Starting phenix.real_space_refine on Mon Jul 6 18:20:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i2g_52584/07_2026/9i2g_52584.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i2g_52584/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9i2g_52584/07_2026/9i2g_52584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i2g_52584/07_2026/9i2g_52584.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i2g_52584/07_2026/9i2g_52584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i2g_52584/07_2026/9i2g_52584.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.84, per 1000 atoms: 0.19 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: 3.79 Conformation dependent library (CDL) restraints added in 897.0 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: 7.20 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: 9.41 Time building geometry restraints manager: 5.24 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=" C1' DC H 10 " pdb=" N1 DC H 10 " ideal model delta sigma weight residual 1.468 1.520 -0.052 1.40e-02 5.10e+03 1.40e+01 bond pdb=" C1' DT H 57 " pdb=" N1 DT H 57 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.58e+00 ... (remaining 37826 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 64539 1.21 - 2.41: 3167 2.41 - 3.62: 639 3.62 - 4.83: 31 4.83 - 6.03: 9 Bond angle restraints: 68385 Sorted by residual: angle pdb=" N3 DT I 57 " pdb=" C4 DT I 57 " pdb=" O4 DT I 57 " ideal model delta sigma weight residual 119.90 122.68 -2.78 6.00e-01 2.78e+00 2.14e+01 angle pdb=" N3 DT G 64 " pdb=" C4 DT G 64 " pdb=" O4 DT G 64 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT H 61 " pdb=" C4 DT H 61 " pdb=" O4 DT H 61 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" C1' U E 18 " pdb=" N1 U E 18 " pdb=" C2 U E 18 " ideal model delta sigma weight residual 117.70 123.07 -5.37 1.20e+00 6.94e-01 2.00e+01 angle pdb=" O4' DC G 67 " pdb=" C4' DC G 67 " pdb=" C3' DC G 67 " ideal model delta sigma weight residual 106.00 103.36 2.64 6.00e-01 2.78e+00 1.94e+01 ... (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 - 0.038: 2566 0.038 - 0.076: 530 0.076 - 0.113: 149 0.113 - 0.151: 90 0.151 - 0.189: 43 Chirality restraints: 3378 Sorted by residual: chirality pdb=" C3' DC H 67 " pdb=" C4' DC H 67 " pdb=" O3' DC H 67 " pdb=" C2' DC H 67 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.92e-01 chirality pdb=" C3' DC I 67 " pdb=" C4' DC I 67 " pdb=" O3' DC I 67 " pdb=" C2' DC I 67 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" C3' DC I 63 " pdb=" C4' DC I 63 " pdb=" O3' DC I 63 " pdb=" C2' DC I 63 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.70e-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: 5.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.240 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 42.700 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 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: 0.020 Load rotamer database and sin/cos tables:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 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 0.052 20539 Z= 0.295 Angle : 0.575 5.868 28880 Z= 0.441 Chirality : 0.044 0.189 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/Z covalent geometry : bond 0.00400 / 0.29 (20539) covalent geometry : angle 0.57535 / 0.44 (28880) hydrogen bonds : bond 0.13210 / 8.49 ( 875) hydrogen bonds : angle 5.72838 / 4.13 ( 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 : 0.879 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: 1.1633 time to fit residues: 187.5946 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 : 0.953 ------------------------------------------------------------------------------- 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: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3970 r_free = 0.3970 target = 0.135889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.088893 restraints weight = 88069.645| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.31 r_work: 0.2979 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.0664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20539 Z= 0.158 Angle : 0.503 6.530 28880 Z= 0.296 Chirality : 0.039 0.283 3378 Planarity : 0.004 0.045 2698 Dihedral : 21.520 173.033 5596 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.45 % Allowed : 5.77 % Favored : 93.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.21), residues: 1722 helix: 1.73 (0.18), residues: 795 sheet: -2.19 (0.35), residues: 174 loop : -0.92 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 473 TYR 0.011 0.001 TYR B 499 PHE 0.022 0.001 PHE C 495 HIS 0.004 0.001 HIS C 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (20539) covalent geometry : angle 0.50274 / 0.30 (28880) hydrogen bonds : bond 0.05287 / 3.48 ( 875) hydrogen bonds : angle 4.87443 / 3.47 ( 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 110 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.911 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 373 THR cc_start: 0.9390 (p) cc_final: 0.9122 (t) REVERT: B 489 MET cc_start: 0.7124 (mtt) cc_final: 0.6877 (mtp) REVERT: B 491 TYR cc_start: 0.8070 (p90) cc_final: 0.7849 (p90) REVERT: C 326 LEU cc_start: 0.8380 (tt) cc_final: 0.7982 (mp) REVERT: C 376 LYS cc_start: 0.8378 (mtmt) cc_final: 0.7890 (pttt) REVERT: C 426 SER cc_start: 0.8821 (t) cc_final: 0.8113 (m) REVERT: C 514 MET cc_start: 0.8110 (mtp) cc_final: 0.7769 (ttm) REVERT: A 420 LYS cc_start: 0.9134 (tttp) cc_final: 0.8927 (tptt) REVERT: A 424 ASP cc_start: 0.8759 (t70) cc_final: 0.8218 (t0) REVERT: A 426 SER cc_start: 0.8973 (p) cc_final: 0.8741 (p) REVERT: A 470 ASN cc_start: 0.7944 (m110) cc_final: 0.7585 (m110) REVERT: A 489 MET cc_start: 0.7439 (mtt) cc_final: 0.7132 (mtt) REVERT: A 551 MET cc_start: 0.7516 (ttt) cc_final: 0.7265 (mmm) REVERT: A 583 MET cc_start: 0.8006 (ttm) cc_final: 0.7794 (ttp) outliers start: 7 outliers final: 3 residues processed: 107 average time/residue: 1.0425 time to fit residues: 131.2634 Evaluate side-chains 99 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 96 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: 5.9990 chunk 176 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 190 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 173 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 69 GLN A 45 GLN A 69 GLN A 327 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.133561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.085988 restraints weight = 88212.025| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.41 r_work: 0.2918 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 20539 Z= 0.265 Angle : 0.518 6.403 28880 Z= 0.307 Chirality : 0.040 0.269 3378 Planarity : 0.004 0.056 2698 Dihedral : 21.618 177.673 5596 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.64 % Allowed : 6.99 % Favored : 92.37 % 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: 0.23 (0.21), residues: 1722 helix: 1.64 (0.18), residues: 795 sheet: -2.20 (0.35), residues: 174 loop : -0.85 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 254 TYR 0.015 0.001 TYR A 439 PHE 0.017 0.002 PHE C 495 HIS 0.008 0.001 HIS C 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.26 (20539) covalent geometry : angle 0.51778 / 0.31 (28880) hydrogen bonds : bond 0.05385 / 3.57 ( 875) hydrogen bonds : angle 4.73403 / 3.37 ( 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 108 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.912 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 216 MET cc_start: 0.8981 (mmt) cc_final: 0.8577 (mmm) REVERT: B 373 THR cc_start: 0.9427 (p) cc_final: 0.9155 (t) REVERT: B 489 MET cc_start: 0.7099 (mtt) cc_final: 0.6820 (mtp) REVERT: B 491 TYR cc_start: 0.8133 (p90) cc_final: 0.7912 (p90) REVERT: C 326 LEU cc_start: 0.8492 (tt) cc_final: 0.8091 (mp) REVERT: C 376 LYS cc_start: 0.8384 (mtmt) cc_final: 0.7855 (pttt) REVERT: C 426 SER cc_start: 0.8899 (t) cc_final: 0.8188 (m) REVERT: C 486 MET cc_start: 0.7899 (mmt) cc_final: 0.7563 (mmm) REVERT: C 514 MET cc_start: 0.8108 (mtp) cc_final: 0.7779 (ttm) REVERT: A 326 LEU cc_start: 0.8490 (tt) cc_final: 0.8080 (mt) REVERT: A 424 ASP cc_start: 0.8871 (t70) cc_final: 0.8340 (t0) REVERT: A 426 SER cc_start: 0.8998 (p) cc_final: 0.8764 (p) REVERT: A 470 ASN cc_start: 0.7897 (m110) cc_final: 0.7555 (m110) REVERT: A 489 MET cc_start: 0.7445 (mtt) cc_final: 0.7141 (mtt) REVERT: A 551 MET cc_start: 0.7531 (ttt) cc_final: 0.7257 (mmm) outliers start: 10 outliers final: 4 residues processed: 102 average time/residue: 1.0073 time to fit residues: 121.6382 Evaluate side-chains 97 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain C residue 437 GLU 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: 0.9990 chunk 179 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN A 69 GLN A 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.134208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.086686 restraints weight = 87901.194| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.33 r_work: 0.2921 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20539 Z= 0.183 Angle : 0.477 6.806 28880 Z= 0.284 Chirality : 0.038 0.266 3378 Planarity : 0.004 0.057 2698 Dihedral : 21.720 179.603 5596 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.58 % Allowed : 7.24 % Favored : 92.18 % 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: 0.32 (0.21), residues: 1722 helix: 1.71 (0.18), residues: 795 sheet: -2.27 (0.35), residues: 174 loop : -0.77 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 332 TYR 0.011 0.001 TYR A 439 PHE 0.017 0.001 PHE C 495 HIS 0.008 0.001 HIS C 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (20539) covalent geometry : angle 0.47672 / 0.28 (28880) hydrogen bonds : bond 0.04989 / 3.30 ( 875) hydrogen bonds : angle 4.57125 / 3.25 ( 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 103 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.921 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 216 MET cc_start: 0.8966 (mmt) cc_final: 0.8427 (mmm) REVERT: B 373 THR cc_start: 0.9479 (p) cc_final: 0.9209 (t) REVERT: B 489 MET cc_start: 0.7120 (mtt) cc_final: 0.6843 (mtp) REVERT: B 491 TYR cc_start: 0.8178 (p90) cc_final: 0.7888 (p90) REVERT: C 326 LEU cc_start: 0.8473 (tt) cc_final: 0.8061 (mp) REVERT: C 376 LYS cc_start: 0.8394 (mtmt) cc_final: 0.7825 (pttp) REVERT: C 426 SER cc_start: 0.8926 (t) cc_final: 0.8207 (m) REVERT: C 486 MET cc_start: 0.7909 (mmt) cc_final: 0.7545 (mmm) REVERT: C 514 MET cc_start: 0.8067 (mtp) cc_final: 0.7866 (ttm) REVERT: A 326 LEU cc_start: 0.8481 (tt) cc_final: 0.8061 (mt) REVERT: A 424 ASP cc_start: 0.8854 (t70) cc_final: 0.8294 (t0) REVERT: A 426 SER cc_start: 0.8942 (p) cc_final: 0.8737 (p) REVERT: A 470 ASN cc_start: 0.7844 (m110) cc_final: 0.7459 (m110) REVERT: A 489 MET cc_start: 0.7357 (mtt) cc_final: 0.7026 (mtt) REVERT: A 551 MET cc_start: 0.7552 (ttt) cc_final: 0.7265 (mmm) outliers start: 9 outliers final: 4 residues processed: 98 average time/residue: 0.9581 time to fit residues: 112.3160 Evaluate side-chains 96 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 437 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 96 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 189 optimal weight: 7.9990 chunk 149 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.134170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.082367 restraints weight = 87989.097| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.68 r_work: 0.2898 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 20539 Z= 0.228 Angle : 0.492 6.422 28880 Z= 0.292 Chirality : 0.039 0.268 3378 Planarity : 0.004 0.059 2698 Dihedral : 21.758 176.570 5596 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.71 % Allowed : 7.82 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.33 (0.21), residues: 1722 helix: 1.70 (0.18), residues: 795 sheet: -2.31 (0.35), residues: 174 loop : -0.73 (0.24), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 254 TYR 0.015 0.001 TYR A 273 PHE 0.018 0.001 PHE C 495 HIS 0.007 0.001 HIS C 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.23 (20539) covalent geometry : angle 0.49241 / 0.29 (28880) hydrogen bonds : bond 0.05052 / 3.35 ( 875) hydrogen bonds : angle 4.52207 / 3.22 ( 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 109 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.870 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: B 216 MET cc_start: 0.8958 (mmt) cc_final: 0.8449 (mmm) REVERT: C 126 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7973 (mp0) REVERT: C 326 LEU cc_start: 0.8412 (tt) cc_final: 0.8030 (mp) REVERT: C 376 LYS cc_start: 0.8347 (mtmt) cc_final: 0.7874 (pttp) REVERT: C 426 SER cc_start: 0.9001 (t) cc_final: 0.8322 (m) REVERT: C 486 MET cc_start: 0.8025 (mmt) cc_final: 0.7709 (mmm) REVERT: A 426 SER cc_start: 0.8932 (p) cc_final: 0.8726 (p) REVERT: A 470 ASN cc_start: 0.7841 (m110) cc_final: 0.7451 (m110) REVERT: A 489 MET cc_start: 0.7412 (mtt) cc_final: 0.7136 (mtt) REVERT: A 551 MET cc_start: 0.7582 (ttt) cc_final: 0.7287 (mmm) REVERT: A 575 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8283 (t70) outliers start: 11 outliers final: 5 residues processed: 103 average time/residue: 1.0257 time to fit residues: 124.9110 Evaluate side-chains 98 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 437 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 157 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 183 optimal weight: 20.0000 chunk 100 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 255 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 = 0.3943 r_free = 0.3943 target = 0.133675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.086146 restraints weight = 87990.154| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.36 r_work: 0.2914 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20539 Z= 0.187 Angle : 0.473 7.086 28880 Z= 0.281 Chirality : 0.038 0.266 3378 Planarity : 0.004 0.061 2698 Dihedral : 21.808 176.696 5596 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.45 % Allowed : 8.53 % Favored : 91.03 % 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: 0.39 (0.21), residues: 1722 helix: 1.76 (0.18), residues: 795 sheet: -2.34 (0.35), residues: 174 loop : -0.69 (0.24), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 552 TYR 0.012 0.001 TYR A 439 PHE 0.016 0.001 PHE C 495 HIS 0.009 0.001 HIS C 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.19 (20539) covalent geometry : angle 0.47349 / 0.28 (28880) hydrogen bonds : bond 0.04857 / 3.20 ( 875) hydrogen bonds : angle 4.44502 / 3.16 ( 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 101 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.932 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 216 MET cc_start: 0.8963 (mmt) cc_final: 0.8468 (mmm) REVERT: B 489 MET cc_start: 0.7118 (mtt) cc_final: 0.6834 (mtp) REVERT: C 326 LEU cc_start: 0.8419 (tt) cc_final: 0.8030 (mp) REVERT: C 376 LYS cc_start: 0.8400 (mtmt) cc_final: 0.7784 (pttp) REVERT: C 426 SER cc_start: 0.9011 (t) cc_final: 0.8351 (m) REVERT: C 486 MET cc_start: 0.8085 (mmt) cc_final: 0.7796 (mmm) REVERT: C 514 MET cc_start: 0.8076 (ttm) cc_final: 0.7651 (ttm) REVERT: A 326 LEU cc_start: 0.8605 (tt) cc_final: 0.8165 (mt) REVERT: A 470 ASN cc_start: 0.7852 (m110) cc_final: 0.7616 (m110) REVERT: A 489 MET cc_start: 0.7421 (mtt) cc_final: 0.7141 (mtt) REVERT: A 551 MET cc_start: 0.7577 (ttt) cc_final: 0.7301 (mmm) REVERT: A 575 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8294 (t70) outliers start: 7 outliers final: 4 residues processed: 97 average time/residue: 0.9324 time to fit residues: 108.4360 Evaluate side-chains 98 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain C residue 437 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 90 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 chunk 188 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 65 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 33 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 189 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 255 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 = 0.3942 r_free = 0.3942 target = 0.133484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.082670 restraints weight = 88141.011| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.60 r_work: 0.2912 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20539 Z= 0.198 Angle : 0.475 6.422 28880 Z= 0.282 Chirality : 0.038 0.266 3378 Planarity : 0.004 0.061 2698 Dihedral : 21.813 178.124 5596 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.77 % Allowed : 8.91 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.21), residues: 1722 helix: 1.76 (0.18), residues: 795 sheet: -2.33 (0.35), residues: 174 loop : -0.66 (0.24), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 254 TYR 0.013 0.001 TYR A 439 PHE 0.015 0.001 PHE C 495 HIS 0.008 0.001 HIS C 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.20 (20539) covalent geometry : angle 0.47502 / 0.28 (28880) hydrogen bonds : bond 0.04829 / 3.18 ( 875) hydrogen bonds : angle 4.41871 / 3.14 ( 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 109 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.883 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: B 216 MET cc_start: 0.8935 (mmt) cc_final: 0.8435 (mmm) REVERT: B 489 MET cc_start: 0.7153 (mtt) cc_final: 0.6855 (mtp) REVERT: C 126 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7968 (mp0) REVERT: C 326 LEU cc_start: 0.8468 (tt) cc_final: 0.8080 (mp) REVERT: C 376 LYS cc_start: 0.8398 (mtmt) cc_final: 0.7783 (pttp) REVERT: C 426 SER cc_start: 0.9006 (t) cc_final: 0.8321 (m) REVERT: C 514 MET cc_start: 0.8177 (ttm) cc_final: 0.7706 (ttm) REVERT: A 470 ASN cc_start: 0.7864 (m110) cc_final: 0.7632 (m110) REVERT: A 489 MET cc_start: 0.7443 (mtt) cc_final: 0.7164 (mtt) REVERT: A 551 MET cc_start: 0.7504 (ttt) cc_final: 0.7188 (mmm) REVERT: A 575 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8288 (t70) outliers start: 12 outliers final: 8 residues processed: 102 average time/residue: 0.9114 time to fit residues: 111.0138 Evaluate side-chains 104 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 126 GLU Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 547 HIS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 426 SER 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: 9.9990 chunk 148 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 95 optimal weight: 9.9990 chunk 66 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3946 r_free = 0.3946 target = 0.133773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.086016 restraints weight = 87585.057| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.36 r_work: 0.2919 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1625 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= 0.167 Angle : 0.466 6.418 28880 Z= 0.275 Chirality : 0.038 0.265 3378 Planarity : 0.004 0.063 2698 Dihedral : 21.837 179.047 5596 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.71 % Allowed : 9.42 % Favored : 89.87 % 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: 0.48 (0.21), residues: 1722 helix: 1.81 (0.18), residues: 795 sheet: -2.29 (0.35), residues: 174 loop : -0.61 (0.24), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 332 TYR 0.013 0.001 TYR C 580 PHE 0.014 0.001 PHE C 495 HIS 0.009 0.001 HIS C 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 (20539) covalent geometry : angle 0.46584 / 0.28 (28880) hydrogen bonds : bond 0.04695 / 3.08 ( 875) hydrogen bonds : angle 4.36171 / 3.10 ( 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 108 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.934 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 216 MET cc_start: 0.8945 (mmt) cc_final: 0.8454 (mmm) REVERT: B 489 MET cc_start: 0.7173 (mtt) cc_final: 0.6845 (mtp) REVERT: C 126 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7978 (mp0) REVERT: C 326 LEU cc_start: 0.8425 (tt) cc_final: 0.8012 (mp) REVERT: C 376 LYS cc_start: 0.8419 (mtmt) cc_final: 0.7776 (pttp) REVERT: C 426 SER cc_start: 0.9004 (t) cc_final: 0.8348 (m) REVERT: C 514 MET cc_start: 0.8177 (ttm) cc_final: 0.7727 (ttp) REVERT: A 470 ASN cc_start: 0.7875 (m110) cc_final: 0.7648 (m110) REVERT: A 489 MET cc_start: 0.7415 (mtt) cc_final: 0.7124 (mtt) REVERT: A 551 MET cc_start: 0.7568 (ttt) cc_final: 0.7227 (mmm) REVERT: A 575 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8290 (t70) outliers start: 11 outliers final: 6 residues processed: 102 average time/residue: 0.9233 time to fit residues: 111.8201 Evaluate side-chains 102 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 437 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 146 optimal weight: 0.0170 chunk 134 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 137 optimal weight: 0.5980 chunk 2 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 50 optimal weight: 0.0070 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 366 ASN A 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.134498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.083944 restraints weight = 87991.121| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.53 r_work: 0.2954 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20539 Z= 0.118 Angle : 0.452 6.440 28880 Z= 0.266 Chirality : 0.037 0.265 3378 Planarity : 0.004 0.064 2698 Dihedral : 21.812 179.137 5596 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.64 % Allowed : 9.87 % 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: 0.66 (0.21), residues: 1722 helix: 1.95 (0.18), residues: 795 sheet: -2.21 (0.36), residues: 174 loop : -0.51 (0.25), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 552 TYR 0.015 0.001 TYR B 499 PHE 0.018 0.001 PHE A 471 HIS 0.008 0.001 HIS C 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.12 (20539) covalent geometry : angle 0.45226 / 0.27 (28880) hydrogen bonds : bond 0.04395 / 2.86 ( 875) hydrogen bonds : angle 4.23804 / 3.00 ( 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 107 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.900 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 216 MET cc_start: 0.8918 (mmt) cc_final: 0.8451 (mmm) REVERT: B 489 MET cc_start: 0.7192 (mtt) cc_final: 0.6862 (mtp) REVERT: C 126 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7953 (mp0) REVERT: C 326 LEU cc_start: 0.8466 (tt) cc_final: 0.8063 (mp) REVERT: C 376 LYS cc_start: 0.8394 (mtmt) cc_final: 0.7743 (pttp) REVERT: C 426 SER cc_start: 0.8981 (t) cc_final: 0.8321 (m) REVERT: C 514 MET cc_start: 0.8182 (ttm) cc_final: 0.7683 (ttp) REVERT: A 470 ASN cc_start: 0.7857 (m110) cc_final: 0.7633 (m110) REVERT: A 489 MET cc_start: 0.7346 (mtt) cc_final: 0.7124 (mtt) REVERT: A 551 MET cc_start: 0.7625 (ttt) cc_final: 0.7247 (mmm) outliers start: 10 outliers final: 3 residues processed: 102 average time/residue: 0.9299 time to fit residues: 113.6022 Evaluate side-chains 100 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 547 HIS Chi-restraints excluded: chain A residue 326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 186 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 135 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 366 ASN A 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.134365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.083512 restraints weight = 88258.455| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.60 r_work: 0.2936 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20539 Z= 0.153 Angle : 0.459 6.407 28880 Z= 0.270 Chirality : 0.037 0.265 3378 Planarity : 0.004 0.058 2698 Dihedral : 21.793 179.440 5596 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.51 % Allowed : 10.13 % Favored : 89.36 % 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: 0.67 (0.21), residues: 1722 helix: 1.94 (0.18), residues: 795 sheet: -2.18 (0.36), residues: 174 loop : -0.49 (0.25), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 552 TYR 0.034 0.001 TYR B 499 PHE 0.031 0.001 PHE C 566 HIS 0.008 0.001 HIS C 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (20539) covalent geometry : angle 0.45923 / 0.27 (28880) hydrogen bonds : bond 0.04443 / 2.90 ( 875) hydrogen bonds : angle 4.24332 / 3.00 ( 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 105 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.920 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 216 MET cc_start: 0.8924 (mmt) cc_final: 0.8438 (mmm) REVERT: B 489 MET cc_start: 0.7177 (mtt) cc_final: 0.6847 (mtp) REVERT: C 126 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7964 (mp0) REVERT: C 326 LEU cc_start: 0.8451 (tt) cc_final: 0.8039 (mp) REVERT: C 376 LYS cc_start: 0.8387 (mtmt) cc_final: 0.7743 (pttp) REVERT: C 426 SER cc_start: 0.8997 (t) cc_final: 0.8337 (m) REVERT: C 514 MET cc_start: 0.8172 (ttm) cc_final: 0.7716 (ttp) REVERT: A 470 ASN cc_start: 0.7859 (m110) cc_final: 0.7451 (m110) REVERT: A 489 MET cc_start: 0.7337 (mtt) cc_final: 0.7024 (mtt) REVERT: A 551 MET cc_start: 0.7604 (ttt) cc_final: 0.7228 (mmm) outliers start: 8 outliers final: 4 residues processed: 102 average time/residue: 0.9521 time to fit residues: 115.5310 Evaluate side-chains 98 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 547 HIS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 372 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 40 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 146 optimal weight: 0.0570 chunk 49 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 161 optimal weight: 0.8980 chunk 164 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 366 ASN C 497 ASN A 45 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.134185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.083659 restraints weight = 87478.317| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.44 r_work: 0.2954 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20539 Z= 0.135 Angle : 0.454 6.403 28880 Z= 0.267 Chirality : 0.037 0.264 3378 Planarity : 0.004 0.057 2698 Dihedral : 21.803 179.723 5596 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.71 % Allowed : 10.00 % Favored : 89.29 % 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: 0.72 (0.21), residues: 1722 helix: 1.97 (0.18), residues: 795 sheet: -2.13 (0.37), residues: 174 loop : -0.45 (0.25), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 552 TYR 0.038 0.001 TYR B 499 PHE 0.017 0.001 PHE C 435 HIS 0.008 0.001 HIS C 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 (20539) covalent geometry : angle 0.45430 / 0.27 (28880) hydrogen bonds : bond 0.04373 / 2.85 ( 875) hydrogen bonds : angle 4.20955 / 2.97 ( 2378) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9775.46 seconds wall clock time: 166 minutes 50.72 seconds (10010.72 seconds total)