Starting phenix.real_space_refine on Sun Aug 9 20:04:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i2g_52584/08_2026/9i2g_52584.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i2g_52584/08_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_52584/08_2026/9i2g_52584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i2g_52584/08_2026/9i2g_52584.map" model { file = "/net/cci-nas-00/data/ceres_data/9i2g_52584/08_2026/9i2g_52584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i2g_52584/08_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-2.2rc3-6140/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: 5.94, per 1000 atoms: 0.16 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: 3.85 Conformation dependent library (CDL) restraints added in 984.8 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: 6.34 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: 8.83 Time building geometry restraints manager: 5.01 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: 64020 1.21 - 2.41: 3650 2.41 - 3.62: 673 3.62 - 4.83: 33 4.83 - 6.03: 9 Bond angle restraints: 68385 Sorted by residual: angle pdb=" O5' G F 59 " pdb=" C5' G F 59 " pdb=" C4' G F 59 " ideal model delta sigma weight residual 109.40 113.86 -4.46 8.00e-01 1.56e+00 3.11e+01 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 ... (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: 2414 0.038 - 0.076: 512 0.076 - 0.113: 316 0.113 - 0.151: 93 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: 4.340 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: 0.220 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 39.730 Find NCS groups from input model: 0.610 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: 0.000 Load rotamer database and sin/cos tables:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 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= 0.303 Angle : 0.631 5.868 28880 Z= 0.499 Chirality : 0.049 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 0.00406 / 0.30 (20539) covalent geometry : angle 0.63072 / 0.50 (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 : 0.896 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: 1.1328 time to fit residues: 183.2189 Evaluate side-chains 96 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.135796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.088714 restraints weight = 88026.238| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.32 r_work: 0.2975 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.0657 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= 0.163 Angle : 0.514 6.926 28880 Z= 0.300 Chirality : 0.040 0.297 3378 Planarity : 0.004 0.044 2698 Dihedral : 21.490 172.070 5596 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.45 % Allowed : 5.58 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.21), residues: 1722 helix: 1.74 (0.18), residues: 795 sheet: -2.20 (0.35), residues: 174 loop : -0.93 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 473 TYR 0.010 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/Z covalent geometry : bond 0.00319 / 0.16 (20539) covalent geometry : angle 0.51385 / 0.30 (28880) hydrogen bonds : bond 0.05564 / 3.66 ( 875) hydrogen bonds : angle 4.91138 / 3.50 ( 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: 7 poor density : 104 time to evaluate : 0.995 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: 0.9392 (p) cc_final: 0.9122 (t) REVERT: B 489 MET cc_start: 0.7128 (mtt) cc_final: 0.6883 (mtp) REVERT: B 491 TYR cc_start: 0.8073 (p90) cc_final: 0.7850 (p90) REVERT: C 326 LEU cc_start: 0.8404 (tt) cc_final: 0.7998 (mp) REVERT: C 376 LYS cc_start: 0.8372 (mtmt) cc_final: 0.7896 (pttt) REVERT: C 426 SER cc_start: 0.8820 (t) cc_final: 0.8113 (m) REVERT: C 514 MET cc_start: 0.8104 (mtp) cc_final: 0.7794 (ttm) REVERT: A 420 LYS cc_start: 0.9138 (tttp) cc_final: 0.8929 (tptt) REVERT: A 424 ASP cc_start: 0.8776 (t70) cc_final: 0.8253 (t0) REVERT: A 426 SER cc_start: 0.8974 (p) cc_final: 0.8743 (p) REVERT: A 470 ASN cc_start: 0.7887 (m110) cc_final: 0.7529 (m110) REVERT: A 489 MET cc_start: 0.7436 (mtt) cc_final: 0.7130 (mtt) REVERT: A 551 MET cc_start: 0.7510 (ttt) cc_final: 0.7262 (mmm) outliers start: 7 outliers final: 3 residues processed: 108 average time/residue: 1.0275 time to fit residues: 131.0442 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 : 0.901 ------------------------------------------------------------------------------- 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: 6.9990 chunk 176 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 190 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 69 GLN C 497 ASN A 45 GLN A 69 GLN A 327 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.133865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.086318 restraints weight = 88165.668| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.33 r_work: 0.2914 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20539 Z= 0.241 Angle : 0.529 6.879 28880 Z= 0.307 Chirality : 0.040 0.295 3378 Planarity : 0.004 0.055 2698 Dihedral : 21.617 177.073 5596 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % 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: 0.25 (0.21), residues: 1722 helix: 1.65 (0.18), residues: 795 sheet: -2.19 (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 254 TYR 0.015 0.001 TYR A 439 PHE 0.019 0.002 PHE C 495 HIS 0.008 0.001 HIS C 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.24 (20539) covalent geometry : angle 0.52880 / 0.31 (28880) hydrogen bonds : bond 0.05390 / 3.58 ( 875) hydrogen bonds : angle 4.72145 / 3.36 ( 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 : 0.950 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: 0.8978 (mmt) cc_final: 0.8585 (mmm) REVERT: B 373 THR cc_start: 0.9430 (p) cc_final: 0.9156 (t) REVERT: B 489 MET cc_start: 0.7091 (mtt) cc_final: 0.6813 (mtp) REVERT: B 491 TYR cc_start: 0.8136 (p90) cc_final: 0.7913 (p90) REVERT: C 326 LEU cc_start: 0.8478 (tt) cc_final: 0.8083 (mp) REVERT: C 376 LYS cc_start: 0.8378 (mtmt) cc_final: 0.7870 (pttp) REVERT: C 426 SER cc_start: 0.8903 (t) cc_final: 0.8193 (m) REVERT: C 437 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8473 (mm-30) REVERT: C 486 MET cc_start: 0.7820 (mmt) cc_final: 0.7564 (mmm) REVERT: C 514 MET cc_start: 0.8124 (mtp) cc_final: 0.7788 (ttm) REVERT: A 326 LEU cc_start: 0.8493 (tt) cc_final: 0.8077 (mt) REVERT: A 424 ASP cc_start: 0.8876 (t70) cc_final: 0.8340 (t0) REVERT: A 426 SER cc_start: 0.8999 (p) cc_final: 0.8764 (p) REVERT: A 470 ASN cc_start: 0.7896 (m110) cc_final: 0.7555 (m110) REVERT: A 489 MET cc_start: 0.7437 (mtt) cc_final: 0.7129 (mtt) REVERT: A 551 MET cc_start: 0.7532 (ttt) cc_final: 0.7246 (mmm) outliers start: 10 outliers final: 4 residues processed: 103 average time/residue: 0.9960 time to fit residues: 121.7592 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 : 0.891 ------------------------------------------------------------------------------- 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 327 ASN 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: 0.3980 chunk 147 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 58 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.134958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.087652 restraints weight = 87849.973| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.31 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: 0.8066 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20539 Z= 0.145 Angle : 0.480 6.974 28880 Z= 0.282 Chirality : 0.038 0.290 3378 Planarity : 0.004 0.052 2698 Dihedral : 21.683 178.442 5596 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.45 % Allowed : 7.24 % 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: 0.36 (0.21), residues: 1722 helix: 1.76 (0.18), residues: 795 sheet: -2.21 (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 A 379 TYR 0.011 0.001 TYR C 580 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 0.00285 / 0.15 (20539) covalent geometry : angle 0.47983 / 0.28 (28880) hydrogen bonds : bond 0.04938 / 3.26 ( 875) hydrogen bonds : angle 4.54728 / 3.23 ( 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 104 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.894 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: 0.9472 (p) cc_final: 0.9205 (t) REVERT: B 489 MET cc_start: 0.7114 (mtt) cc_final: 0.6853 (mtp) REVERT: B 491 TYR cc_start: 0.8171 (p90) cc_final: 0.7939 (p90) REVERT: C 326 LEU cc_start: 0.8461 (tt) cc_final: 0.8067 (mp) REVERT: C 376 LYS cc_start: 0.8353 (mtmt) cc_final: 0.7826 (pttp) REVERT: C 426 SER cc_start: 0.8906 (t) cc_final: 0.8194 (m) REVERT: C 486 MET cc_start: 0.7897 (mmt) cc_final: 0.7536 (mmm) REVERT: A 326 LEU cc_start: 0.8466 (tt) cc_final: 0.8058 (mt) REVERT: A 424 ASP cc_start: 0.8838 (t70) cc_final: 0.8277 (t0) REVERT: A 470 ASN cc_start: 0.7777 (m110) cc_final: 0.7399 (m110) REVERT: A 489 MET cc_start: 0.7445 (mtt) cc_final: 0.7191 (mtt) REVERT: A 551 MET cc_start: 0.7548 (ttt) cc_final: 0.7261 (mmm) outliers start: 7 outliers final: 5 residues processed: 101 average time/residue: 0.9009 time to fit residues: 109.6146 Evaluate side-chains 97 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 ASP 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: 8.9990 chunk 33 optimal weight: 9.9990 chunk 127 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 189 optimal weight: 8.9990 chunk 149 optimal weight: 1.9990 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: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3937 r_free = 0.3937 target = 0.133292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.085728 restraints weight = 87879.932| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.30 r_work: 0.2904 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20539 Z= 0.239 Angle : 0.518 7.116 28880 Z= 0.300 Chirality : 0.039 0.293 3378 Planarity : 0.004 0.060 2698 Dihedral : 21.734 177.397 5596 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.71 % Allowed : 7.69 % Favored : 91.60 % 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: 1.66 (0.18), residues: 795 sheet: -2.29 (0.35), residues: 174 loop : -0.75 (0.24), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 254 TYR 0.016 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 0.00496 / 0.24 (20539) covalent geometry : angle 0.51807 / 0.30 (28880) hydrogen bonds : bond 0.05166 / 3.42 ( 875) hydrogen bonds : angle 4.54808 / 3.24 ( 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 106 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.913 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 489 MET cc_start: 0.7086 (mtt) cc_final: 0.6787 (mtp) REVERT: B 491 TYR cc_start: 0.8185 (p90) cc_final: 0.7867 (p90) REVERT: C 126 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7961 (mp0) REVERT: C 326 LEU cc_start: 0.8442 (tt) cc_final: 0.8045 (mp) REVERT: C 376 LYS cc_start: 0.8301 (mtmt) cc_final: 0.7834 (pttp) REVERT: C 426 SER cc_start: 0.8989 (t) cc_final: 0.8300 (m) REVERT: C 486 MET cc_start: 0.7992 (mmt) cc_final: 0.7695 (mmm) REVERT: C 514 MET cc_start: 0.8206 (ttm) cc_final: 0.7778 (ttm) REVERT: A 326 LEU cc_start: 0.8559 (tt) cc_final: 0.8172 (mt) REVERT: A 470 ASN cc_start: 0.7837 (m110) cc_final: 0.7422 (m110) REVERT: A 489 MET cc_start: 0.7428 (mtt) cc_final: 0.7160 (mtt) REVERT: A 551 MET cc_start: 0.7585 (ttt) cc_final: 0.7293 (mmm) REVERT: A 575 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8285 (t70) outliers start: 11 outliers final: 3 residues processed: 101 average time/residue: 1.0232 time to fit residues: 122.2633 Evaluate side-chains 95 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 51 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.133839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.085988 restraints weight = 87907.604| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.34 r_work: 0.2919 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1401 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= 0.178 Angle : 0.486 6.924 28880 Z= 0.283 Chirality : 0.039 0.289 3378 Planarity : 0.004 0.060 2698 Dihedral : 21.781 176.098 5596 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.38 % Allowed : 8.33 % Favored : 91.28 % 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: 0.35 (0.21), residues: 1722 helix: 1.71 (0.18), residues: 795 sheet: -2.30 (0.35), residues: 174 loop : -0.70 (0.24), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 184 TYR 0.018 0.001 TYR B 499 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 0.00365 / 0.18 (20539) covalent geometry : angle 0.48570 / 0.28 (28880) hydrogen bonds : bond 0.04918 / 3.25 ( 875) hydrogen bonds : angle 4.46602 / 3.17 ( 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: 6 poor density : 95 time to evaluate : 0.710 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 489 MET cc_start: 0.7106 (mtt) cc_final: 0.6808 (mtp) REVERT: B 491 TYR cc_start: 0.8176 (p90) cc_final: 0.7843 (p90) REVERT: C 326 LEU cc_start: 0.8418 (tt) cc_final: 0.8034 (mp) REVERT: C 376 LYS cc_start: 0.8423 (mtmt) cc_final: 0.7832 (pttp) REVERT: C 426 SER cc_start: 0.9002 (t) cc_final: 0.8336 (m) REVERT: C 486 MET cc_start: 0.8119 (mmt) cc_final: 0.7816 (mmm) REVERT: C 514 MET cc_start: 0.8161 (ttm) cc_final: 0.7705 (ttm) REVERT: A 470 ASN cc_start: 0.7839 (m110) cc_final: 0.7431 (m110) REVERT: A 489 MET cc_start: 0.7416 (mtt) cc_final: 0.7139 (mtt) REVERT: A 551 MET cc_start: 0.7566 (ttt) cc_final: 0.7290 (mmm) REVERT: A 575 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8294 (t70) outliers start: 6 outliers final: 4 residues processed: 98 average time/residue: 0.9467 time to fit residues: 111.4380 Evaluate side-chains 99 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 ASP 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: 10.0000 chunk 64 optimal weight: 0.9980 chunk 188 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 65 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 189 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.133853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.086434 restraints weight = 88118.404| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.36 r_work: 0.2918 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1543 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= 0.185 Angle : 0.485 6.897 28880 Z= 0.282 Chirality : 0.038 0.289 3378 Planarity : 0.004 0.063 2698 Dihedral : 21.787 178.266 5596 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.64 % Allowed : 8.46 % Favored : 90.90 % 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: 1.74 (0.18), residues: 795 sheet: -2.27 (0.36), residues: 174 loop : -0.66 (0.24), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 332 TYR 0.014 0.001 TYR C 491 PHE 0.018 0.001 PHE A 471 HIS 0.009 0.001 HIS C 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.19 (20539) covalent geometry : angle 0.48516 / 0.28 (28880) hydrogen bonds : bond 0.04817 / 3.17 ( 875) hydrogen bonds : angle 4.39859 / 3.12 ( 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 108 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.984 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 489 MET cc_start: 0.7157 (mtt) cc_final: 0.6864 (mtp) REVERT: B 491 TYR cc_start: 0.8193 (p90) cc_final: 0.7868 (p90) REVERT: C 126 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7976 (mp0) REVERT: C 326 LEU cc_start: 0.8422 (tt) cc_final: 0.8016 (mp) REVERT: C 376 LYS cc_start: 0.8401 (mtmt) cc_final: 0.7772 (pttp) REVERT: C 426 SER cc_start: 0.9006 (t) cc_final: 0.8344 (m) REVERT: C 486 MET cc_start: 0.8115 (mmt) cc_final: 0.7830 (mmm) REVERT: C 514 MET cc_start: 0.8174 (ttm) cc_final: 0.7735 (ttm) REVERT: A 470 ASN cc_start: 0.7866 (m110) cc_final: 0.7633 (m110) REVERT: A 489 MET cc_start: 0.7426 (mtt) cc_final: 0.7134 (mtt) REVERT: A 551 MET cc_start: 0.7502 (ttt) cc_final: 0.7187 (mmm) REVERT: A 575 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8294 (t70) outliers start: 10 outliers final: 5 residues processed: 103 average time/residue: 0.9545 time to fit residues: 116.9970 Evaluate side-chains 105 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 58 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3952 r_free = 0.3952 target = 0.134747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.083865 restraints weight = 87542.812| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.63 r_work: 0.2909 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20539 Z= 0.173 Angle : 0.480 6.882 28880 Z= 0.278 Chirality : 0.038 0.288 3378 Planarity : 0.004 0.062 2698 Dihedral : 21.819 179.411 5596 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.77 % Allowed : 8.97 % 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: 0.47 (0.21), residues: 1722 helix: 1.80 (0.18), residues: 795 sheet: -2.25 (0.36), residues: 174 loop : -0.63 (0.24), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 552 TYR 0.015 0.001 TYR B 499 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 0.00353 / 0.17 (20539) covalent geometry : angle 0.47969 / 0.28 (28880) hydrogen bonds : bond 0.04737 / 3.11 ( 875) hydrogen bonds : angle 4.36290 / 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 112 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 489 MET cc_start: 0.7140 (mtt) cc_final: 0.6816 (mtp) REVERT: B 491 TYR cc_start: 0.8293 (p90) cc_final: 0.7956 (p90) REVERT: C 126 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7984 (mp0) REVERT: C 326 LEU cc_start: 0.8443 (tt) cc_final: 0.8025 (mp) REVERT: C 376 LYS cc_start: 0.8405 (mtmt) cc_final: 0.7780 (pttp) REVERT: C 426 SER cc_start: 0.9004 (t) cc_final: 0.8321 (m) REVERT: C 486 MET cc_start: 0.8161 (mmt) cc_final: 0.7899 (mmm) REVERT: C 514 MET cc_start: 0.8196 (ttm) cc_final: 0.7740 (ttp) REVERT: A 470 ASN cc_start: 0.7856 (m110) cc_final: 0.7463 (m110) REVERT: A 489 MET cc_start: 0.7370 (mtt) cc_final: 0.7075 (mtt) REVERT: A 551 MET cc_start: 0.7501 (ttt) cc_final: 0.7170 (mmm) REVERT: A 575 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8284 (t70) outliers start: 12 outliers final: 8 residues processed: 105 average time/residue: 0.8533 time to fit residues: 108.0168 Evaluate side-chains 105 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 372 ILE 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 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: 2.9990 chunk 146 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 2 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 50 optimal weight: 0.0570 overall best weight: 0.7098 ------------------------------------------------------------------------------- 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 = 0.3956 r_free = 0.3956 target = 0.134521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.087028 restraints weight = 88225.145| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.34 r_work: 0.2939 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20539 Z= 0.135 Angle : 0.469 6.894 28880 Z= 0.271 Chirality : 0.038 0.289 3378 Planarity : 0.004 0.060 2698 Dihedral : 21.811 179.793 5596 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.64 % Allowed : 9.29 % Favored : 90.06 % 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: 0.57 (0.21), residues: 1722 helix: 1.89 (0.18), residues: 795 sheet: -2.23 (0.36), residues: 174 loop : -0.58 (0.24), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 552 TYR 0.020 0.001 TYR C 580 PHE 0.032 0.001 PHE C 566 HIS 0.009 0.001 HIS C 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (20539) covalent geometry : angle 0.46945 / 0.27 (28880) hydrogen bonds : bond 0.04562 / 2.99 ( 875) hydrogen bonds : angle 4.29140 / 3.04 ( 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 104 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 489 MET cc_start: 0.7207 (mtt) cc_final: 0.6882 (mtp) REVERT: B 491 TYR cc_start: 0.8205 (p90) cc_final: 0.7884 (p90) REVERT: C 126 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: C 326 LEU cc_start: 0.8484 (tt) cc_final: 0.8074 (mp) REVERT: C 376 LYS cc_start: 0.8408 (mtmt) cc_final: 0.7766 (pttp) REVERT: C 426 SER cc_start: 0.8987 (t) cc_final: 0.8326 (m) REVERT: C 486 MET cc_start: 0.8210 (mmt) cc_final: 0.7921 (mmm) REVERT: C 514 MET cc_start: 0.8112 (ttm) cc_final: 0.7672 (ttp) REVERT: A 470 ASN cc_start: 0.7855 (m110) cc_final: 0.7626 (m110) REVERT: A 489 MET cc_start: 0.7391 (mtt) cc_final: 0.7089 (mtt) REVERT: A 551 MET cc_start: 0.7601 (ttt) cc_final: 0.7237 (mmm) outliers start: 10 outliers final: 5 residues processed: 99 average time/residue: 0.8590 time to fit residues: 102.5470 Evaluate side-chains 99 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 547 HIS Chi-restraints excluded: chain A residue 372 ILE 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 186 optimal weight: 4.9990 chunk 100 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.133787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.083212 restraints weight = 87831.329| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.58 r_work: 0.2930 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20539 Z= 0.153 Angle : 0.475 6.868 28880 Z= 0.274 Chirality : 0.038 0.289 3378 Planarity : 0.004 0.081 2698 Dihedral : 21.808 179.887 5596 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.51 % Allowed : 9.68 % Favored : 89.81 % 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: 0.60 (0.21), residues: 1722 helix: 1.90 (0.18), residues: 795 sheet: -2.21 (0.36), residues: 174 loop : -0.54 (0.25), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 332 TYR 0.012 0.001 TYR B 499 PHE 0.016 0.001 PHE A 471 HIS 0.008 0.001 HIS C 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (20539) covalent geometry : angle 0.47459 / 0.27 (28880) hydrogen bonds : bond 0.04548 / 2.97 ( 875) hydrogen bonds : angle 4.26793 / 3.02 ( 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 103 residues out of total 1560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.851 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: 0.7176 (mtt) cc_final: 0.6844 (mtp) REVERT: B 491 TYR cc_start: 0.8211 (p90) cc_final: 0.7879 (p90) REVERT: C 126 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: C 326 LEU cc_start: 0.8472 (tt) cc_final: 0.8060 (mp) REVERT: C 376 LYS cc_start: 0.8385 (mtmt) cc_final: 0.7743 (pttp) REVERT: C 426 SER cc_start: 0.8995 (t) cc_final: 0.8328 (m) REVERT: C 486 MET cc_start: 0.8227 (mmt) cc_final: 0.7930 (mmm) REVERT: C 514 MET cc_start: 0.8139 (ttm) cc_final: 0.7672 (ttp) REVERT: A 470 ASN cc_start: 0.7859 (m110) cc_final: 0.7468 (m110) REVERT: A 489 MET cc_start: 0.7364 (mtt) cc_final: 0.7059 (mtt) REVERT: A 551 MET cc_start: 0.7597 (ttt) cc_final: 0.7221 (mmm) outliers start: 8 outliers final: 5 residues processed: 99 average time/residue: 0.9085 time to fit residues: 107.5681 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 : 0.845 ------------------------------------------------------------------------------- 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 547 HIS Chi-restraints excluded: chain A residue 372 ILE 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: 3.9990 chunk 3 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 146 optimal weight: 0.0570 chunk 49 optimal weight: 0.5980 chunk 148 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 161 optimal weight: 0.0870 chunk 164 optimal weight: 0.1980 chunk 99 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 366 ASN C 547 HIS A 45 GLN A 366 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.135651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.088293 restraints weight = 87766.874| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.38 r_work: 0.2956 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20539 Z= 0.104 Angle : 0.461 6.906 28880 Z= 0.265 Chirality : 0.038 0.288 3378 Planarity : 0.004 0.057 2698 Dihedral : 21.791 179.975 5596 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.51 % Allowed : 9.81 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.75 (0.21), residues: 1722 helix: 2.02 (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 0.007 0.000 ARG A 552 TYR 0.018 0.001 TYR C 580 PHE 0.020 0.001 PHE C 435 HIS 0.008 0.001 HIS C 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.10 (20539) covalent geometry : angle 0.46140 / 0.27 (28880) hydrogen bonds : bond 0.04334 / 2.83 ( 875) hydrogen bonds : angle 4.16913 / 2.94 ( 2378) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9296.46 seconds wall clock time: 158 minutes 34.47 seconds (9514.47 seconds total)