Starting phenix.real_space_refine on Fri Jul 3 02:50:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g6d_51098/07_2026/9g6d_51098.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g6d_51098/07_2026/9g6d_51098.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9g6d_51098/07_2026/9g6d_51098.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g6d_51098/07_2026/9g6d_51098.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9g6d_51098/07_2026/9g6d_51098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g6d_51098/07_2026/9g6d_51098.map" } resolution = 2.7 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= 0.021 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: 5 Type Number sf(0) Gaussians S 87 5.16 5 Cl 6 4.86 5 C 7377 2.51 5 N 1786 2.21 5 O 2036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 11292 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3780 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 475, 3608 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 17, 'TRANS': 457} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 475, 3608 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 17, 'TRANS': 457} Chain breaks: 1 bond proxies already assigned to first conformer: 3523 Chain: "B" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1735 Classifications: {'peptide': 218} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 207} Chain breaks: 2 Chain: "C" Number of atoms: 3749 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 475, 3608 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 17, 'TRANS': 457} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 475, 3608 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 17, 'TRANS': 457} Chain breaks: 1 bond proxies already assigned to first conformer: 3554 Chain: "D" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1690 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain breaks: 2 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 105 Ad-hoc single atom residues: {' CL': 3} Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 3 Chain: "C" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 105 Ad-hoc single atom residues: {' CL': 3} Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 3 Residues with excluded nonbonded symmetry interactions: 40 residue: pdb=" N AMET A 584 " occ=0.46 ... (14 atoms not shown) pdb=" CE BMET A 584 " occ=0.54 residue: pdb=" N ALEU A 585 " occ=0.46 ... (14 atoms not shown) pdb=" CD2BLEU A 585 " occ=0.54 residue: pdb=" N AVAL A 586 " occ=0.46 ... (12 atoms not shown) pdb=" CG2BVAL A 586 " occ=0.54 residue: pdb=" N ALEU A 587 " occ=0.46 ... (14 atoms not shown) pdb=" CD2BLEU A 587 " occ=0.54 residue: pdb=" N AMET A 588 " occ=0.46 ... (14 atoms not shown) pdb=" CE BMET A 588 " occ=0.54 residue: pdb=" N ATHR A 589 " occ=0.46 ... (12 atoms not shown) pdb=" CG2BTHR A 589 " occ=0.54 residue: pdb=" N AALA A 590 " occ=0.46 ... (8 atoms not shown) pdb=" CB BALA A 590 " occ=0.54 residue: pdb=" N ALYS A 591 " occ=0.46 ... (16 atoms not shown) pdb=" NZ BLYS A 591 " occ=0.54 residue: pdb=" N AILE A 592 " occ=0.46 ... (14 atoms not shown) pdb=" CD1BILE A 592 " occ=0.54 residue: pdb=" N AVAL A 593 " occ=0.46 ... (12 atoms not shown) pdb=" CG2BVAL A 593 " occ=0.54 residue: pdb=" N AGLY A 594 " occ=0.46 ... (6 atoms not shown) pdb=" O BGLY A 594 " occ=0.54 residue: pdb=" N AASP A 595 " occ=0.46 ... (14 atoms not shown) pdb=" OD2BASP A 595 " occ=0.54 ... (remaining 28 not shown) Time building chain proxies: 4.20, per 1000 atoms: 0.37 Number of scatterers: 11292 At special positions: 0 Unit cell: (89.397, 110.187, 102.564, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 6 17.00 S 87 16.00 O 2036 8.00 N 1786 7.00 C 7377 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 438 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 112 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 174 " - pdb=" SG CYS B 255 " distance=2.03 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 221 " - pdb=" SG CYS B 275 " distance=2.03 Simple disulfide: pdb=" SG CYS C 438 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 115 " distance=2.03 Simple disulfide: pdb=" SG CYS D 112 " - pdb=" SG CYS D 171 " distance=2.03 Simple disulfide: pdb=" SG CYS D 174 " - pdb=" SG CYS D 255 " distance=2.03 Simple disulfide: pdb=" SG CYS D 199 " - pdb=" SG CYS D 224 " distance=2.03 Simple disulfide: pdb=" SG CYS D 221 " - pdb=" SG CYS D 275 " distance=2.03 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 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA H 3 " - " MAN H 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA H 3 " - " MAN H 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 698.4 milliseconds 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2632 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 2 sheets defined 79.8% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 115 through 170 removed outlier: 4.845A pdb=" N GLU A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS A 169 " --> pdb=" O LYS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 197 removed outlier: 3.908A pdb=" N SER A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 223 through 240 Processing helix chain 'A' and resid 248 through 262 removed outlier: 4.363A pdb=" N HIS A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 302 Processing helix chain 'A' and resid 303 through 316 Processing helix chain 'A' and resid 320 through 346 Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 374 through 407 Processing helix chain 'A' and resid 409 through 435 Processing helix chain 'A' and resid 461 through 468 removed outlier: 3.520A pdb=" N ALA A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 466 " --> pdb=" O MET A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 479 Processing helix chain 'A' and resid 486 through 506 removed outlier: 3.633A pdb=" N PHE A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLY A 506 " --> pdb=" O CYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 536 Processing helix chain 'A' and resid 543 through 561 Processing helix chain 'A' and resid 563 through 575 removed outlier: 3.777A pdb=" N VAL A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 578 No H-bonds generated for 'chain 'A' and resid 576 through 578' Processing helix chain 'A' and resid 579 through 598 removed outlier: 4.079A pdb=" N APHE A 597 " --> pdb=" O AVAL A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'B' and resid 81 through 105 removed outlier: 3.749A pdb=" N LEU B 87 " --> pdb=" O GLU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 115 through 130 Processing helix chain 'B' and resid 153 through 170 Processing helix chain 'B' and resid 170 through 175 removed outlier: 4.538A pdb=" N CYS B 174 " --> pdb=" O ASN B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 202 removed outlier: 3.535A pdb=" N LEU B 192 " --> pdb=" O TYR B 188 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 225 through 246 Processing helix chain 'B' and resid 255 through 271 Processing helix chain 'B' and resid 281 through 309 Proline residue: B 296 - end of helix removed outlier: 4.156A pdb=" N GLN B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 170 removed outlier: 4.486A pdb=" N GLU C 168 " --> pdb=" O ASP C 164 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS C 169 " --> pdb=" O LYS C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 197 removed outlier: 3.874A pdb=" N SER C 175 " --> pdb=" O GLY C 171 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL C 194 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 202 Processing helix chain 'C' and resid 205 through 215 Processing helix chain 'C' and resid 223 through 240 Processing helix chain 'C' and resid 248 through 262 removed outlier: 4.238A pdb=" N HIS C 252 " --> pdb=" O GLY C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 302 removed outlier: 3.583A pdb=" N ASP C 287 " --> pdb=" O THR C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 316 Processing helix chain 'C' and resid 320 through 347 Processing helix chain 'C' and resid 371 through 373 No H-bonds generated for 'chain 'C' and resid 371 through 373' Processing helix chain 'C' and resid 374 through 407 Processing helix chain 'C' and resid 409 through 435 Processing helix chain 'C' and resid 461 through 468 Processing helix chain 'C' and resid 469 through 479 Processing helix chain 'C' and resid 486 through 505 removed outlier: 3.515A pdb=" N PHE C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 536 Processing helix chain 'C' and resid 543 through 561 Processing helix chain 'C' and resid 563 through 575 Processing helix chain 'C' and resid 579 through 598 removed outlier: 3.501A pdb=" N AVAL C 596 " --> pdb=" O AILE C 592 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N APHE C 597 " --> pdb=" O AVAL C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 605 removed outlier: 3.503A pdb=" N AHIS C 605 " --> pdb=" O ALEU C 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 105 removed outlier: 4.174A pdb=" N LEU D 88 " --> pdb=" O CYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 115 through 131 Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 153 through 169 Processing helix chain 'D' and resid 170 through 175 removed outlier: 3.677A pdb=" N CYS D 174 " --> pdb=" O ASN D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 205 removed outlier: 3.546A pdb=" N PHE D 200 " --> pdb=" O THR D 196 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS D 202 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLN D 205 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 222 removed outlier: 3.637A pdb=" N LYS D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 218 through 222' Processing helix chain 'D' and resid 224 through 247 removed outlier: 3.590A pdb=" N TYR D 228 " --> pdb=" O CYS D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 271 Processing helix chain 'D' and resid 281 through 308 Proline residue: D 296 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 438 through 440 Processing sheet with id=AA2, first strand: chain 'C' and resid 438 through 440 849 hydrogen bonds defined for protein. 2535 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1859 1.32 - 1.45: 3048 1.45 - 1.57: 6511 1.57 - 1.69: 1 1.69 - 1.81: 134 Bond restraints: 11553 Sorted by residual: bond pdb=" C LEU A 431 " pdb=" N ILE A 432 " ideal model delta sigma weight residual 1.335 1.412 -0.077 1.20e-02 6.94e+03 4.10e+01 bond pdb=" C3 BMA E 3 " pdb=" O3 BMA E 3 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" C ILE A 432 " pdb=" O ILE A 432 " ideal model delta sigma weight residual 1.237 1.203 0.035 1.29e-02 6.01e+03 7.16e+00 bond pdb=" C3 BMA H 3 " pdb=" O3 BMA H 3 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.31e+00 bond pdb=" C1 MAN E 5 " pdb=" C2 MAN E 5 " ideal model delta sigma weight residual 1.526 1.565 -0.039 2.00e-02 2.50e+03 3.84e+00 ... (remaining 11548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 15439 1.66 - 3.32: 202 3.32 - 4.98: 64 4.98 - 6.64: 20 6.64 - 8.30: 2 Bond angle restraints: 15727 Sorted by residual: angle pdb=" CA ILE A 432 " pdb=" C ILE A 432 " pdb=" O ILE A 432 " ideal model delta sigma weight residual 120.47 125.24 -4.77 1.08e+00 8.57e-01 1.95e+01 angle pdb=" CB LYS B 240 " pdb=" CG LYS B 240 " pdb=" CD LYS B 240 " ideal model delta sigma weight residual 111.30 119.60 -8.30 2.30e+00 1.89e-01 1.30e+01 angle pdb=" C ASN C 348 " pdb=" CA ASN C 348 " pdb=" CB ASN C 348 " ideal model delta sigma weight residual 111.91 117.16 -5.25 1.52e+00 4.33e-01 1.19e+01 angle pdb=" N VAL C 221 " pdb=" CA VAL C 221 " pdb=" C VAL C 221 " ideal model delta sigma weight residual 112.96 109.81 3.15 1.00e+00 1.00e+00 9.91e+00 angle pdb=" CA ASN C 348 " pdb=" CB ASN C 348 " pdb=" CG ASN C 348 " ideal model delta sigma weight residual 112.60 115.70 -3.10 1.00e+00 1.00e+00 9.60e+00 ... (remaining 15722 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.28: 6398 20.28 - 40.56: 634 40.56 - 60.85: 136 60.85 - 81.13: 35 81.13 - 101.41: 11 Dihedral angle restraints: 7214 sinusoidal: 3128 harmonic: 4086 Sorted by residual: dihedral pdb=" CB CYS D 199 " pdb=" SG CYS D 199 " pdb=" SG CYS D 224 " pdb=" CB CYS D 224 " ideal model delta sinusoidal sigma weight residual -86.00 -165.29 79.29 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CB CYS D 84 " pdb=" SG CYS D 84 " pdb=" SG CYS D 142 " pdb=" CB CYS D 142 " ideal model delta sinusoidal sigma weight residual -86.00 -164.22 78.22 1 1.00e+01 1.00e-02 7.64e+01 dihedral pdb=" CB CYS B 199 " pdb=" SG CYS B 199 " pdb=" SG CYS B 224 " pdb=" CB CYS B 224 " ideal model delta sinusoidal sigma weight residual 93.00 151.05 -58.05 1 1.00e+01 1.00e-02 4.52e+01 ... (remaining 7211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1527 0.049 - 0.098: 312 0.098 - 0.148: 34 0.148 - 0.197: 2 0.197 - 0.246: 2 Chirality restraints: 1877 Sorted by residual: chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA ASN C 348 " pdb=" N ASN C 348 " pdb=" C ASN C 348 " pdb=" CB ASN C 348 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.32e-01 ... (remaining 1874 not shown) Planarity restraints: 1914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 81 " 0.051 5.00e-02 4.00e+02 7.57e-02 9.16e+00 pdb=" N PRO B 82 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 82 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 82 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 348 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.80e+00 pdb=" C ASN C 348 " 0.034 2.00e-02 2.50e+03 pdb=" O ASN C 348 " -0.013 2.00e-02 2.50e+03 pdb=" N MET C 349 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 277 " -0.032 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO D 278 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 278 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 278 " -0.026 5.00e-02 4.00e+02 ... (remaining 1911 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 2423 2.78 - 3.31: 11498 3.31 - 3.84: 19408 3.84 - 4.37: 22870 4.37 - 4.90: 39331 Nonbonded interactions: 95530 Sorted by model distance: nonbonded pdb=" O LEU A 500 " pdb=" OG1 THR A 504 " model vdw 2.244 3.040 nonbonded pdb=" O ILE C 163 " pdb=" OG1 THR C 167 " model vdw 2.248 3.040 nonbonded pdb=" O THR C 563 " pdb=" OG1 THR C 567 " model vdw 2.251 3.040 nonbonded pdb=" O SER B 95 " pdb=" OG1 THR B 99 " model vdw 2.276 3.040 nonbonded pdb=" OD1 ASN A 576 " pdb=" OG1 THR A 578 " model vdw 2.277 3.040 ... (remaining 95525 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' and (resid 115 through 583 or resid 901 through 906)) selection = (chain 'C' and (resid 115 through 583 or resid 901 through 906)) } ncs_group { reference = (chain 'B' and resid 79 through 310) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=0.97 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: 10.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.550 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:7.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 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 0.080 11574 Z= 0.160 Angle : 0.568 8.302 15777 Z= 0.277 Chirality : 0.038 0.246 1877 Planarity : 0.004 0.076 1914 Dihedral : 16.811 101.410 4543 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.84 % Allowed : 22.74 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.22), residues: 1400 helix: 2.12 (0.15), residues: 1027 sheet: None (None), residues: 0 loop : -1.70 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 271 TYR 0.017 0.001 TYR A 459 PHE 0.009 0.001 PHE D 294 TRP 0.022 0.001 TRP C 350 HIS 0.005 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (11553) covalent geometry : angle 0.55819 / 0.27 (15727) SS BOND : bond 0.00241 / 0.15 ( 13) SS BOND : angle 1.52282 / 1.20 ( 26) hydrogen bonds : bond 0.18922 / 12.94 ( 849) hydrogen bonds : angle 6.72005 / 4.95 ( 2535) link_ALPHA1-3 : bond 0.00747 / 0.38 ( 2) link_ALPHA1-3 : angle 4.12949 / 3.24 ( 6) link_ALPHA1-6 : bond 0.00504 / 0.26 ( 2) link_ALPHA1-6 : angle 1.49764 / 1.10 ( 6) link_BETA1-4 : bond 0.00550 / 0.27 ( 4) link_BETA1-4 : angle 1.02185 / 0.66 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 24 residues processed: 139 average time/residue: 0.5740 time to fit residues: 86.6065 Evaluate side-chains 132 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 CYS Chi-restraints excluded: chain D residue 280 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0770 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 202 HIS C 321 GLN C 348 ASN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.113942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.082792 restraints weight = 78161.363| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 4.92 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11574 Z= 0.158 Angle : 0.582 6.243 15777 Z= 0.301 Chirality : 0.040 0.230 1877 Planarity : 0.004 0.057 1914 Dihedral : 9.121 77.174 2159 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.60 % Allowed : 21.15 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.50 (0.22), residues: 1400 helix: 2.75 (0.15), residues: 1027 sheet: None (None), residues: 0 loop : -1.69 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 271 TYR 0.020 0.001 TYR A 505 PHE 0.015 0.001 PHE A 392 TRP 0.015 0.001 TRP C 524 HIS 0.004 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (11553) covalent geometry : angle 0.57285 / 0.30 (15727) SS BOND : bond 0.00314 / 0.19 ( 13) SS BOND : angle 1.24305 / 0.95 ( 26) hydrogen bonds : bond 0.05219 / 3.47 ( 849) hydrogen bonds : angle 4.54702 / 3.37 ( 2535) link_ALPHA1-3 : bond 0.00078 / 0.04 ( 2) link_ALPHA1-3 : angle 3.85789 / 3.07 ( 6) link_ALPHA1-6 : bond 0.01040 / 0.54 ( 2) link_ALPHA1-6 : angle 1.94627 / 1.63 ( 6) link_BETA1-4 : bond 0.00580 / 0.29 ( 4) link_BETA1-4 : angle 1.48227 / 0.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: C 348 ASN cc_start: 0.6777 (OUTLIER) cc_final: 0.6543 (p0) outliers start: 35 outliers final: 11 residues processed: 138 average time/residue: 0.5848 time to fit residues: 87.4529 Evaluate side-chains 121 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain C residue 348 ASN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 192 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 131 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 95 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 202 HIS C 321 GLN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.113271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.081981 restraints weight = 81917.380| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 5.01 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11574 Z= 0.170 Angle : 0.584 7.970 15777 Z= 0.296 Chirality : 0.040 0.186 1877 Planarity : 0.004 0.055 1914 Dihedral : 8.323 65.644 2135 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.01 % Allowed : 20.07 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.51 (0.22), residues: 1400 helix: 2.77 (0.15), residues: 1027 sheet: None (None), residues: 0 loop : -1.72 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 362 TYR 0.014 0.001 TYR A 547 PHE 0.015 0.001 PHE A 392 TRP 0.015 0.001 TRP A 524 HIS 0.004 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (11553) covalent geometry : angle 0.57437 / 0.29 (15727) SS BOND : bond 0.00290 / 0.19 ( 13) SS BOND : angle 1.40586 / 1.06 ( 26) hydrogen bonds : bond 0.04718 / 3.15 ( 849) hydrogen bonds : angle 4.31917 / 3.19 ( 2535) link_ALPHA1-3 : bond 0.00014 / 0.01 ( 2) link_ALPHA1-3 : angle 3.83106 / 3.12 ( 6) link_ALPHA1-6 : bond 0.00817 / 0.42 ( 2) link_ALPHA1-6 : angle 1.72702 / 1.42 ( 6) link_BETA1-4 : bond 0.00633 / 0.31 ( 4) link_BETA1-4 : angle 1.57020 / 0.97 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 112 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: D 240 LYS cc_start: 0.8872 (ptpp) cc_final: 0.8576 (mppt) REVERT: D 271 ARG cc_start: 0.8201 (ttp-110) cc_final: 0.7919 (tpp-160) outliers start: 41 outliers final: 19 residues processed: 145 average time/residue: 0.5125 time to fit residues: 81.2000 Evaluate side-chains 127 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 437 ASP Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 174 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 93 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 129 optimal weight: 0.2980 chunk 122 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 GLN B 202 HIS C 321 GLN C 348 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.113907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.082712 restraints weight = 77283.401| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 4.92 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11574 Z= 0.140 Angle : 0.555 6.380 15777 Z= 0.280 Chirality : 0.039 0.219 1877 Planarity : 0.004 0.053 1914 Dihedral : 7.410 58.801 2134 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.10 % Allowed : 20.40 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.59 (0.22), residues: 1400 helix: 2.79 (0.15), residues: 1039 sheet: None (None), residues: 0 loop : -1.74 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 271 TYR 0.013 0.001 TYR A 547 PHE 0.014 0.001 PHE A 392 TRP 0.017 0.001 TRP A 524 HIS 0.005 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (11553) covalent geometry : angle 0.54623 / 0.28 (15727) SS BOND : bond 0.00199 / 0.12 ( 13) SS BOND : angle 1.14840 / 0.84 ( 26) hydrogen bonds : bond 0.04261 / 2.84 ( 849) hydrogen bonds : angle 4.18001 / 3.09 ( 2535) link_ALPHA1-3 : bond 0.00158 / 0.08 ( 2) link_ALPHA1-3 : angle 3.92699 / 3.15 ( 6) link_ALPHA1-6 : bond 0.00617 / 0.32 ( 2) link_ALPHA1-6 : angle 1.53454 / 1.25 ( 6) link_BETA1-4 : bond 0.00695 / 0.34 ( 4) link_BETA1-4 : angle 1.58439 / 0.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 111 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ARG cc_start: 0.5311 (OUTLIER) cc_final: 0.5071 (ptm-80) REVERT: A 285 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.6936 (tptt) REVERT: C 439 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.6999 (pp30) REVERT: D 199 CYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7191 (t) outliers start: 42 outliers final: 19 residues processed: 144 average time/residue: 0.5306 time to fit residues: 82.7876 Evaluate side-chains 130 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 439 GLN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 199 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 104 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 GLN B 202 HIS C 321 GLN C 348 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.112916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.081572 restraints weight = 96061.963| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 5.29 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11574 Z= 0.163 Angle : 0.574 6.388 15777 Z= 0.290 Chirality : 0.040 0.215 1877 Planarity : 0.004 0.053 1914 Dihedral : 6.821 59.784 2133 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.77 % Allowed : 19.65 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.62 (0.22), residues: 1400 helix: 2.81 (0.15), residues: 1038 sheet: None (None), residues: 0 loop : -1.71 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 271 TYR 0.014 0.001 TYR A 547 PHE 0.014 0.001 PHE A 392 TRP 0.017 0.001 TRP C 350 HIS 0.005 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (11553) covalent geometry : angle 0.56467 / 0.29 (15727) SS BOND : bond 0.00246 / 0.15 ( 13) SS BOND : angle 1.30558 / 0.93 ( 26) hydrogen bonds : bond 0.04266 / 2.85 ( 849) hydrogen bonds : angle 4.15357 / 3.07 ( 2535) link_ALPHA1-3 : bond 0.00190 / 0.09 ( 2) link_ALPHA1-3 : angle 3.80468 / 3.07 ( 6) link_ALPHA1-6 : bond 0.00436 / 0.23 ( 2) link_ALPHA1-6 : angle 1.62078 / 1.11 ( 6) link_BETA1-4 : bond 0.00599 / 0.30 ( 4) link_BETA1-4 : angle 1.63248 / 1.01 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 110 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.6921 (tptt) REVERT: C 314 GLU cc_start: 0.7633 (mp0) cc_final: 0.7099 (mp0) REVERT: C 439 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6941 (pp30) REVERT: D 199 CYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7294 (t) REVERT: D 240 LYS cc_start: 0.8912 (ptpp) cc_final: 0.8581 (mppt) outliers start: 50 outliers final: 26 residues processed: 151 average time/residue: 0.5305 time to fit residues: 87.2341 Evaluate side-chains 134 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 437 ASP Chi-restraints excluded: chain C residue 439 GLN Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 199 CYS Chi-restraints excluded: chain D residue 224 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 24 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 52 optimal weight: 0.0470 chunk 119 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 134 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 129 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 GLN B 202 HIS C 321 GLN C 348 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.113947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.082633 restraints weight = 86247.601| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 5.12 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 0.035 11574 Z= 0.133 Angle : 0.559 7.238 15777 Z= 0.281 Chirality : 0.039 0.181 1877 Planarity : 0.004 0.053 1914 Dihedral : 6.677 57.868 2133 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.68 % Allowed : 20.90 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.73 (0.22), residues: 1400 helix: 2.89 (0.15), residues: 1038 sheet: None (None), residues: 0 loop : -1.69 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 271 TYR 0.013 0.001 TYR D 235 PHE 0.017 0.001 PHE D 294 TRP 0.020 0.001 TRP C 350 HIS 0.005 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (11553) covalent geometry : angle 0.55097 / 0.28 (15727) SS BOND : bond 0.00191 / 0.11 ( 13) SS BOND : angle 1.16371 / 0.82 ( 26) hydrogen bonds : bond 0.03979 / 2.66 ( 849) hydrogen bonds : angle 4.07428 / 3.01 ( 2535) link_ALPHA1-3 : bond 0.00102 / 0.05 ( 2) link_ALPHA1-3 : angle 3.67647 / 2.96 ( 6) link_ALPHA1-6 : bond 0.00425 / 0.22 ( 2) link_ALPHA1-6 : angle 1.54397 / 1.12 ( 6) link_BETA1-4 : bond 0.00605 / 0.30 ( 4) link_BETA1-4 : angle 1.43645 / 0.84 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 108 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.6908 (tptt) REVERT: A 314 GLU cc_start: 0.7731 (mp0) cc_final: 0.7174 (mp0) REVERT: C 314 GLU cc_start: 0.7572 (mp0) cc_final: 0.7009 (mp0) REVERT: C 439 GLN cc_start: 0.7138 (OUTLIER) cc_final: 0.6876 (pp30) REVERT: D 199 CYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7315 (t) outliers start: 37 outliers final: 20 residues processed: 140 average time/residue: 0.5394 time to fit residues: 81.8932 Evaluate side-chains 128 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 221 CYS Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 439 GLN Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 199 CYS Chi-restraints excluded: chain D residue 224 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 26 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 133 optimal weight: 0.0000 chunk 132 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 GLN B 202 HIS C 321 GLN ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.113381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.082258 restraints weight = 81417.148| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 5.03 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11574 Z= 0.149 Angle : 0.576 10.689 15777 Z= 0.290 Chirality : 0.039 0.188 1877 Planarity : 0.004 0.092 1914 Dihedral : 6.570 57.443 2133 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.43 % Allowed : 20.82 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.72 (0.22), residues: 1400 helix: 2.88 (0.15), residues: 1040 sheet: None (None), residues: 0 loop : -1.68 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 362 TYR 0.015 0.001 TYR D 235 PHE 0.014 0.001 PHE A 392 TRP 0.022 0.001 TRP C 350 HIS 0.006 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (11553) covalent geometry : angle 0.56821 / 0.29 (15727) SS BOND : bond 0.00214 / 0.13 ( 13) SS BOND : angle 1.20636 / 0.85 ( 26) hydrogen bonds : bond 0.04035 / 2.70 ( 849) hydrogen bonds : angle 4.05352 / 2.99 ( 2535) link_ALPHA1-3 : bond 0.00084 / 0.04 ( 2) link_ALPHA1-3 : angle 3.71155 / 2.95 ( 6) link_ALPHA1-6 : bond 0.00313 / 0.16 ( 2) link_ALPHA1-6 : angle 1.53166 / 1.08 ( 6) link_BETA1-4 : bond 0.00568 / 0.28 ( 4) link_BETA1-4 : angle 1.47643 / 0.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.6919 (tptt) REVERT: A 314 GLU cc_start: 0.7744 (mp0) cc_final: 0.7174 (mp0) REVERT: C 314 GLU cc_start: 0.7617 (mp0) cc_final: 0.7195 (mp0) REVERT: C 439 GLN cc_start: 0.6928 (pp30) cc_final: 0.6622 (pp30) REVERT: D 199 CYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7339 (t) REVERT: D 240 LYS cc_start: 0.8877 (ptpp) cc_final: 0.8612 (mppt) outliers start: 34 outliers final: 23 residues processed: 136 average time/residue: 0.4858 time to fit residues: 72.1102 Evaluate side-chains 130 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 199 CYS Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 224 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 67 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 77 optimal weight: 0.1980 chunk 51 optimal weight: 0.6980 chunk 31 optimal weight: 0.0030 chunk 123 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 GLN B 202 HIS D 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.114604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.083235 restraints weight = 98127.051| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 5.33 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11574 Z= 0.126 Angle : 0.572 12.986 15777 Z= 0.285 Chirality : 0.038 0.176 1877 Planarity : 0.004 0.053 1914 Dihedral : 6.424 57.609 2132 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.18 % Allowed : 20.99 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.84 (0.22), residues: 1400 helix: 3.02 (0.15), residues: 1028 sheet: None (None), residues: 0 loop : -1.64 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 362 TYR 0.017 0.001 TYR A 459 PHE 0.022 0.001 PHE D 294 TRP 0.021 0.001 TRP C 350 HIS 0.006 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (11553) covalent geometry : angle 0.56507 / 0.28 (15727) SS BOND : bond 0.00169 / 0.10 ( 13) SS BOND : angle 1.07380 / 0.75 ( 26) hydrogen bonds : bond 0.03813 / 2.56 ( 849) hydrogen bonds : angle 3.97695 / 2.94 ( 2535) link_ALPHA1-3 : bond 0.00079 / 0.04 ( 2) link_ALPHA1-3 : angle 3.59157 / 2.86 ( 6) link_ALPHA1-6 : bond 0.00351 / 0.18 ( 2) link_ALPHA1-6 : angle 1.47632 / 1.05 ( 6) link_BETA1-4 : bond 0.00583 / 0.29 ( 4) link_BETA1-4 : angle 1.34151 / 0.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 285 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.6892 (tptt) REVERT: A 314 GLU cc_start: 0.7728 (mp0) cc_final: 0.7162 (mp0) REVERT: C 314 GLU cc_start: 0.7572 (mp0) cc_final: 0.7140 (mp0) REVERT: D 199 CYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7369 (t) REVERT: D 240 LYS cc_start: 0.8906 (ptpp) cc_final: 0.8643 (mppt) outliers start: 31 outliers final: 16 residues processed: 137 average time/residue: 0.5006 time to fit residues: 74.5164 Evaluate side-chains 123 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 199 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 97 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 22 optimal weight: 0.0050 chunk 14 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 GLN B 202 HIS D 239 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.114126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.082895 restraints weight = 96134.697| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 5.30 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11574 Z= 0.136 Angle : 0.580 15.353 15777 Z= 0.289 Chirality : 0.038 0.176 1877 Planarity : 0.004 0.053 1914 Dihedral : 6.279 57.577 2130 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.51 % Allowed : 21.74 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.84 (0.22), residues: 1400 helix: 3.02 (0.15), residues: 1028 sheet: None (None), residues: 0 loop : -1.63 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 271 TYR 0.023 0.001 TYR A 459 PHE 0.013 0.001 PHE A 392 TRP 0.020 0.001 TRP C 350 HIS 0.007 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (11553) covalent geometry : angle 0.57216 / 0.29 (15727) SS BOND : bond 0.00164 / 0.09 ( 13) SS BOND : angle 1.42330 / 1.03 ( 26) hydrogen bonds : bond 0.03882 / 2.61 ( 849) hydrogen bonds : angle 3.97622 / 2.94 ( 2535) link_ALPHA1-3 : bond 0.00102 / 0.05 ( 2) link_ALPHA1-3 : angle 3.57397 / 2.84 ( 6) link_ALPHA1-6 : bond 0.00336 / 0.17 ( 2) link_ALPHA1-6 : angle 1.52339 / 1.07 ( 6) link_BETA1-4 : bond 0.00557 / 0.27 ( 4) link_BETA1-4 : angle 1.38420 / 0.84 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.6879 (tptt) REVERT: A 314 GLU cc_start: 0.7764 (mp0) cc_final: 0.7190 (mp0) REVERT: C 314 GLU cc_start: 0.7601 (mp0) cc_final: 0.7170 (mp0) REVERT: D 144 ARG cc_start: 0.7375 (mtm-85) cc_final: 0.6709 (mpp-170) REVERT: D 199 CYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7299 (t) REVERT: D 240 LYS cc_start: 0.8898 (ptpp) cc_final: 0.8650 (mppt) outliers start: 23 outliers final: 16 residues processed: 125 average time/residue: 0.5314 time to fit residues: 72.0313 Evaluate side-chains 123 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 199 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 69 optimal weight: 0.3980 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 90 optimal weight: 0.0870 chunk 112 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 GLN B 202 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.114179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.082925 restraints weight = 91389.350| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 5.21 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11574 Z= 0.137 Angle : 0.574 12.507 15777 Z= 0.287 Chirality : 0.038 0.173 1877 Planarity : 0.004 0.053 1914 Dihedral : 6.245 57.763 2130 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.51 % Allowed : 21.82 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.85 (0.22), residues: 1400 helix: 3.02 (0.15), residues: 1028 sheet: None (None), residues: 0 loop : -1.63 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 271 TYR 0.026 0.001 TYR A 459 PHE 0.028 0.001 PHE D 294 TRP 0.021 0.001 TRP C 350 HIS 0.008 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (11553) covalent geometry : angle 0.56604 / 0.29 (15727) SS BOND : bond 0.00166 / 0.10 ( 13) SS BOND : angle 1.39875 / 1.02 ( 26) hydrogen bonds : bond 0.03880 / 2.61 ( 849) hydrogen bonds : angle 3.95388 / 2.92 ( 2535) link_ALPHA1-3 : bond 0.00158 / 0.08 ( 2) link_ALPHA1-3 : angle 3.53721 / 2.81 ( 6) link_ALPHA1-6 : bond 0.00389 / 0.20 ( 2) link_ALPHA1-6 : angle 1.53136 / 1.08 ( 6) link_BETA1-4 : bond 0.00572 / 0.28 ( 4) link_BETA1-4 : angle 1.33891 / 0.80 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ARG cc_start: 0.5280 (OUTLIER) cc_final: 0.4535 (ptm-80) REVERT: A 285 LYS cc_start: 0.7523 (OUTLIER) cc_final: 0.6853 (tptt) REVERT: A 314 GLU cc_start: 0.7772 (mp0) cc_final: 0.7191 (mp0) REVERT: A 349 MET cc_start: 0.8264 (mtp) cc_final: 0.7786 (mtp) REVERT: C 314 GLU cc_start: 0.7600 (mp0) cc_final: 0.7069 (mp0) REVERT: D 144 ARG cc_start: 0.7379 (mtm-85) cc_final: 0.6723 (mpp-170) REVERT: D 199 CYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7321 (t) REVERT: D 240 LYS cc_start: 0.8887 (ptpp) cc_final: 0.8660 (mppt) outliers start: 23 outliers final: 17 residues processed: 122 average time/residue: 0.6009 time to fit residues: 79.0542 Evaluate side-chains 121 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 199 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 130 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 55 optimal weight: 0.0970 chunk 87 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 GLN B 202 HIS D 239 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.113864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.082773 restraints weight = 93369.883| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 5.23 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11574 Z= 0.138 Angle : 0.581 15.468 15777 Z= 0.289 Chirality : 0.038 0.171 1877 Planarity : 0.004 0.053 1914 Dihedral : 6.215 57.883 2130 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.42 % Allowed : 21.66 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 2.89 (0.22), residues: 1400 helix: 3.05 (0.15), residues: 1028 sheet: None (None), residues: 0 loop : -1.60 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 271 TYR 0.023 0.001 TYR A 459 PHE 0.014 0.001 PHE A 392 TRP 0.021 0.001 TRP C 350 HIS 0.008 0.001 HIS B 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (11553) covalent geometry : angle 0.57283 / 0.29 (15727) SS BOND : bond 0.00179 / 0.11 ( 13) SS BOND : angle 1.36230 / 0.99 ( 26) hydrogen bonds : bond 0.03874 / 2.60 ( 849) hydrogen bonds : angle 3.95449 / 2.92 ( 2535) link_ALPHA1-3 : bond 0.00128 / 0.06 ( 2) link_ALPHA1-3 : angle 3.52532 / 2.79 ( 6) link_ALPHA1-6 : bond 0.00325 / 0.17 ( 2) link_ALPHA1-6 : angle 1.52136 / 1.08 ( 6) link_BETA1-4 : bond 0.00554 / 0.27 ( 4) link_BETA1-4 : angle 1.32869 / 0.80 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3264.40 seconds wall clock time: 56 minutes 40.95 seconds (3400.95 seconds total)