042 3.00e-02 1.11e+03 1.92e+00 ... (remaining 37826 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 64833 1.21 - 2.41: 2993 2.41 - 3.62: 528 3.62 - 4.83: 23 4.83 - 6.03: 8 Bond angle restraints: 68385 Sorted by residual: angle pdb=" CA LYS C 558 " pdb=" CB LYS C 558 " pdb=" CG LYS C 558 " ideal model delta sigma weight residual 114.10 119.97 -5.87 2.00e+00 2.50e-01 8.61e+00 angle pdb=" C3' DC H 10 " pdb=" C2' DC H 10 " pdb=" C1' DC H 10 " ideal model delta sigma weight residual 101.60 105.09 -3.49 1.50e+00 4.44e-01 5.42e+00 angle pdb=" O3' DG H 55 " pdb=" C3' DG H 55 " pdb=" C2' DG H 55 " ideal model delta sigma weight residual 111.50 114.96 -3.46 1.50e+00 4.44e-01 5.33e+00 angle pdb=" C LYS C 557 " pdb=" N LYS C 558 " pdb=" CA LYS C 558 " ideal model delta sigma weight residual 125.02 128.98 -3.96 1.76e+00 3.23e-01 5.06e+00 angle pdb=" C3' DA G 9 " pdb=" O3' DA G 9 " pdb=" P DC G 10 " ideal model delta sigma weight residual 120.20 123.57 -3.37 1.50e+00 4.44e-01 5.04e+00 ... (remaining 68380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.40: 16583 34.40 - 68.80: 920 68.80 - 103.21: 51 103.21 - 137.61: 1 137.61 - 172.01: 11 Dihedral angle restraints: 17566 sinusoidal: 11554 harmonic: 6012 Sorted by residual: dihedral pdb=" O4' C E 39 " pdb=" C1' C E 39 " pdb=" N1 C E 39 " pdb=" C2 C E 39 " ideal model delta sinusoidal sigma weight residual -160.00 4.08 -164.08 1 1.50e+01 4.44e-03 8.37e+01 dihedral pdb=" O4' C F 46 " pdb=" C1' C F 46 " pdb=" N1 C F 46 " pdb=" C2 C F 46 " ideal model delta sinusoidal sigma weight residual 200.00 58.03 141.97 1 1.50e+01 4.44e-03 7.63e+01 dihedral pdb=" O4' U D 18 " pdb=" C1' U D 18 " pdb=" N1 U D 18 " pdb=" C2 U D 18 " ideal model delta sinusoidal sigma weight residual -128.00 26.21 -154.21 1 1.70e+01 3.46e-03 6.31e+01 ... (remaining 17563 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2372 0.033 - 0.066: 690 0.066 - 0.099: 209 0.099 - 0.132: 96 0.132 - 0.165: 11 Chirality restraints: 3378 Sorted by residual: chirality pdb=" CB ILE A 372 " pdb=" CA ILE A 372 " pdb=" CG1 ILE A 372 " pdb=" CG2 ILE A 372 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA ILE C 561 " pdb=" N ILE C 561 " pdb=" C ILE C 561 " pdb=" CB ILE C 561 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.89e-01 chirality pdb=" CA ILE B 119 " pdb=" N ILE B 119 " pdb=" C ILE B 119 " pdb=" CB ILE B 119 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.46e-01 ... (remaining 3375 not shown) Planarity restraints: 4569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 557 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.68e+00 pdb=" C LYS C 557 " -0.037 2.00e-02 2.50e+03 pdb=" O LYS C 557 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS C 558 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 580 " -0.016 2.00e-02 2.50e+03 1.20e-02 4.30e+00 pdb=" CG TYR C 580 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR C 580 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR C 580 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR C 580 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR C 580 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 580 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 580 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TYR C 580 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 TYR C 580 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 TYR C 580 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR C 580 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 68 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.79e+00 pdb=" C ILE C 68 " -0.034 2.00e-02 2.50e+03 pdb=" O ILE C 68 " 0.013 2.00e-02 2.50e+03 pdb=" N GLN C 69 " 0.011 2.00e-02 2.50e+03 ... (remaining 4566 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 231 2.06 - 2.70: 55915 2.70 - 3.33: 107460 3.33 - 3.97: 140987 3.97 - 4.60: 218755 Nonbonded interactions: 523348 Sorted by model distance: nonbonded pdb=" P DT I 1 " pdb=" O2' G F 15 " model vdw 1.430 3.200 nonbonded pdb=" O2' G E 15 " pdb=" OP1 DT H 1 " model vdw 1.456 2.800 nonbonded pdb=" P DT G 1 " pdb=" O2' G D 15 " model vdw 1.472 3.200 nonbonded pdb=" O2' G E 15 " pdb=" P DT H 1 " model vdw 1.481 3.200 nonbonded pdb=" OP2 DT I 1 " pdb=" O2' G F 15 " model vdw 1.764 2.800 ... (remaining 523343 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 'B' and resid 4 through 602) selection = (chain 'C' and resid 4 through 602) } ncs_group { reference = (chain 'D' and (resid 11 through 63 or resid 121 through 202)) selection = (chain 'E' and resid 11 through 202) selection = (chain 'F' and (resid 11 through 63 or resid 121 through 202)) } ncs_group { reference = (chain 'G' and (resid 1 through 27 or resid 54 through 101)) selection = (chain 'H' and (resid 1 through 27 or resid 54 through 101)) selection = (chain 'I' and resid 1 through 101) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.210 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 36.970 Find NCS groups from input model: 0.560 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: 0.010 Load rotamer database and sin/cos tables:5.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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 : 0.004 0.046 20539 Z= 0.163 Angle : 0.520 5.868 28880 Z= 0.292 Chirality : 0.038 0.165 3378 Planarity : 0.004 0.037 2698 Dihedral : 19.197 172.009 9163 Min Nonbonded Distance : 1.430 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.08 (0.20), residues: 1722 helix: 1.57 (0.18), residues: 786 sheet: -2.40 (0.33), residues: 174 loop : -1.21 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 559 TYR 0.033 0.001 TYR C 580 PHE 0.033 0.001 PHE C 495 HIS 0.008 0.001 HIS C 547 Details of bonding type rmsd covalent geometry : bond 0.00351 (20539) covalent geometry : angle 0.52047 (28880) hydrogen bonds : bond 0.13210 ( 875) hydrogen bonds : angle 5.72838 ( 2378) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 373 THR cc_start: 0.9354 (p) cc_final: 0.9033 (t) REVERT: B 489 MET cc_start: 0.6804 (mtt) cc_final: 0.6518 (mtp) REVERT: B 491 TYR cc_start: 0.8074 (p90) cc_final: 0.7804 (p90) REVERT: C 326 LEU cc_start: 0.8531 (tt) cc_final: 0.8138 (mp) REVERT: C 376 LYS cc_start: 0.8393 (mtmt) cc_final: 0.7945 (pttp) REVERT: C 426 SER cc_start: 0.8727 (t) cc_final: 0.7955 (m) REVERT: C 497 ASN cc_start: 0.7095 (p0) cc_final: 0.6783 (p0) REVERT: C 514 MET cc_start: 0.8082 (mtp) cc_final: 0.7605 (ttm) REVERT: A 45 GLN cc_start: 0.8630 (mt0) cc_final: 0.8415 (mt0) REVERT: A 326 LEU cc_start: 0.8678 (tt) cc_final: 0.8310 (mt) REVERT: A 420 LYS cc_start: 0.9004 (tttp) cc_final: 0.8774 (tptt) REVERT: A 424 ASP cc_start: 0.8664 (t70) cc_final: 0.8075 (t0) REVERT: A 426 SER cc_start: 0.8967 (p) cc_final: 0.8720 (p) REVERT: A 470 ASN cc_start: 0.7706 (m110) cc_final: 0.7456 (m110) REVERT: A 489 MET cc_start: 0.7445 (mtt) cc_final: 0.6811 (mtt) REVERT: A 551 MET cc_start: 0.7418 (ttt) cc_final: 0.7046 (mmm) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 1.1746 time to fit residues: 187.1452 Evaluate side-chains 97 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN A 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.135563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.088404 restraints weight = 88081.828| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.34 r_work: 0.2968 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20539 Z= 0.158 Angle : 0.485 4.486 28880 Z= 0.271 Chirality : 0.037 0.153 3378 Planarity : 0.004 0.040 2698 Dihedral : 21.533 176.334 5596 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.51 % Allowed : 5.90 % Favored : 93.59 % 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: 0.38 (0.21), residues: 1722 helix: 1.83 (0.18), residues: 795 sheet: -2.20 (0.35), residues: 174 loop : -0.84 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 332 TYR 0.015 0.001 TYR B 499 PHE 0.020 0.001 PHE C 495 HIS 0.004 0.001 HIS C 547 Details of bonding type rmsd covalent geometry : bond 0.00337 (20539) covalent geometry : angle 0.48455 (28880) hydrogen bonds : bond 0.04530 ( 875) hydrogen bonds : angle 4.58800 ( 2378) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.795 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: B 373 THR cc_start: 0.9403 (p) cc_final: 0.9135 (t) REVERT: B 489 MET cc_start: 0.7141 (mtt) cc_final: 0.6894 (mtp) REVERT: B 491 TYR cc_start: 0.8100 (p90) cc_final: 0.7878 (p90) REVERT: C 326 LEU cc_start: 0.8395 (tt) cc_final: 0.8044 (mp) REVERT: C 376 LYS cc_start: 0.8328 (mtmt) cc_final: 0.7840 (pttt) REVERT: C 426 SER cc_start: 0.8853 (t) cc_final: 0.8159 (m) REVERT: C 514 MET cc_start: 0.8147 (mtp) cc_final: 0.7633 (ttm) REVERT: C 551 MET cc_start: 0.6556 (mtt) cc_final: 0.5715 (mtt) REVERT: A 424 ASP cc_start: 0.8854 (t70) cc_final: 0.8294 (t0) REVERT: A 426 SER cc_start: 0.8988 (p) cc_final: 0.8763 (p) REVERT: A 470 ASN cc_start: 0.7771 (m110) cc_final: 0.7364 (m110) REVERT: A 489 MET cc_start: 0.7439 (mtt) cc_final: 0.7188 (mtt) REVERT: A 551 MET cc_start: 0.7455 (ttt) cc_final: 0.7251 (mmm) outliers start: 8 outliers final: 3 residues processed: 106 average time/residue: 0.9777 time to fit residues: 120.9893 Evaluate side-chains 97 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 94 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 575 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 193 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 190 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN A 45 GLN A 69 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.133776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.082664 restraints weight = 88208.914| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.61 r_work: 0.2890 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20539 Z= 0.252 Angle : 0.508 4.931 28880 Z= 0.288 Chirality : 0.039 0.146 3378 Planarity : 0.004 0.057 2698 Dihedral : 21.744 179.089 5596 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.64 % Allowed : 7.05 % Favored : 92.31 % 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: 0.29 (0.21), residues: 1722 helix: 1.69 (0.18), residues: 795 sheet: -2.37 (0.34), residues: 174 loop : -0.78 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 438 TYR 0.016 0.001 TYR A 439 PHE 0.015 0.002 PHE B 357 HIS 0.004 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00546 (20539) covalent geometry : angle 0.50795 (28880) hydrogen bonds : bond 0.05036 ( 875) hydrogen bonds : angle 4.55410 ( 2378) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.733 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: B 326 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8067 (mt) REVERT: B 489 MET cc_start: 0.7194 (mtt) cc_final: 0.6894 (mtp) REVERT: B 491 TYR cc_start: 0.8181 (p90) cc_final: 0.7839 (p90) REVERT: C 326 LEU cc_start: 0.8428 (tt) cc_final: 0.8069 (mp) REVERT: C 376 LYS cc_start: 0.8341 (mtmt) cc_final: 0.7823 (pttp) REVERT: C 426 SER cc_start: 0.8983 (t) cc_final: 0.8292 (m) REVERT: C 489 MET cc_start: 0.6983 (mtt) cc_final: 0.6733 (mpp) REVERT: C 514 MET cc_start: 0.7975 (mtp) cc_final: 0.7677 (ttm) REVERT: C 551 MET cc_start: 0.6596 (mtt) cc_final: 0.5715 (mtt) REVERT: A 326 LEU cc_start: 0.8359 (tt) cc_final: 0.8042 (mt) REVERT: A 470 ASN cc_start: 0.7906 (m110) cc_final: 0.7511 (m110) REVERT: A 489 MET cc_start: 0.7400 (mtt) cc_final: 0.7190 (mtt) REVERT: A 551 MET cc_start: 0.7521 (ttt) cc_final: 0.7161 (mmm) REVERT: A 575 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8293 (t70) outliers start: 10 outliers final: 4 residues processed: 108 average time/residue: 1.1266 time to fit residues: 139.8559 Evaluate side-chains 101 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 398 ARG Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 575 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 174 optimal weight: 0.9980 chunk 179 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 47 optimal weight: 0.1980 chunk 106 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 58 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 GLN C 255 GLN A 45 GLN A 69 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.134856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.084098 restraints weight = 88095.671| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.59 r_work: 0.2942 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20539 Z= 0.140 Angle : 0.466 5.228 28880 Z= 0.261 Chirality : 0.036 0.167 3378 Planarity : 0.004 0.054 2698 Dihedral : 21.702 178.091 5596 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.51 % Allowed : 8.14 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.53 (0.21), residues: 1722 helix: 1.89 (0.18), residues: 795 sheet: -2.32 (0.35), residues: 174 loop : -0.62 (0.24), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 552 TYR 0.011 0.001 TYR C 491 PHE 0.015 0.001 PHE C 495 HIS 0.003 0.001 HIS C 547 Details of bonding type rmsd covalent geometry : bond 0.00293 (20539) covalent geometry : angle 0.46631 (28880) hydrogen bonds : bond 0.04211 ( 875) hydrogen bonds : angle 4.31927 ( 2378) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.938 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: B 489 MET cc_start: 0.7133 (mtt) cc_final: 0.6814 (mtp) REVERT: B 491 TYR cc_start: 0.8194 (p90) cc_final: 0.7861 (p90) REVERT: C 326 LEU cc_start: 0.8399 (tt) cc_final: 0.8032 (mp) REVERT: C 376 LYS cc_start: 0.8217 (mtmt) cc_final: 0.7696 (pttp) REVERT: C 426 SER cc_start: 0.8950 (t) cc_final: 0.8254 (m) REVERT: C 514 MET cc_start: 0.8009 (mtp) cc_final: 0.7748 (ttm) REVERT: A 470 ASN cc_start: 0.7902 (m110) cc_final: 0.7649 (m110) REVERT: A 489 MET cc_start: 0.7356 (mtt) cc_final: 0.7102 (mtt) REVERT: A 551 MET cc_start: 0.7577 (ttt) cc_final: 0.7185 (mmm) outliers start: 8 outliers final: 2 residues processed: 102 average time/residue: 1.0181 time to fit residues: 121.6263 Evaluate side-chains 96 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 575 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 96 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 189 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.134131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.083050 restraints weight = 88057.986| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.72 r_work: 0.2894 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20539 Z= 0.211 Angle : 0.484 5.307 28880 Z= 0.273 Chirality : 0.038 0.141 3378 Planarity : 0.004 0.060 2698 Dihedral : 21.756 179.927 5596 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.90 % Allowed : 8.85 % Favored : 90.26 % 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: 0.52 (0.21), residues: 1722 helix: 1.85 (0.18), residues: 795 sheet: -2.31 (0.35), residues: 174 loop : -0.59 (0.24), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 552 TYR 0.014 0.001 TYR A 439 PHE 0.013 0.001 PHE C 495 HIS 0.003 0.001 HIS A 547 Details of bonding type rmsd covalent geometry : bond 0.00455 (20539) covalent geometry : angle 0.48375 (28880) hydrogen bonds : bond 0.04522 ( 875) hydrogen bonds : angle 4.34031 ( 2378) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.835 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: B 326 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8068 (mt) REVERT: B 489 MET cc_start: 0.7174 (mtt) cc_final: 0.6857 (mtp) REVERT: B 491 TYR cc_start: 0.8246 (p90) cc_final: 0.7884 (p90) REVERT: C 326 LEU cc_start: 0.8463 (tt) cc_final: 0.8076 (mp) REVERT: C 376 LYS cc_start: 0.8244 (mtmt) cc_final: 0.7685 (pttp) REVERT: C 426 SER cc_start: 0.9007 (t) cc_final: 0.8323 (m) REVERT: C 514 MET cc_start: 0.7951 (mtp) cc_final: 0.7673 (ttm) REVERT: A 470 ASN cc_start: 0.7860 (m110) cc_final: 0.7644 (m110) REVERT: A 489 MET cc_start: 0.7385 (mtt) cc_final: 0.7152 (mtt) REVERT: A 551 MET cc_start: 0.7633 (ttt) cc_final: 0.7199 (mmm) REVERT: A 575 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8344 (t70) outliers start: 14 outliers final: 4 residues processed: 105 average time/residue: 1.0573 time to fit residues: 129.3916 Evaluate side-chains 98 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 575 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 157 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 183 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 81 optimal weight: 0.5980 chunk 138 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.132325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.081524 restraints weight = 88097.849| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.55 r_work: 0.2891 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20539 Z= 0.246 Angle : 0.500 6.080 28880 Z= 0.282 Chirality : 0.039 0.153 3378 Planarity : 0.004 0.064 2698 Dihedral : 21.842 178.616 5596 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.96 % Allowed : 9.55 % Favored : 89.49 % 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: 0.37 (0.21), residues: 1722 helix: 1.63 (0.18), residues: 816 sheet: -2.36 (0.35), residues: 174 loop : -0.63 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 332 TYR 0.017 0.001 TYR B 499 PHE 0.013 0.002 PHE A 471 HIS 0.004 0.001 HIS A 547 Details of bonding type rmsd covalent geometry : bond 0.00532 (20539) covalent geometry : angle 0.49985 (28880) hydrogen bonds : bond 0.04649 ( 875) hydrogen bonds : angle 4.35807 ( 2378) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 326 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8111 (mt) REVERT: B 489 MET cc_start: 0.7023 (mtt) cc_final: 0.6740 (mtp) REVERT: C 326 LEU cc_start: 0.8530 (tt) cc_final: 0.8120 (mp) REVERT: C 376 LYS cc_start: 0.8305 (mtmt) cc_final: 0.7824 (pttp) REVERT: C 426 SER cc_start: 0.9029 (t) cc_final: 0.8371 (m) REVERT: C 514 MET cc_start: 0.8053 (mtp) cc_final: 0.7804 (ttm) REVERT: A 11 ARG cc_start: 0.8649 (mtp85) cc_final: 0.8408 (mtt90) REVERT: A 470 ASN cc_start: 0.7968 (m110) cc_final: 0.7624 (m110) REVERT: A 489 MET cc_start: 0.7447 (mtt) cc_final: 0.7083 (mtt) REVERT: A 551 MET cc_start: 0.7662 (ttt) cc_final: 0.7255 (mmm) REVERT: A 575 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8338 (t70) outliers start: 15 outliers final: 6 residues processed: 104 average time/residue: 1.0538 time to fit residues: 127.6171 Evaluate side-chains 101 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain C residue 547 HIS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 575 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 90 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 189 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.133223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.082176 restraints weight = 88134.426| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.45 r_work: 0.2915 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20539 Z= 0.190 Angle : 0.479 4.576 28880 Z= 0.269 Chirality : 0.038 0.151 3378 Planarity : 0.004 0.064 2698 Dihedral : 21.807 178.723 5596 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.90 % Allowed : 10.26 % Favored : 88.85 % 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: 0.47 (0.21), residues: 1722 helix: 1.72 (0.18), residues: 816 sheet: -2.36 (0.36), residues: 174 loop : -0.56 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 552 TYR 0.022 0.001 TYR B 499 PHE 0.018 0.001 PHE C 566 HIS 0.004 0.001 HIS C 547 Details of bonding type rmsd covalent geometry : bond 0.00407 (20539) covalent geometry : angle 0.47917 (28880) hydrogen bonds : bond 0.04348 ( 875) hydrogen bonds : angle 4.25994 ( 2378) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 326 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8111 (mt) REVERT: B 489 MET cc_start: 0.7255 (mtt) cc_final: 0.6948 (mtp) REVERT: C 326 LEU cc_start: 0.8464 (tt) cc_final: 0.8033 (mp) REVERT: C 376 LYS cc_start: 0.8388 (mtmt) cc_final: 0.7788 (pttp) REVERT: C 426 SER cc_start: 0.9063 (t) cc_final: 0.8423 (m) REVERT: C 514 MET cc_start: 0.8049 (mtp) cc_final: 0.7112 (mmm) REVERT: A 11 ARG cc_start: 0.8699 (mtp85) cc_final: 0.8411 (mtt90) REVERT: A 470 ASN cc_start: 0.7942 (m110) cc_final: 0.7609 (m110) REVERT: A 489 MET cc_start: 0.7443 (mtt) cc_final: 0.7062 (mtt) REVERT: A 551 MET cc_start: 0.7641 (ttt) cc_final: 0.7192 (mmm) REVERT: A 575 ASP cc_start: 0.8812 (OUTLIER) cc_final: 0.8534 (t70) outliers start: 14 outliers final: 5 residues processed: 104 average time/residue: 1.0060 time to fit residues: 122.5176 Evaluate side-chains 102 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain C residue 489 MET Chi-restraints excluded: chain C residue 547 HIS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 575 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 57 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.131373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.083498 restraints weight = 87659.433| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.40 r_work: 0.2869 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 20539 Z= 0.289 Angle : 0.520 4.689 28880 Z= 0.293 Chirality : 0.040 0.156 3378 Planarity : 0.004 0.066 2698 Dihedral : 21.905 178.230 5596 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.90 % Allowed : 10.58 % Favored : 88.53 % 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: 0.27 (0.21), residues: 1722 helix: 1.46 (0.18), residues: 819 sheet: -2.40 (0.36), residues: 174 loop : -0.56 (0.25), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 332 TYR 0.022 0.001 TYR B 499 PHE 0.018 0.002 PHE C 435 HIS 0.008 0.001 HIS C 547 Details of bonding type rmsd covalent geometry : bond 0.00631 (20539) covalent geometry : angle 0.51975 (28880) hydrogen bonds : bond 0.04843 ( 875) hydrogen bonds : angle 4.39414 ( 2378) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 216 MET cc_start: 0.8997 (mmt) cc_final: 0.8393 (mmm) REVERT: B 326 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8136 (mt) REVERT: B 489 MET cc_start: 0.7182 (mtt) cc_final: 0.6900 (mtp) REVERT: C 326 LEU cc_start: 0.8557 (tt) cc_final: 0.8117 (mp) REVERT: C 376 LYS cc_start: 0.8395 (mtmt) cc_final: 0.7819 (pttp) REVERT: C 426 SER cc_start: 0.9034 (t) cc_final: 0.8394 (m) REVERT: C 514 MET cc_start: 0.8055 (mtp) cc_final: 0.7224 (mmm) REVERT: A 11 ARG cc_start: 0.8662 (mtp85) cc_final: 0.8410 (mtt90) REVERT: A 470 ASN cc_start: 0.7903 (m110) cc_final: 0.7628 (m110) REVERT: A 551 MET cc_start: 0.7630 (ttt) cc_final: 0.7183 (mmm) REVERT: A 552 ARG cc_start: 0.8387 (mmm-85) cc_final: 0.7891 (mmp80) REVERT: A 575 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.8405 (t70) outliers start: 14 outliers final: 7 residues processed: 112 average time/residue: 1.0186 time to fit residues: 133.5662 Evaluate side-chains 104 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain C residue 547 HIS Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 575 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 146 optimal weight: 0.5980 chunk 134 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 137 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 170 optimal weight: 0.0970 chunk 111 optimal weight: 4.9990 chunk 50 optimal weight: 0.0270 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 69 GLN A 366 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.134439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.087094 restraints weight = 88365.824| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.36 r_work: 0.2940 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20539 Z= 0.119 Angle : 0.474 6.980 28880 Z= 0.264 Chirality : 0.036 0.148 3378 Planarity : 0.004 0.060 2698 Dihedral : 21.773 178.836 5596 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.83 % Allowed : 11.09 % Favored : 88.08 % 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: 0.62 (0.22), residues: 1722 helix: 1.81 (0.18), residues: 816 sheet: -2.25 (0.37), residues: 174 loop : -0.45 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 552 TYR 0.026 0.001 TYR B 499 PHE 0.016 0.001 PHE C 435 HIS 0.008 0.001 HIS C 547 Details of bonding type rmsd covalent geometry : bond 0.00251 (20539) covalent geometry : angle 0.47411 (28880) hydrogen bonds : bond 0.04024 ( 875) hydrogen bonds : angle 4.15429 ( 2378) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 181 MET cc_start: 0.8911 (ttp) cc_final: 0.8609 (ttt) REVERT: B 216 MET cc_start: 0.8958 (mmt) cc_final: 0.8497 (mmm) REVERT: B 326 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8103 (mt) REVERT: C 206 SER cc_start: 0.9251 (p) cc_final: 0.8978 (m) REVERT: C 326 LEU cc_start: 0.8526 (tt) cc_final: 0.8096 (mp) REVERT: C 376 LYS cc_start: 0.8366 (mtmt) cc_final: 0.7778 (pttp) REVERT: C 426 SER cc_start: 0.8999 (t) cc_final: 0.8359 (m) REVERT: A 11 ARG cc_start: 0.8622 (mtp85) cc_final: 0.8409 (mtt90) REVERT: A 470 ASN cc_start: 0.7911 (m110) cc_final: 0.7563 (m110) REVERT: A 551 MET cc_start: 0.7619 (ttt) cc_final: 0.7153 (mmm) REVERT: A 552 ARG cc_start: 0.8258 (mmm-85) cc_final: 0.7763 (mmp80) REVERT: A 575 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8347 (t70) outliers start: 13 outliers final: 3 residues processed: 108 average time/residue: 1.0787 time to fit residues: 135.5434 Evaluate side-chains 103 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain C residue 547 HIS Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 575 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 186 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 73 optimal weight: 0.0870 chunk 137 optimal weight: 0.7980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 45 GLN A 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.133905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.086725 restraints weight = 88182.974| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.39 r_work: 0.2941 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20539 Z= 0.150 Angle : 0.478 9.587 28880 Z= 0.266 Chirality : 0.037 0.146 3378 Planarity : 0.004 0.065 2698 Dihedral : 21.745 178.972 5596 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.58 % Allowed : 11.41 % Favored : 88.01 % 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: 0.70 (0.21), residues: 1722 helix: 1.86 (0.18), residues: 813 sheet: -2.20 (0.37), residues: 174 loop : -0.38 (0.25), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 332 TYR 0.025 0.001 TYR B 499 PHE 0.015 0.001 PHE C 435 HIS 0.009 0.001 HIS C 547 Details of bonding type rmsd covalent geometry : bond 0.00322 (20539) covalent geometry : angle 0.47824 (28880) hydrogen bonds : bond 0.04106 ( 875) hydrogen bonds : angle 4.13267 ( 2378) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.895 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: B 181 MET cc_start: 0.8915 (ttp) cc_final: 0.8661 (ttt) REVERT: B 216 MET cc_start: 0.8957 (mmt) cc_final: 0.8491 (mmm) REVERT: B 326 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8116 (mt) REVERT: C 206 SER cc_start: 0.9249 (p) cc_final: 0.8987 (m) REVERT: C 326 LEU cc_start: 0.8526 (tt) cc_final: 0.8087 (mp) REVERT: C 376 LYS cc_start: 0.8356 (mtmt) cc_final: 0.7764 (pttp) REVERT: C 426 SER cc_start: 0.9006 (t) cc_final: 0.8394 (m) REVERT: A 11 ARG cc_start: 0.8619 (mtp85) cc_final: 0.8412 (mtt90) REVERT: A 470 ASN cc_start: 0.7883 (m110) cc_final: 0.7548 (m110) REVERT: A 551 MET cc_start: 0.7687 (ttt) cc_final: 0.7221 (mmm) REVERT: A 552 ARG cc_start: 0.8176 (mmm-85) cc_final: 0.7705 (mmp80) outliers start: 9 outliers final: 2 residues processed: 105 average time/residue: 1.0130 time to fit residues: 124.7712 Evaluate side-chains 100 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 97 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain C residue 547 HIS Chi-restraints excluded: chain A residue 567 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 40 optimal weight: 0.3980 chunk 3 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 146 optimal weight: 0.0070 chunk 49 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 161 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 GLN C 547 HIS A 45 GLN A 69 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.134643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.084490 restraints weight = 87535.536| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.51 r_work: 0.2951 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20539 Z= 0.133 Angle : 0.479 8.994 28880 Z= 0.265 Chirality : 0.036 0.142 3378 Planarity : 0.004 0.058 2698 Dihedral : 21.713 179.183 5596 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.45 % Allowed : 11.86 % Favored : 87.69 % 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 (0.22), residues: 1722 helix: 1.90 (0.18), residues: 813 sheet: -2.09 (0.38), residues: 174 loop : -0.35 (0.25), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 552 TYR 0.024 0.001 TYR B 499 PHE 0.016 0.001 PHE C 435 HIS 0.009 0.001 HIS C 547 Details of bonding type rmsd covalent geometry : bond 0.00284 (20539) covalent geometry : angle 0.47912 (28880) hydrogen bonds : bond 0.03994 ( 875) hydrogen bonds : angle 4.07668 ( 2378) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10214.90 seconds wall clock time: 173 minutes 55.20 seconds (10435.20 seconds total)