Starting phenix.real_space_refine on Wed Oct 28 20:33:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m77_63677/10_2026/9m77_63677.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m77_63677/10_2026/9m77_63677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m77_63677/10_2026/9m77_63677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m77_63677/10_2026/9m77_63677.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m77_63677/10_2026/9m77_63677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m77_63677/10_2026/9m77_63677.map" } resolution = 3.7 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= -0.000 sd= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 288 5.49 5 S 38 5.16 5 C 9019 2.51 5 N 2976 2.21 5 O 3525 1.98 5 H 13378 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29227 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1388 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1737 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1564 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1676 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1437 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1758 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1540 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "I" Number of atoms: 4556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 4556 Classifications: {'DNA': 144} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 143} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "J" Number of atoms: 4583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 4583 Classifications: {'DNA': 144} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 143} Chain: "A" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1833 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain breaks: 1 Chain: "K" Number of atoms: 7152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 7152 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 435} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 24672 SG CYS K 302 74.850 63.795 36.171 1.00159.52 S ATOM 24721 SG CYS K 305 78.071 64.636 33.145 1.00165.97 S ATOM 24850 SG CYS K 313 75.764 61.744 33.215 1.00159.78 S ATOM 24900 SG CYS K 316 75.012 64.372 30.957 1.00161.94 S ATOM 24920 SG CYS K 318 70.726 55.905 25.839 1.00155.52 S ATOM 24966 SG CYS K 321 73.646 55.379 24.312 1.00156.82 S ATOM 25307 SG CYS K 344 70.933 54.011 23.114 1.00159.71 S ATOM 25144 SG CYS K 333 60.970 57.951 33.339 1.00157.45 S ATOM 25181 SG CYS K 336 63.389 57.464 35.156 1.00164.93 S ATOM 25545 SG CYS K 360 62.175 54.576 33.510 1.00160.59 S ATOM 25584 SG CYS K 363 61.274 54.441 36.310 1.00167.69 S Time building chain proxies: 4.77, per 1000 atoms: 0.16 Number of scatterers: 29227 At special positions: 0 Unit cell: (153.819, 120.285, 115.911, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 38 16.00 P 288 15.00 O 3525 8.00 N 2976 7.00 C 9019 6.00 H 13378 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 592.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 801 " pdb="ZN ZN K 801 " - pdb=" SG CYS K 313 " pdb="ZN ZN K 801 " - pdb=" SG CYS K 305 " pdb="ZN ZN K 801 " - pdb=" SG CYS K 302 " pdb="ZN ZN K 801 " - pdb=" SG CYS K 316 " pdb=" ZN K 802 " pdb="ZN ZN K 802 " - pdb=" ND1 HIS K 341 " pdb="ZN ZN K 802 " - pdb=" SG CYS K 344 " pdb="ZN ZN K 802 " - pdb=" SG CYS K 321 " pdb="ZN ZN K 802 " - pdb=" SG CYS K 318 " pdb=" ZN K 803 " pdb="ZN ZN K 803 " - pdb=" SG CYS K 336 " pdb="ZN ZN K 803 " - pdb=" SG CYS K 360 " pdb="ZN ZN K 803 " - pdb=" SG CYS K 363 " pdb="ZN ZN K 803 " - pdb=" SG CYS K 333 " Number of angles added : 15 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2324 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 16 sheets defined 51.6% alpha, 11.6% beta 137 base pairs and 244 stacking pairs defined. Time for finding SS restraints: 5.14 Creating SS restraints... Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.935A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.142A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.507A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 122 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.574A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.572A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.288A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 122 removed outlier: 3.587A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.614A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.629A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.555A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 149 Processing helix chain 'K' and resid 213 through 217 removed outlier: 3.510A pdb=" N LEU K 217 " --> pdb=" O TRP K 214 " (cutoff:3.500A) Processing helix chain 'K' and resid 273 through 277 removed outlier: 4.055A pdb=" N VAL K 277 " --> pdb=" O VAL K 274 " (cutoff:3.500A) Processing helix chain 'K' and resid 343 through 345 No H-bonds generated for 'chain 'K' and resid 343 through 345' Processing helix chain 'K' and resid 360 through 366 removed outlier: 3.899A pdb=" N ASP K 366 " --> pdb=" O GLU K 362 " (cutoff:3.500A) Processing helix chain 'K' and resid 366 through 377 Processing helix chain 'K' and resid 400 through 404 removed outlier: 4.295A pdb=" N VAL K 404 " --> pdb=" O MET K 401 " (cutoff:3.500A) Processing helix chain 'K' and resid 432 through 439 removed outlier: 3.843A pdb=" N VAL K 436 " --> pdb=" O PHE K 432 " (cutoff:3.500A) Processing helix chain 'K' and resid 502 through 510 Processing helix chain 'K' and resid 526 through 530 Processing helix chain 'K' and resid 540 through 544 removed outlier: 3.550A pdb=" N LYS K 543 " --> pdb=" O LYS K 540 " (cutoff:3.500A) Processing helix chain 'K' and resid 591 through 602 Processing helix chain 'K' and resid 610 through 619 Processing sheet with id=AA1, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.218A pdb=" N ARG B 45 " --> pdb=" O ILE A 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.745A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.790A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.036A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.258A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 128 through 129 removed outlier: 6.859A pdb=" N HIS K 185 " --> pdb=" O VAL K 157 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL K 159 " --> pdb=" O ILE K 183 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE K 183 " --> pdb=" O VAL K 159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'K' and resid 222 through 227 removed outlier: 4.569A pdb=" N ASP K 240 " --> pdb=" O VAL K 260 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TYR K 256 " --> pdb=" O SER K 244 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LYS K 246 " --> pdb=" O GLU K 254 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLU K 254 " --> pdb=" O LYS K 246 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU K 255 " --> pdb=" O ILE K 271 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL K 259 " --> pdb=" O ASN K 267 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ASN K 267 " --> pdb=" O VAL K 259 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 330 through 332 Processing sheet with id=AB6, first strand: chain 'K' and resid 449 through 450 removed outlier: 3.597A pdb=" N SER K 459 " --> pdb=" O HIS K 450 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL K 533 " --> pdb=" O ILE K 558 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE K 558 " --> pdb=" O VAL K 533 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL K 535 " --> pdb=" O ASP K 556 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 470 through 471 removed outlier: 3.553A pdb=" N VAL K 470 " --> pdb=" O THR K 477 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ARG K 581 " --> pdb=" O VAL K 561 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL K 561 " --> pdb=" O ARG K 581 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N MET K 429 " --> pdb=" O GLN K 606 " (cutoff:3.500A) 502 hydrogen bonds defined for protein. 1443 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 351 hydrogen bonds 702 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 244 stacking parallelities Total time for adding SS restraints: 7.71 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 13371 1.04 - 1.23: 291 1.23 - 1.43: 7474 1.43 - 1.63: 8909 1.63 - 1.82: 58 Bond restraints: 30103 Sorted by residual: bond pdb=" P 5CM I -62 " pdb=" O5' 5CM I -62 " ideal model delta sigma weight residual 1.714 1.623 0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C3' DG I -68 " pdb=" C2' DG I -68 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C1' DC I -64 " pdb=" N1 DC I -64 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.05e+01 bond pdb=" C3' DT J -29 " pdb=" C2' DT J -29 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.22e+00 bond pdb=" C3' DT J 14 " pdb=" C2' DT J 14 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.90e+00 ... (remaining 30098 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 50031 1.23 - 2.46: 3902 2.46 - 3.69: 512 3.69 - 4.92: 12 4.92 - 6.15: 8 Bond angle restraints: 54465 Sorted by residual: angle pdb=" N3 DT I -39 " pdb=" C4 DT I -39 " pdb=" O4 DT I -39 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT I 71 " pdb=" C4 DT I 71 " pdb=" O4 DT I 71 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT I 30 " pdb=" C4 DT I 30 " pdb=" O4 DT I 30 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT J 22 " pdb=" C4 DT J 22 " pdb=" O4 DT J 22 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT I 62 " pdb=" C4 DT I 62 " pdb=" O4 DT I 62 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 ... (remaining 54460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 10003 17.05 - 34.09: 1265 34.09 - 51.14: 1016 51.14 - 68.18: 621 68.18 - 85.23: 29 Dihedral angle restraints: 12934 sinusoidal: 8840 harmonic: 4094 Sorted by residual: dihedral pdb=" CA ILE F 29 " pdb=" C ILE F 29 " pdb=" N THR F 30 " pdb=" CA THR F 30 " ideal model delta harmonic sigma weight residual 180.00 -158.89 -21.11 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA THR K 411 " pdb=" C THR K 411 " pdb=" N ILE K 412 " pdb=" CA ILE K 412 " ideal model delta harmonic sigma weight residual -180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ILE B 29 " pdb=" C ILE B 29 " pdb=" N THR B 30 " pdb=" CA THR B 30 " ideal model delta harmonic sigma weight residual -180.00 -162.45 -17.55 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 12931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2258 0.072 - 0.144: 358 0.144 - 0.216: 33 0.216 - 0.289: 0 0.289 - 0.361: 1 Chirality restraints: 2650 Sorted by residual: chirality pdb=" C3' 5CM I -62 " pdb=" C4' 5CM I -62 " pdb=" O3' 5CM I -62 " pdb=" C2' 5CM I -62 " both_signs ideal model delta sigma weight residual False -2.36 -2.72 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" C3' DG I 9 " pdb=" C4' DG I 9 " pdb=" O3' DG I 9 " pdb=" C2' DG I 9 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" C3' DC I 8 " pdb=" C4' DC I 8 " pdb=" O3' DC I 8 " pdb=" C2' DC I 8 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.51e-01 ... (remaining 2647 not shown) Planarity restraints: 3468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 5CM I -62 " 0.172 2.00e-02 2.50e+03 7.39e-02 1.50e+02 pdb=" N1 5CM I -62 " -0.022 2.00e-02 2.50e+03 pdb=" C2 5CM I -62 " -0.035 2.00e-02 2.50e+03 pdb=" O2 5CM I -62 " -0.032 2.00e-02 2.50e+03 pdb=" N3 5CM I -62 " -0.050 2.00e-02 2.50e+03 pdb=" C4 5CM I -62 " -0.056 2.00e-02 2.50e+03 pdb=" N4 5CM I -62 " 0.036 2.00e-02 2.50e+03 pdb=" C5 5CM I -62 " -0.086 2.00e-02 2.50e+03 pdb=" C6 5CM I -62 " -0.062 2.00e-02 2.50e+03 pdb="HN41 5CM I -62 " 0.051 2.00e-02 2.50e+03 pdb="HN42 5CM I -62 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 99 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO D 100 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO D 100 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 100 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO B 32 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.021 5.00e-02 4.00e+02 ... (remaining 3465 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1102 2.18 - 2.79: 51613 2.79 - 3.39: 76580 3.39 - 4.00: 105356 4.00 - 4.60: 162409 Nonbonded interactions: 397060 Sorted by model distance: nonbonded pdb=" O CYS K 302 " pdb=" H LYS K 306 " model vdw 1.577 2.450 nonbonded pdb=" OE1 GLU A 59 " pdb=" H GLU A 59 " model vdw 1.581 2.450 nonbonded pdb=" HG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 1.585 2.450 nonbonded pdb=" HH TYR K 418 " pdb=" OD1 ASP K 455 " model vdw 1.604 2.450 nonbonded pdb=" OE1 GLU E 59 " pdb=" H GLU E 59 " model vdw 1.605 2.450 ... (remaining 397055 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 37 through 134) selection = (chain 'E' and resid 37 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 19 through 101) } ncs_group { reference = (chain 'C' and (resid 11 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 75 through 117 or (resid \ 118 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 119)) selection = (chain 'G' and (resid 11 through 12 or (resid 13 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 14 through 119)) } ncs_group { reference = (chain 'D' and resid 27 through 122) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.630 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: 0.060 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 37.470 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 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 : 0.009 0.568 16737 Z= 0.514 Angle : 0.875 31.022 23832 Z= 0.634 Chirality : 0.053 0.361 2650 Planarity : 0.004 0.066 2054 Dihedral : 23.217 85.230 7044 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 0.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.29 % Allowed : 1.82 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.23), residues: 1225 helix: 1.71 (0.22), residues: 602 sheet: -0.69 (0.54), residues: 80 loop : -0.27 (0.24), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 433 TYR 0.008 0.001 TYR K 343 PHE 0.008 0.001 PHE K 273 TRP 0.003 0.001 TRP K 238 HIS 0.003 0.001 HIS K 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.45 (16725) covalent geometry : angle 0.72856 / 0.63 (23817) hydrogen bonds : bond 0.16359 / 11.23 ( 851) hydrogen bonds : angle 6.00906 / 4.26 ( 2145) metal coordination : bond 0.28610 / 17.16 ( 12) metal coordination : angle 19.29772 / 14.07 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 543 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Evaluate side-chains 268 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 265 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 SER cc_start: 0.8346 (t) cc_final: 0.8138 (p) REVERT: C 110 ASN cc_start: 0.7271 (t0) cc_final: 0.6986 (p0) REVERT: D 56 MET cc_start: 0.6909 (tpp) cc_final: 0.6507 (tpp) REVERT: F 22 LEU cc_start: 0.5914 (mt) cc_final: 0.5632 (mp) REVERT: G 38 ASN cc_start: 0.7240 (m110) cc_final: 0.7039 (m-40) REVERT: G 113 SER cc_start: 0.7255 (m) cc_final: 0.6995 (p) REVERT: K 199 MET cc_start: 0.1247 (pmm) cc_final: 0.0945 (ptp) REVERT: K 408 LYS cc_start: 0.4747 (OUTLIER) cc_final: 0.4019 (tptm) REVERT: K 436 VAL cc_start: 0.8225 (t) cc_final: 0.8024 (t) REVERT: K 446 VAL cc_start: 0.8148 (m) cc_final: 0.7901 (p) REVERT: K 460 LEU cc_start: 0.7782 (pt) cc_final: 0.7482 (pt) outliers start: 3 outliers final: 1 residues processed: 268 average time/residue: 0.4334 time to fit residues: 151.3965 Evaluate side-chains 135 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 408 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 50.0000 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 ASN D 92 GLN D 106 HIS F 75 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.119145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.086650 restraints weight = 144317.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.087015 restraints weight = 77638.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.086983 restraints weight = 55798.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.087710 restraints weight = 52390.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.087738 restraints weight = 47121.019| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 16737 Z= 0.251 Angle : 0.801 21.443 23832 Z= 0.462 Chirality : 0.046 0.187 2650 Planarity : 0.006 0.054 2054 Dihedral : 27.494 81.080 4571 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.77 % Allowed : 6.51 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.23), residues: 1225 helix: 1.50 (0.21), residues: 602 sheet: -1.29 (0.50), residues: 97 loop : -0.43 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 253 TYR 0.026 0.002 TYR F 88 PHE 0.009 0.001 PHE K 273 TRP 0.007 0.001 TRP K 430 HIS 0.012 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.25 (16725) covalent geometry : angle 0.77304 / 0.46 (23817) hydrogen bonds : bond 0.06359 / 4.27 ( 851) hydrogen bonds : angle 4.44392 / 3.15 ( 2145) metal coordination : bond 0.02126 / 1.71 ( 12) metal coordination : angle 8.36745 / 7.35 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 543 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 SER cc_start: 0.8652 (t) cc_final: 0.8221 (p) REVERT: C 110 ASN cc_start: 0.7411 (t0) cc_final: 0.7116 (p0) REVERT: D 110 GLU cc_start: 0.7845 (mp0) cc_final: 0.7600 (mp0) REVERT: E 59 GLU cc_start: 0.6592 (pm20) cc_final: 0.6332 (pm20) REVERT: G 38 ASN cc_start: 0.7457 (m110) cc_final: 0.7245 (m-40) REVERT: G 113 SER cc_start: 0.7373 (m) cc_final: 0.7040 (p) REVERT: A 97 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7142 (mt-10) REVERT: K 303 LYS cc_start: 0.7146 (mttt) cc_final: 0.6781 (ttpp) REVERT: K 408 LYS cc_start: 0.4746 (OUTLIER) cc_final: 0.4369 (tptt) REVERT: K 446 VAL cc_start: 0.8487 (m) cc_final: 0.8122 (t) REVERT: K 485 ASP cc_start: 0.7727 (m-30) cc_final: 0.7495 (m-30) outliers start: 8 outliers final: 7 residues processed: 148 average time/residue: 0.3504 time to fit residues: 71.0765 Evaluate side-chains 135 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 368 SER Chi-restraints excluded: chain K residue 378 ARG Chi-restraints excluded: chain K residue 408 LYS Chi-restraints excluded: chain K residue 472 HIS Chi-restraints excluded: chain K residue 492 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: [60, 32, 45, 24, 128, 35, 10, 88, 50, 68, 101] chunk 60 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 45 optimal weight: 0.3980 chunk 24 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 88 optimal weight: 40.0000 chunk 50 optimal weight: 6.9990 chunk 68 optimal weight: 40.0000 chunk 101 optimal weight: 4.9990 overall best weight: 6.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN K 200 ASN K 365 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.117272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.083274 restraints weight = 144907.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.082926 restraints weight = 81232.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.083522 restraints weight = 63370.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.083881 restraints weight = 52446.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.083939 restraints weight = 52053.020| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 16737 Z= 0.316 Angle : 0.760 10.226 23832 Z= 0.449 Chirality : 0.045 0.175 2650 Planarity : 0.007 0.073 2054 Dihedral : 28.157 84.983 4571 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.72 % Allowed : 7.56 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.23), residues: 1225 helix: 1.12 (0.21), residues: 597 sheet: -1.15 (0.56), residues: 83 loop : -0.79 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 116 TYR 0.040 0.002 TYR K 418 PHE 0.010 0.002 PHE K 273 TRP 0.009 0.001 TRP K 565 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.32 (16725) covalent geometry : angle 0.74124 / 0.45 (23817) hydrogen bonds : bond 0.06961 / 4.75 ( 851) hydrogen bonds : angle 4.51011 / 3.21 ( 2145) metal coordination : bond 0.01201 / 0.90 ( 12) metal coordination : angle 6.76491 / 4.85 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 543 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 SER cc_start: 0.8890 (t) cc_final: 0.8518 (p) REVERT: B 53 GLU cc_start: 0.7099 (tp30) cc_final: 0.6857 (tp30) REVERT: C 110 ASN cc_start: 0.7457 (t0) cc_final: 0.7121 (p0) REVERT: D 56 MET cc_start: 0.6999 (tpp) cc_final: 0.6638 (tpp) REVERT: K 303 LYS cc_start: 0.7081 (mttt) cc_final: 0.6862 (ttpp) outliers start: 18 outliers final: 14 residues processed: 132 average time/residue: 0.3307 time to fit residues: 60.4350 Evaluate side-chains 122 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 368 SER Chi-restraints excluded: chain K residue 378 ARG Chi-restraints excluded: chain K residue 436 VAL Chi-restraints excluded: chain K residue 453 SER Chi-restraints excluded: chain K residue 460 LEU Chi-restraints excluded: chain K residue 461 VAL Chi-restraints excluded: chain K residue 472 HIS Chi-restraints excluded: chain K residue 492 THR Chi-restraints excluded: chain K residue 611 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: [41, 53, 56, 102, 76, 80, 20, 93, 104, 4, 31] chunk 41 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 102 optimal weight: 40.0000 chunk 76 optimal weight: 50.0000 chunk 80 optimal weight: 50.0000 chunk 20 optimal weight: 30.0000 chunk 93 optimal weight: 0.4980 chunk 104 optimal weight: 30.0000 chunk 4 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 505 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.118639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.085872 restraints weight = 143880.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.086364 restraints weight = 80553.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.086624 restraints weight = 55480.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.087248 restraints weight = 48228.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.087305 restraints weight = 45663.571| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16737 Z= 0.167 Angle : 0.639 8.663 23832 Z= 0.391 Chirality : 0.041 0.141 2650 Planarity : 0.005 0.062 2054 Dihedral : 28.054 79.826 4567 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.77 % Allowed : 9.19 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.23), residues: 1225 helix: 1.54 (0.21), residues: 597 sheet: -1.27 (0.52), residues: 93 loop : -0.67 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 71 TYR 0.014 0.001 TYR B 51 PHE 0.009 0.001 PHE K 273 TRP 0.005 0.001 TRP K 430 HIS 0.011 0.001 HIS K 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.17 (16725) covalent geometry : angle 0.62597 / 0.39 (23817) hydrogen bonds : bond 0.05045 / 3.42 ( 851) hydrogen bonds : angle 4.07126 / 2.90 ( 2145) metal coordination : bond 0.00725 / 0.55 ( 12) metal coordination : angle 5.15056 / 3.80 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 543 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 SER cc_start: 0.8829 (t) cc_final: 0.8404 (p) REVERT: B 53 GLU cc_start: 0.7051 (tp30) cc_final: 0.6815 (tp30) REVERT: C 110 ASN cc_start: 0.7403 (t0) cc_final: 0.7062 (p0) REVERT: D 56 MET cc_start: 0.7093 (tpp) cc_final: 0.6725 (tpp) REVERT: A 97 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6995 (mt-10) outliers start: 8 outliers final: 8 residues processed: 122 average time/residue: 0.3522 time to fit residues: 58.6114 Evaluate side-chains 117 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 368 SER Chi-restraints excluded: chain K residue 378 ARG Chi-restraints excluded: chain K residue 410 CYS Chi-restraints excluded: chain K residue 472 HIS Chi-restraints excluded: chain K residue 492 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: [24, 130, 77, 102, 134, 71, 5, 95, 23, 103, 76] chunk 24 optimal weight: 10.0000 chunk 130 optimal weight: 0.2980 chunk 77 optimal weight: 50.0000 chunk 102 optimal weight: 0.6980 chunk 134 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 5 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 76 optimal weight: 50.0000 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 505 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.118202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.087651 restraints weight = 144039.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.087788 restraints weight = 95881.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.088715 restraints weight = 67854.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.088645 restraints weight = 58457.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.088633 restraints weight = 58950.917| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16737 Z= 0.196 Angle : 0.638 7.505 23832 Z= 0.388 Chirality : 0.041 0.146 2650 Planarity : 0.005 0.058 2054 Dihedral : 28.085 81.250 4567 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.24 % Allowed : 9.38 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.24), residues: 1225 helix: 1.77 (0.21), residues: 597 sheet: -1.30 (0.53), residues: 88 loop : -0.62 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 116 TYR 0.013 0.001 TYR B 51 PHE 0.009 0.001 PHE K 273 TRP 0.006 0.001 TRP K 430 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.20 (16725) covalent geometry : angle 0.62645 / 0.39 (23817) hydrogen bonds : bond 0.04896 / 3.34 ( 851) hydrogen bonds : angle 3.96799 / 2.82 ( 2145) metal coordination : bond 0.00507 / 0.32 ( 12) metal coordination : angle 4.75335 / 3.37 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 543 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 SER cc_start: 0.8755 (t) cc_final: 0.8319 (p) REVERT: B 53 GLU cc_start: 0.7054 (tp30) cc_final: 0.6820 (tp30) REVERT: C 112 GLN cc_start: 0.7208 (mm-40) cc_final: 0.6997 (mp10) REVERT: D 56 MET cc_start: 0.7245 (tpp) cc_final: 0.6853 (tpp) REVERT: D 65 ASP cc_start: 0.7427 (t0) cc_final: 0.7018 (m-30) REVERT: A 49 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7916 (ttp80) REVERT: A 97 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6830 (mt-10) REVERT: K 378 ARG cc_start: 0.5209 (OUTLIER) cc_final: 0.4708 (mtm180) outliers start: 13 outliers final: 10 residues processed: 121 average time/residue: 0.3405 time to fit residues: 56.9573 Evaluate side-chains 117 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 368 SER Chi-restraints excluded: chain K residue 378 ARG Chi-restraints excluded: chain K residue 436 VAL Chi-restraints excluded: chain K residue 472 HIS Chi-restraints excluded: chain K residue 492 THR Chi-restraints excluded: chain K residue 503 ASN Chi-restraints excluded: chain K residue 505 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: [143, 114, 129, 124, 20, 34, 38, 100, 72, 76, 117] chunk 143 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 chunk 20 optimal weight: 50.0000 chunk 34 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 76 optimal weight: 50.0000 chunk 117 optimal weight: 9.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN H 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.115808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.085431 restraints weight = 144975.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.085187 restraints weight = 115485.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.086269 restraints weight = 78077.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.086579 restraints weight = 62337.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.086758 restraints weight = 63519.226| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 16737 Z= 0.419 Angle : 0.829 9.504 23832 Z= 0.478 Chirality : 0.048 0.204 2650 Planarity : 0.007 0.082 2054 Dihedral : 28.430 81.411 4567 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.34 % Allowed : 10.05 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.23), residues: 1225 helix: 0.97 (0.21), residues: 597 sheet: -0.98 (0.59), residues: 78 loop : -1.13 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 36 TYR 0.020 0.003 TYR A 54 PHE 0.013 0.002 PHE F 100 TRP 0.008 0.002 TRP K 576 HIS 0.009 0.002 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00837 / 0.42 (16725) covalent geometry : angle 0.81956 / 0.48 (23817) hydrogen bonds : bond 0.07217 / 4.92 ( 851) hydrogen bonds : angle 4.52893 / 3.23 ( 2145) metal coordination : bond 0.02571 / 1.35 ( 12) metal coordination : angle 5.15566 / 2.94 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 543 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 SER cc_start: 0.8853 (t) cc_final: 0.8459 (p) REVERT: D 56 MET cc_start: 0.7266 (tpp) cc_final: 0.6924 (tpp) REVERT: A 97 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6978 (mt-10) outliers start: 14 outliers final: 11 residues processed: 116 average time/residue: 0.3280 time to fit residues: 53.4546 Evaluate side-chains 110 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 368 SER Chi-restraints excluded: chain K residue 378 ARG Chi-restraints excluded: chain K residue 436 VAL Chi-restraints excluded: chain K residue 461 VAL Chi-restraints excluded: chain K residue 472 HIS Chi-restraints excluded: chain K residue 492 THR Chi-restraints excluded: chain K residue 503 ASN Chi-restraints excluded: chain K residue 611 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: [32, 47, 100, 81, 36, 122, 95, 109, 16, 101, 79] chunk 32 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 81 optimal weight: 40.0000 chunk 36 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 79 optimal weight: 50.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.117593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.084436 restraints weight = 144381.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.084544 restraints weight = 79448.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.085119 restraints weight = 60076.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.085624 restraints weight = 52987.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.085583 restraints weight = 47878.150| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16737 Z= 0.193 Angle : 0.659 13.046 23832 Z= 0.393 Chirality : 0.042 0.246 2650 Planarity : 0.005 0.075 2054 Dihedral : 28.364 86.060 4567 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.05 % Allowed : 11.00 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.24), residues: 1225 helix: 1.30 (0.21), residues: 603 sheet: -1.07 (0.57), residues: 83 loop : -0.95 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 39 TYR 0.014 0.001 TYR B 51 PHE 0.027 0.002 PHE K 152 TRP 0.007 0.001 TRP K 430 HIS 0.007 0.001 HIS K 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.19 (16725) covalent geometry : angle 0.63622 / 0.39 (23817) hydrogen bonds : bond 0.05149 / 3.52 ( 851) hydrogen bonds : angle 4.11523 / 2.93 ( 2145) metal coordination : bond 0.01828 / 0.98 ( 12) metal coordination : angle 6.88761 / 3.87 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 543 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 SER cc_start: 0.8937 (t) cc_final: 0.8437 (p) REVERT: D 56 MET cc_start: 0.7184 (tpp) cc_final: 0.6865 (tpp) REVERT: A 97 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6952 (mt-10) REVERT: K 378 ARG cc_start: 0.5346 (ttm110) cc_final: 0.4663 (mtm180) outliers start: 11 outliers final: 10 residues processed: 109 average time/residue: 0.3368 time to fit residues: 51.3905 Evaluate side-chains 104 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 368 SER Chi-restraints excluded: chain K residue 436 VAL Chi-restraints excluded: chain K residue 492 THR Chi-restraints excluded: chain K residue 503 ASN Chi-restraints excluded: chain K residue 508 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: [35, 146, 121, 144, 23, 56, 44, 18, 103, 141, 30] chunk 35 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 30.0000 chunk 103 optimal weight: 20.0000 chunk 141 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 505 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.116845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.085802 restraints weight = 144601.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.085779 restraints weight = 97784.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.086631 restraints weight = 67386.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.086723 restraints weight = 57739.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.086838 restraints weight = 57083.490| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16737 Z= 0.252 Angle : 0.691 11.640 23832 Z= 0.407 Chirality : 0.043 0.165 2650 Planarity : 0.006 0.079 2054 Dihedral : 28.410 87.790 4567 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.24 % Allowed : 11.39 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.24), residues: 1225 helix: 1.39 (0.21), residues: 597 sheet: -1.20 (0.57), residues: 73 loop : -0.96 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 534 TYR 0.017 0.002 TYR K 418 PHE 0.017 0.002 PHE K 152 TRP 0.007 0.001 TRP K 430 HIS 0.006 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.25 (16725) covalent geometry : angle 0.67418 / 0.41 (23817) hydrogen bonds : bond 0.05460 / 3.73 ( 851) hydrogen bonds : angle 4.15552 / 2.95 ( 2145) metal coordination : bond 0.01252 / 0.69 ( 12) metal coordination : angle 5.99588 / 3.33 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 543 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 SER cc_start: 0.8739 (t) cc_final: 0.8317 (p) REVERT: D 56 MET cc_start: 0.7259 (tpp) cc_final: 0.6909 (tpp) REVERT: A 97 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6836 (mt-10) REVERT: K 368 SER cc_start: 0.6555 (OUTLIER) cc_final: 0.6258 (t) outliers start: 13 outliers final: 12 residues processed: 104 average time/residue: 0.2946 time to fit residues: 44.1839 Evaluate side-chains 107 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 368 SER Chi-restraints excluded: chain K residue 436 VAL Chi-restraints excluded: chain K residue 461 VAL Chi-restraints excluded: chain K residue 472 HIS Chi-restraints excluded: chain K residue 492 THR Chi-restraints excluded: chain K residue 503 ASN Chi-restraints excluded: chain K residue 505 ASN Chi-restraints excluded: chain K residue 508 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: [105, 15, 101, 51, 59, 137, 33, 104, 11, 76, 81] chunk 105 optimal weight: 30.0000 chunk 15 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 76 optimal weight: 50.0000 chunk 81 optimal weight: 40.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN K 505 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.116806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.085728 restraints weight = 144491.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.085797 restraints weight = 104249.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.086641 restraints weight = 73640.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.086700 restraints weight = 62986.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.086817 restraints weight = 57847.598| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16737 Z= 0.249 Angle : 0.681 11.657 23832 Z= 0.404 Chirality : 0.042 0.160 2650 Planarity : 0.006 0.067 2054 Dihedral : 28.444 88.948 4567 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.44 % Allowed : 11.10 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.24), residues: 1225 helix: 1.38 (0.21), residues: 597 sheet: -1.18 (0.59), residues: 67 loop : -1.07 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 247 TYR 0.014 0.002 TYR B 51 PHE 0.041 0.002 PHE K 152 TRP 0.006 0.001 TRP K 430 HIS 0.008 0.001 HIS K 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.25 (16725) covalent geometry : angle 0.66483 / 0.40 (23817) hydrogen bonds : bond 0.05428 / 3.72 ( 851) hydrogen bonds : angle 4.07238 / 2.93 ( 2145) metal coordination : bond 0.01142 / 0.63 ( 12) metal coordination : angle 5.91565 / 3.26 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 543 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 SER cc_start: 0.8732 (t) cc_final: 0.8317 (p) REVERT: D 56 MET cc_start: 0.7266 (tpp) cc_final: 0.6893 (tpp) REVERT: A 97 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6858 (mt-10) REVERT: K 368 SER cc_start: 0.6488 (OUTLIER) cc_final: 0.6207 (t) REVERT: K 547 TYR cc_start: 0.3523 (OUTLIER) cc_final: 0.2523 (m-80) outliers start: 15 outliers final: 12 residues processed: 106 average time/residue: 0.3025 time to fit residues: 46.6543 Evaluate side-chains 104 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 368 SER Chi-restraints excluded: chain K residue 436 VAL Chi-restraints excluded: chain K residue 472 HIS Chi-restraints excluded: chain K residue 474 ASN Chi-restraints excluded: chain K residue 492 THR Chi-restraints excluded: chain K residue 503 ASN Chi-restraints excluded: chain K residue 505 ASN Chi-restraints excluded: chain K residue 508 LEU Chi-restraints excluded: chain K residue 547 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: [98, 15, 108, 133, 53, 137, 135, 54, 145, 36, 45] chunk 98 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 108 optimal weight: 30.0000 chunk 133 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 137 optimal weight: 0.0970 chunk 135 optimal weight: 9.9990 chunk 54 optimal weight: 0.0060 chunk 145 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 505 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.118300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.087385 restraints weight = 144288.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.087665 restraints weight = 92683.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.088469 restraints weight = 63788.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.088441 restraints weight = 53621.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.088463 restraints weight = 53149.223| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16737 Z= 0.140 Angle : 0.614 11.560 23832 Z= 0.373 Chirality : 0.041 0.231 2650 Planarity : 0.005 0.057 2054 Dihedral : 28.334 92.899 4567 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.84 % Favored : 96.08 % Rotamer: Outliers : 0.96 % Allowed : 11.48 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.24), residues: 1225 helix: 1.75 (0.21), residues: 597 sheet: -1.07 (0.59), residues: 70 loop : -0.81 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 484 TYR 0.013 0.001 TYR H 37 PHE 0.032 0.002 PHE K 152 TRP 0.007 0.001 TRP K 590 HIS 0.006 0.001 HIS K 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.14 (16725) covalent geometry : angle 0.59732 / 0.37 (23817) hydrogen bonds : bond 0.04585 / 3.15 ( 851) hydrogen bonds : angle 3.72115 / 2.68 ( 2145) metal coordination : bond 0.01054 / 0.58 ( 12) metal coordination : angle 5.66941 / 3.17 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 525 is missing expected H atoms. Skipping. Residue LYS 543 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue LYS 599 is missing expected H atoms. Skipping. Residue LYS 600 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 SER cc_start: 0.8671 (t) cc_final: 0.8267 (p) REVERT: C 112 GLN cc_start: 0.7491 (mm-40) cc_final: 0.7009 (mp10) REVERT: D 56 MET cc_start: 0.7217 (tpp) cc_final: 0.6867 (tpp) REVERT: A 97 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6687 (mt-10) REVERT: K 368 SER cc_start: 0.6365 (OUTLIER) cc_final: 0.6074 (t) outliers start: 10 outliers final: 7 residues processed: 103 average time/residue: 0.3071 time to fit residues: 44.9957 Evaluate side-chains 100 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain K residue 266 LEU Chi-restraints excluded: chain K residue 368 SER Chi-restraints excluded: chain K residue 474 ASN Chi-restraints excluded: chain K residue 503 ASN Chi-restraints excluded: chain K residue 508 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: [147, 53, 109, 88, 30, 112, 97, 20, 89, 96, 92] chunk 147 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 88 optimal weight: 40.0000 chunk 30 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 20 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 96 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 505 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.117682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.086577 restraints weight = 146117.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.086754 restraints weight = 96164.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.087287 restraints weight = 72131.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.087411 restraints weight = 61195.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.087548 restraints weight = 58546.687| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16737 Z= 0.178 Angle : 0.625 11.173 23832 Z= 0.376 Chirality : 0.040 0.143 2650 Planarity : 0.005 0.060 2054 Dihedral : 28.302 93.069 4567 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.86 % Allowed : 11.77 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.24), residues: 1225 helix: 1.85 (0.21), residues: 597 sheet: -1.09 (0.59), residues: 70 loop : -0.81 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 35 TYR 0.011 0.001 TYR K 478 PHE 0.029 0.001 PHE K 152 TRP 0.007 0.001 TRP K 430 HIS 0.004 0.001 HIS K 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.18 (16725) covalent geometry : angle 0.61018 / 0.37 (23817) hydrogen bonds : bond 0.04649 / 3.17 ( 851) hydrogen bonds : angle 3.83144 / 2.72 ( 2145) metal coordination : bond 0.00960 / 0.53 ( 12) metal coordination : angle 5.37674 / 2.96 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4937.87 seconds wall clock time: 84 minutes 34.13 seconds (5074.13 seconds total)