Starting phenix.real_space_refine on Wed Mar 4 11:52:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a08_11601/03_2026/7a08_11601.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a08_11601/03_2026/7a08_11601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7a08_11601/03_2026/7a08_11601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a08_11601/03_2026/7a08_11601.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7a08_11601/03_2026/7a08_11601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a08_11601/03_2026/7a08_11601.map" } resolution = 3.11 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= 0.007 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 262 5.49 5 S 23 5.16 5 C 7994 2.51 5 N 2569 2.21 5 O 3120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13969 Number of models: 1 Model: "" Number of chains: 12 Chain: "a" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2977 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 15, 'TRANS': 344} Chain: "I" Number of atoms: 2691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2691 Classifications: {'DNA': 132} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 131} Chain: "J" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2698 Classifications: {'DNA': 131} Link IDs: {'rna3p': 130} Chain: "b" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 808 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "c" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "d" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 780 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "e" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 618 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "f" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 717 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "g" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "h" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 628 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain: "i" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1987 SG CYS a 392 76.301 40.287 17.746 1.00 76.33 S Time building chain proxies: 2.71, per 1000 atoms: 0.19 Number of scatterers: 13969 At special positions: 0 Unit cell: (113.313, 120.726, 122.844, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 23 16.00 P 262 15.00 O 3120 8.00 N 2569 7.00 C 7994 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS a 397 " - pdb=" SG CYS a 448 " distance=2.04 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: 0.90 Conformation dependent library (CDL) restraints added in 410.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 601 " pdb="ZN ZN a 601 " - pdb=" SG CYS a 392 " 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2008 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 12 sheets defined 62.2% alpha, 6.6% beta 93 base pairs and 224 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'a' and resid 148 through 185 removed outlier: 4.207A pdb=" N THR a 170 " --> pdb=" O GLU a 166 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS a 173 " --> pdb=" O GLU a 169 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG a 177 " --> pdb=" O LYS a 173 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ARG a 180 " --> pdb=" O GLU a 176 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ARG a 181 " --> pdb=" O ARG a 177 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N MET a 182 " --> pdb=" O LEU a 178 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN a 183 " --> pdb=" O LEU a 179 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS a 184 " --> pdb=" O ARG a 180 " (cutoff:3.500A) Processing helix chain 'a' and resid 258 through 277 removed outlier: 3.696A pdb=" N MET a 262 " --> pdb=" O SER a 258 " (cutoff:3.500A) Processing helix chain 'a' and resid 319 through 323 removed outlier: 3.814A pdb=" N LYS a 323 " --> pdb=" O ILE a 320 " (cutoff:3.500A) Processing helix chain 'a' and resid 328 through 333 Processing helix chain 'a' and resid 333 through 339 Processing helix chain 'a' and resid 367 through 377 Processing helix chain 'a' and resid 394 through 412 Processing helix chain 'a' and resid 413 through 418 removed outlier: 3.668A pdb=" N ALA a 417 " --> pdb=" O GLU a 414 " (cutoff:3.500A) Processing helix chain 'a' and resid 420 through 432 removed outlier: 3.978A pdb=" N LYS a 424 " --> pdb=" O SER a 420 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR a 432 " --> pdb=" O PHE a 428 " (cutoff:3.500A) Processing helix chain 'a' and resid 444 through 463 Processing helix chain 'a' and resid 482 through 498 removed outlier: 4.135A pdb=" N LYS a 486 " --> pdb=" O ASP a 482 " (cutoff:3.500A) Processing helix chain 'a' and resid 501 through 505 Processing helix chain 'b' and resid 16 through 21 removed outlier: 3.582A pdb=" N ARG b 20 " --> pdb=" O SER b 16 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA b 21 " --> pdb=" O ARG b 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 16 through 21' Processing helix chain 'b' and resid 26 through 37 Processing helix chain 'b' and resid 46 through 73 removed outlier: 3.676A pdb=" N LEU b 65 " --> pdb=" O GLU b 61 " (cutoff:3.500A) Processing helix chain 'b' and resid 90 through 97 Processing helix chain 'c' and resid 37 through 48 removed outlier: 3.588A pdb=" N GLN c 47 " --> pdb=" O LYS c 43 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL c 48 " --> pdb=" O VAL c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 57 through 84 removed outlier: 3.559A pdb=" N GLU c 71 " --> pdb=" O ASN c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 90 through 102 removed outlier: 3.620A pdb=" N THR c 96 " --> pdb=" O ARG c 92 " (cutoff:3.500A) Processing helix chain 'c' and resid 104 through 115 removed outlier: 3.750A pdb=" N LYS c 108 " --> pdb=" O GLY c 104 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL c 111 " --> pdb=" O ALA c 107 " (cutoff:3.500A) Processing helix chain 'c' and resid 115 through 123 removed outlier: 3.712A pdb=" N LYS c 120 " --> pdb=" O LYS c 116 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR c 122 " --> pdb=" O VAL c 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 44 through 50 removed outlier: 3.917A pdb=" N GLU d 50 " --> pdb=" O VAL d 46 " (cutoff:3.500A) Processing helix chain 'd' and resid 50 through 55 removed outlier: 3.641A pdb=" N TYR d 54 " --> pdb=" O GLU d 50 " (cutoff:3.500A) Processing helix chain 'd' and resid 63 through 76 Processing helix chain 'd' and resid 85 through 114 removed outlier: 3.551A pdb=" N ALA d 98 " --> pdb=" O GLU d 94 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR d 99 " --> pdb=" O ALA d 95 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU d 109 " --> pdb=" O GLU d 105 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA d 114 " --> pdb=" O CYS d 110 " (cutoff:3.500A) Processing helix chain 'd' and resid 120 through 131 removed outlier: 3.680A pdb=" N ARG d 131 " --> pdb=" O ALA d 127 " (cutoff:3.500A) Processing helix chain 'e' and resid 25 through 29 Processing helix chain 'e' and resid 30 through 42 Processing helix chain 'e' and resid 50 through 76 removed outlier: 3.626A pdb=" N GLY e 56 " --> pdb=" O GLU e 52 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP e 68 " --> pdb=" O ASN e 64 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA e 76 " --> pdb=" O TYR e 72 " (cutoff:3.500A) Processing helix chain 'e' and resid 82 through 93 removed outlier: 3.587A pdb=" N GLN e 93 " --> pdb=" O ALA e 89 " (cutoff:3.500A) Processing helix chain 'f' and resid 16 through 22 Processing helix chain 'f' and resid 26 through 36 Processing helix chain 'f' and resid 46 through 74 removed outlier: 3.654A pdb=" N ASN f 68 " --> pdb=" O GLU f 64 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP f 72 " --> pdb=" O ASN f 68 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN f 73 " --> pdb=" O ALA f 69 " (cutoff:3.500A) Processing helix chain 'f' and resid 79 through 90 Processing helix chain 'f' and resid 92 through 97 Processing helix chain 'g' and resid 39 through 49 removed outlier: 3.636A pdb=" N GLN g 47 " --> pdb=" O LYS g 43 " (cutoff:3.500A) Processing helix chain 'g' and resid 55 through 84 removed outlier: 3.819A pdb=" N ARG g 79 " --> pdb=" O GLY g 75 " (cutoff:3.500A) Processing helix chain 'g' and resid 90 through 102 removed outlier: 3.692A pdb=" N THR g 96 " --> pdb=" O ARG g 92 " (cutoff:3.500A) Processing helix chain 'g' and resid 104 through 122 removed outlier: 3.822A pdb=" N SER g 112 " --> pdb=" O LYS g 108 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA g 117 " --> pdb=" O GLU g 113 " (cutoff:3.500A) Processing helix chain 'h' and resid 63 through 76 Processing helix chain 'h' and resid 86 through 113 removed outlier: 3.615A pdb=" N GLY h 90 " --> pdb=" O SER h 86 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU h 92 " --> pdb=" O ALA h 88 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA h 98 " --> pdb=" O GLU h 94 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU h 109 " --> pdb=" O GLU h 105 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N CYS h 110 " --> pdb=" O ASP h 106 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA h 111 " --> pdb=" O THR h 107 " (cutoff:3.500A) Processing helix chain 'h' and resid 124 through 130 removed outlier: 3.514A pdb=" N ARG h 128 " --> pdb=" O ILE h 124 " (cutoff:3.500A) Processing helix chain 'i' and resid 25 through 29 Processing helix chain 'i' and resid 30 through 41 Processing helix chain 'i' and resid 49 through 77 removed outlier: 3.804A pdb=" N GLY i 56 " --> pdb=" O GLU i 52 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL i 60 " --> pdb=" O GLY i 56 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN i 64 " --> pdb=" O VAL i 60 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP i 68 " --> pdb=" O ASN i 64 " (cutoff:3.500A) Processing helix chain 'i' and resid 82 through 93 removed outlier: 3.566A pdb=" N VAL i 86 " --> pdb=" O THR i 82 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN i 93 " --> pdb=" O ALA i 89 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 193 through 194 removed outlier: 3.505A pdb=" N GLU a 193 " --> pdb=" O LYS a 217 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL a 214 " --> pdb=" O ILE a 309 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ALA a 311 " --> pdb=" O VAL a 214 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N PHE a 216 " --> pdb=" O ALA a 311 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLU a 313 " --> pdb=" O PHE a 216 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU a 218 " --> pdb=" O GLU a 313 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE a 308 " --> pdb=" O VAL a 294 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL a 294 " --> pdb=" O ILE a 308 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 193 through 194 removed outlier: 3.505A pdb=" N GLU a 193 " --> pdb=" O LYS a 217 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL a 214 " --> pdb=" O ILE a 309 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ALA a 311 " --> pdb=" O VAL a 214 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N PHE a 216 " --> pdb=" O ALA a 311 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLU a 313 " --> pdb=" O PHE a 216 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU a 218 " --> pdb=" O GLU a 313 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LEU a 310 " --> pdb=" O PRO a 349 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 223 through 226 Processing sheet with id=AA4, first strand: chain 'b' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'b' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'd' and resid 83 through 84 removed outlier: 7.177A pdb=" N ARG d 83 " --> pdb=" O VAL i 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'd' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'e' and resid 45 through 46 removed outlier: 7.588A pdb=" N ARG e 45 " --> pdb=" O ILE h 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'e' and resid 80 through 81 Processing sheet with id=AB1, first strand: chain 'e' and resid 96 through 98 removed outlier: 6.706A pdb=" N THR e 96 " --> pdb=" O THR f 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'f' and resid 42 through 43 removed outlier: 7.148A pdb=" N ARG f 42 " --> pdb=" O ILE g 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'f' and resid 77 through 78 454 hydrogen bonds defined for protein. 1326 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 235 hydrogen bonds 470 hydrogen bond angles 0 basepair planarities 93 basepair parallelities 224 stacking parallelities Total time for adding SS restraints: 2.95 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3726 1.34 - 1.46: 4721 1.46 - 1.59: 5759 1.59 - 1.71: 517 1.71 - 1.84: 36 Bond restraints: 14759 Sorted by residual: bond pdb=" C1' DG I -70 " pdb=" N9 DG I -70 " ideal model delta sigma weight residual 1.460 1.397 0.063 2.00e-02 2.50e+03 9.98e+00 bond pdb=" C1' DA J 72 " pdb=" N9 DA J 72 " ideal model delta sigma weight residual 1.460 1.398 0.062 2.00e-02 2.50e+03 9.72e+00 bond pdb=" N GLU a 313 " pdb=" CA GLU a 313 " ideal model delta sigma weight residual 1.456 1.421 0.036 1.21e-02 6.83e+03 8.66e+00 bond pdb=" C1' DG J 33 " pdb=" N9 DG J 33 " ideal model delta sigma weight residual 1.460 1.405 0.055 2.00e-02 2.50e+03 7.59e+00 bond pdb=" C1' DG I -71 " pdb=" N9 DG I -71 " ideal model delta sigma weight residual 1.460 1.407 0.053 2.00e-02 2.50e+03 6.92e+00 ... (remaining 14754 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 20458 1.85 - 3.71: 552 3.71 - 5.56: 20 5.56 - 7.41: 2 7.41 - 9.26: 1 Bond angle restraints: 21033 Sorted by residual: angle pdb=" N LYS c 57 " pdb=" CA LYS c 57 " pdb=" C LYS c 57 " ideal model delta sigma weight residual 113.88 109.71 4.17 1.23e+00 6.61e-01 1.15e+01 angle pdb=" N LEU a 445 " pdb=" CA LEU a 445 " pdb=" CB LEU a 445 " ideal model delta sigma weight residual 110.22 105.54 4.68 1.54e+00 4.22e-01 9.24e+00 angle pdb=" N ASN a 300 " pdb=" CA ASN a 300 " pdb=" C ASN a 300 " ideal model delta sigma weight residual 109.81 103.18 6.63 2.21e+00 2.05e-01 9.00e+00 angle pdb=" CA VAL a 220 " pdb=" C VAL a 220 " pdb=" N PRO a 221 " ideal model delta sigma weight residual 116.57 119.40 -2.83 9.80e-01 1.04e+00 8.36e+00 angle pdb=" N ARG a 394 " pdb=" CA ARG a 394 " pdb=" C ARG a 394 " ideal model delta sigma weight residual 113.18 109.39 3.79 1.33e+00 5.65e-01 8.13e+00 ... (remaining 21028 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.74: 6957 34.74 - 69.47: 1218 69.47 - 104.21: 43 104.21 - 138.94: 0 138.94 - 173.68: 4 Dihedral angle restraints: 8222 sinusoidal: 5114 harmonic: 3108 Sorted by residual: dihedral pdb=" CB CYS a 397 " pdb=" SG CYS a 397 " pdb=" SG CYS a 448 " pdb=" CB CYS a 448 " ideal model delta sinusoidal sigma weight residual 93.00 139.31 -46.31 1 1.00e+01 1.00e-02 2.97e+01 dihedral pdb=" CA ASP h 123 " pdb=" C ASP h 123 " pdb=" N ILE h 124 " pdb=" CA ILE h 124 " ideal model delta harmonic sigma weight residual 180.00 159.53 20.47 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" C4' DG I -53 " pdb=" C3' DG I -53 " pdb=" O3' DG I -53 " pdb=" P DG I -52 " ideal model delta sinusoidal sigma weight residual 220.00 46.32 173.68 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 8219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1352 0.033 - 0.065: 688 0.065 - 0.098: 250 0.098 - 0.130: 70 0.130 - 0.163: 8 Chirality restraints: 2368 Sorted by residual: chirality pdb=" CA ASN a 300 " pdb=" N ASN a 300 " pdb=" C ASN a 300 " pdb=" CB ASN a 300 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" C1' DG I -70 " pdb=" O4' DG I -70 " pdb=" C2' DG I -70 " pdb=" N9 DG I -70 " both_signs ideal model delta sigma weight residual False 2.42 2.26 0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" C1' DA I -32 " pdb=" O4' DA I -32 " pdb=" C2' DA I -32 " pdb=" N9 DA I -32 " both_signs ideal model delta sigma weight residual False 2.42 2.26 0.16 2.00e-01 2.50e+01 6.27e-01 ... (remaining 2365 not shown) Planarity restraints: 1755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE a 449 " -0.020 2.00e-02 2.50e+03 1.51e-02 3.98e+00 pdb=" CG PHE a 449 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE a 449 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE a 449 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE a 449 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE a 449 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE a 449 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT J 32 " 0.022 2.00e-02 2.50e+03 1.13e-02 3.21e+00 pdb=" N1 DT J 32 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DT J 32 " -0.005 2.00e-02 2.50e+03 pdb=" O2 DT J 32 " -0.013 2.00e-02 2.50e+03 pdb=" N3 DT J 32 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT J 32 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT J 32 " 0.018 2.00e-02 2.50e+03 pdb=" C5 DT J 32 " -0.007 2.00e-02 2.50e+03 pdb=" C7 DT J 32 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DT J 32 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER a 291 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.59e+00 pdb=" N PRO a 292 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO a 292 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO a 292 " 0.022 5.00e-02 4.00e+02 ... (remaining 1752 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 72 2.53 - 3.12: 10230 3.12 - 3.72: 22504 3.72 - 4.31: 35011 4.31 - 4.90: 51127 Nonbonded interactions: 118944 Sorted by model distance: nonbonded pdb=" OG1 THR h 107 " pdb=" O ASP h 123 " model vdw 1.939 3.040 nonbonded pdb=" OG1 THR i 73 " pdb=" OD2 ASP i 85 " model vdw 1.982 3.040 nonbonded pdb=" OP1 DG I 48 " pdb=" OH TYR g 40 " model vdw 2.055 3.040 nonbonded pdb=" O LYS a 205 " pdb=" CG1 ILE a 206 " model vdw 2.090 3.440 nonbonded pdb=" NZ LYS a 409 " pdb=" O PHE a 418 " model vdw 2.100 3.120 ... (remaining 118939 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 'b' and resid 14 through 106) selection = chain 'f' } ncs_group { reference = (chain 'c' and resid 35 through 124) selection = chain 'g' } ncs_group { reference = chain 'e' selection = (chain 'i' and resid 24 through 100) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.810 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 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 : 0.006 0.063 14761 Z= 0.269 Angle : 0.670 9.263 21035 Z= 0.409 Chirality : 0.044 0.163 2368 Planarity : 0.004 0.040 1755 Dihedral : 26.055 173.677 6211 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.22 % Allowed : 0.11 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.24), residues: 1052 helix: -1.02 (0.20), residues: 659 sheet: -0.92 (0.76), residues: 47 loop : -2.61 (0.29), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG c 86 TYR 0.013 0.002 TYR b 57 PHE 0.033 0.002 PHE a 449 TRP 0.014 0.002 TRP a 363 HIS 0.005 0.001 HIS c 82 Details of bonding type rmsd covalent geometry : bond 0.00585 (14759) covalent geometry : angle 0.66975 (21033) SS BOND : bond 0.01012 ( 1) SS BOND : angle 1.95129 ( 2) hydrogen bonds : bond 0.22776 ( 688) hydrogen bonds : angle 8.08322 ( 1796) metal coordination : bond 0.00261 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 401 MET cc_start: 0.5012 (tpt) cc_final: 0.4803 (tpp) REVERT: b 64 GLU cc_start: 0.7542 (tt0) cc_final: 0.7219 (tt0) REVERT: b 71 ARG cc_start: 0.8074 (mtp-110) cc_final: 0.7674 (ttm-80) REVERT: i 78 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7696 (mtm-85) outliers start: 2 outliers final: 1 residues processed: 161 average time/residue: 0.1610 time to fit residues: 34.4013 Evaluate side-chains 134 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 313 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 203 HIS ** a 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 407 GLN c 84 ASN e 27 GLN ** i 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.195128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.162366 restraints weight = 14746.057| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 0.86 r_work: 0.3384 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14761 Z= 0.172 Angle : 0.624 10.423 21035 Z= 0.359 Chirality : 0.039 0.212 2368 Planarity : 0.005 0.045 1755 Dihedral : 29.540 178.654 4039 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.53 % Allowed : 6.10 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.25), residues: 1052 helix: 0.00 (0.20), residues: 658 sheet: -1.09 (0.78), residues: 45 loop : -2.06 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG c 86 TYR 0.015 0.001 TYR a 346 PHE 0.019 0.001 PHE h 67 TRP 0.019 0.002 TRP a 363 HIS 0.005 0.001 HIS a 369 Details of bonding type rmsd covalent geometry : bond 0.00382 (14759) covalent geometry : angle 0.62386 (21033) SS BOND : bond 0.01316 ( 1) SS BOND : angle 1.95701 ( 2) hydrogen bonds : bond 0.04703 ( 688) hydrogen bonds : angle 3.99229 ( 1796) metal coordination : bond 0.00122 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: a 449 PHE cc_start: 0.4938 (OUTLIER) cc_final: 0.4354 (m-80) REVERT: a 462 THR cc_start: 0.7691 (p) cc_final: 0.7404 (p) REVERT: b 71 ARG cc_start: 0.8107 (mtp-110) cc_final: 0.7803 (ttm-80) outliers start: 14 outliers final: 7 residues processed: 146 average time/residue: 0.1640 time to fit residues: 32.1779 Evaluate side-chains 131 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain a residue 297 LEU Chi-restraints excluded: chain a residue 449 PHE Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain g residue 87 SER Chi-restraints excluded: chain h residue 117 VAL Chi-restraints excluded: chain h residue 118 THR Chi-restraints excluded: chain h residue 134 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 109 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 63 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 422 HIS e 27 GLN g 47 GLN i 25 ASN i 27 GLN i 75 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.194833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.161758 restraints weight = 14909.560| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 0.77 r_work: 0.3388 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14761 Z= 0.184 Angle : 0.591 9.912 21035 Z= 0.341 Chirality : 0.037 0.141 2368 Planarity : 0.004 0.043 1755 Dihedral : 29.520 179.309 4036 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.18 % Allowed : 9.15 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.25), residues: 1052 helix: 0.44 (0.20), residues: 655 sheet: -1.02 (0.79), residues: 45 loop : -1.89 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG c 86 TYR 0.012 0.001 TYR b 57 PHE 0.016 0.001 PHE a 476 TRP 0.013 0.001 TRP a 363 HIS 0.003 0.001 HIS h 113 Details of bonding type rmsd covalent geometry : bond 0.00418 (14759) covalent geometry : angle 0.59086 (21033) SS BOND : bond 0.00936 ( 1) SS BOND : angle 1.57005 ( 2) hydrogen bonds : bond 0.04648 ( 688) hydrogen bonds : angle 3.81387 ( 1796) metal coordination : bond 0.00133 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 449 PHE cc_start: 0.5105 (OUTLIER) cc_final: 0.4388 (m-80) REVERT: b 71 ARG cc_start: 0.8097 (mtp-110) cc_final: 0.7776 (ttm-80) REVERT: h 123 ASP cc_start: 0.8010 (p0) cc_final: 0.7782 (p0) REVERT: i 78 ARG cc_start: 0.8087 (mtm-85) cc_final: 0.7691 (mtm-85) outliers start: 20 outliers final: 11 residues processed: 141 average time/residue: 0.1537 time to fit residues: 29.3527 Evaluate side-chains 137 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain a residue 297 LEU Chi-restraints excluded: chain a residue 445 LEU Chi-restraints excluded: chain a residue 449 PHE Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain g residue 64 SER Chi-restraints excluded: chain g residue 87 SER Chi-restraints excluded: chain h residue 117 VAL Chi-restraints excluded: chain h residue 118 THR Chi-restraints excluded: chain h residue 134 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 53 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 27 GLN i 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.188686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.151493 restraints weight = 14976.277| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 0.93 r_work: 0.3299 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14761 Z= 0.216 Angle : 0.612 9.754 21035 Z= 0.351 Chirality : 0.039 0.173 2368 Planarity : 0.005 0.047 1755 Dihedral : 29.635 178.823 4036 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.07 % Allowed : 11.11 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.25), residues: 1052 helix: 0.50 (0.20), residues: 654 sheet: -1.25 (0.78), residues: 47 loop : -1.75 (0.29), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG e 45 TYR 0.013 0.002 TYR b 57 PHE 0.018 0.002 PHE a 476 TRP 0.014 0.001 TRP a 363 HIS 0.004 0.001 HIS h 113 Details of bonding type rmsd covalent geometry : bond 0.00500 (14759) covalent geometry : angle 0.61225 (21033) SS BOND : bond 0.00759 ( 1) SS BOND : angle 1.69233 ( 2) hydrogen bonds : bond 0.04673 ( 688) hydrogen bonds : angle 3.81456 ( 1796) metal coordination : bond 0.00177 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 449 PHE cc_start: 0.4922 (OUTLIER) cc_final: 0.4283 (m-80) REVERT: b 71 ARG cc_start: 0.8148 (mtp-110) cc_final: 0.7792 (ttm-80) outliers start: 19 outliers final: 13 residues processed: 140 average time/residue: 0.1507 time to fit residues: 28.5380 Evaluate side-chains 138 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 204 VAL Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain a residue 297 LEU Chi-restraints excluded: chain a residue 322 THR Chi-restraints excluded: chain a residue 445 LEU Chi-restraints excluded: chain a residue 449 PHE Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain g residue 64 SER Chi-restraints excluded: chain g residue 87 SER Chi-restraints excluded: chain h residue 117 VAL Chi-restraints excluded: chain h residue 118 THR Chi-restraints excluded: chain h residue 134 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 4 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 23 optimal weight: 20.0000 chunk 85 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 359 GLN e 27 GLN i 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.194386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.162171 restraints weight = 14856.878| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 0.81 r_work: 0.3385 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14761 Z= 0.160 Angle : 0.580 10.450 21035 Z= 0.336 Chirality : 0.037 0.246 2368 Planarity : 0.004 0.045 1755 Dihedral : 29.570 178.549 4036 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.29 % Allowed : 12.64 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.25), residues: 1052 helix: 0.71 (0.21), residues: 654 sheet: -1.01 (0.78), residues: 47 loop : -1.62 (0.29), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG c 86 TYR 0.012 0.001 TYR b 57 PHE 0.015 0.001 PHE a 476 TRP 0.010 0.001 TRP a 363 HIS 0.003 0.001 HIS a 369 Details of bonding type rmsd covalent geometry : bond 0.00357 (14759) covalent geometry : angle 0.57938 (21033) SS BOND : bond 0.00772 ( 1) SS BOND : angle 1.85154 ( 2) hydrogen bonds : bond 0.04213 ( 688) hydrogen bonds : angle 3.72990 ( 1796) metal coordination : bond 0.00089 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 449 PHE cc_start: 0.4896 (OUTLIER) cc_final: 0.4325 (m-80) REVERT: b 71 ARG cc_start: 0.8110 (mtp-110) cc_final: 0.7779 (ttm-80) REVERT: d 120 MET cc_start: 0.8576 (mtt) cc_final: 0.8370 (mtt) REVERT: f 63 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8070 (mt) REVERT: i 78 ARG cc_start: 0.8007 (mtm-85) cc_final: 0.7525 (mtm180) outliers start: 21 outliers final: 11 residues processed: 138 average time/residue: 0.1575 time to fit residues: 29.3789 Evaluate side-chains 136 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain a residue 297 LEU Chi-restraints excluded: chain a residue 322 THR Chi-restraints excluded: chain a residue 445 LEU Chi-restraints excluded: chain a residue 449 PHE Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 63 LEU Chi-restraints excluded: chain g residue 87 SER Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 117 VAL Chi-restraints excluded: chain h residue 118 THR Chi-restraints excluded: chain h residue 134 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 73 optimal weight: 0.0980 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 23 optimal weight: 20.0000 chunk 127 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 407 GLN e 27 GLN i 25 ASN i 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.197370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.165335 restraints weight = 14765.953| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 0.80 r_work: 0.3428 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14761 Z= 0.142 Angle : 0.558 10.272 21035 Z= 0.325 Chirality : 0.036 0.209 2368 Planarity : 0.004 0.045 1755 Dihedral : 29.445 177.891 4036 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.07 % Allowed : 13.07 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.26), residues: 1052 helix: 1.08 (0.21), residues: 650 sheet: -0.78 (0.79), residues: 47 loop : -1.55 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG c 86 TYR 0.013 0.001 TYR a 235 PHE 0.013 0.001 PHE h 67 TRP 0.007 0.001 TRP a 363 HIS 0.003 0.001 HIS a 369 Details of bonding type rmsd covalent geometry : bond 0.00306 (14759) covalent geometry : angle 0.55822 (21033) SS BOND : bond 0.00696 ( 1) SS BOND : angle 1.64628 ( 2) hydrogen bonds : bond 0.03869 ( 688) hydrogen bonds : angle 3.61154 ( 1796) metal coordination : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 449 PHE cc_start: 0.4934 (OUTLIER) cc_final: 0.4499 (m-80) REVERT: b 71 ARG cc_start: 0.8107 (mtp-110) cc_final: 0.7790 (ttm-80) REVERT: c 67 ASN cc_start: 0.8822 (m-40) cc_final: 0.8430 (m110) REVERT: h 123 ASP cc_start: 0.8063 (p0) cc_final: 0.7792 (p0) REVERT: i 78 ARG cc_start: 0.7977 (mtm-85) cc_final: 0.7740 (mtm-85) REVERT: i 95 ARG cc_start: 0.8359 (mtt90) cc_final: 0.7993 (mtp85) outliers start: 19 outliers final: 11 residues processed: 143 average time/residue: 0.1655 time to fit residues: 31.7304 Evaluate side-chains 136 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 204 VAL Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain a residue 297 LEU Chi-restraints excluded: chain a residue 322 THR Chi-restraints excluded: chain a residue 445 LEU Chi-restraints excluded: chain a residue 449 PHE Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain g residue 87 SER Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 118 THR Chi-restraints excluded: chain h residue 134 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 81 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 125 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 27 GLN i 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.194257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.160897 restraints weight = 14868.114| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 0.81 r_work: 0.3379 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 14761 Z= 0.173 Angle : 0.569 9.964 21035 Z= 0.330 Chirality : 0.036 0.157 2368 Planarity : 0.004 0.044 1755 Dihedral : 29.435 178.509 4036 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.29 % Allowed : 12.85 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.26), residues: 1052 helix: 1.09 (0.21), residues: 651 sheet: -0.66 (0.79), residues: 47 loop : -1.51 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG g 79 TYR 0.011 0.001 TYR b 57 PHE 0.015 0.001 PHE a 476 TRP 0.009 0.001 TRP a 331 HIS 0.003 0.001 HIS h 113 Details of bonding type rmsd covalent geometry : bond 0.00392 (14759) covalent geometry : angle 0.56878 (21033) SS BOND : bond 0.00662 ( 1) SS BOND : angle 1.52943 ( 2) hydrogen bonds : bond 0.04034 ( 688) hydrogen bonds : angle 3.64040 ( 1796) metal coordination : bond 0.00233 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 449 PHE cc_start: 0.4912 (OUTLIER) cc_final: 0.4539 (m-80) REVERT: b 71 ARG cc_start: 0.8136 (mtp-110) cc_final: 0.7779 (ttm-80) REVERT: c 67 ASN cc_start: 0.8884 (m-40) cc_final: 0.8453 (m110) REVERT: d 56 LYS cc_start: 0.8269 (ttpp) cc_final: 0.8030 (ttpt) REVERT: e 92 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7907 (ttp80) REVERT: h 123 ASP cc_start: 0.8084 (p0) cc_final: 0.7824 (p0) outliers start: 21 outliers final: 14 residues processed: 137 average time/residue: 0.1551 time to fit residues: 28.6999 Evaluate side-chains 133 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 204 VAL Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain a residue 223 ILE Chi-restraints excluded: chain a residue 297 LEU Chi-restraints excluded: chain a residue 322 THR Chi-restraints excluded: chain a residue 445 LEU Chi-restraints excluded: chain a residue 449 PHE Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain e residue 92 ARG Chi-restraints excluded: chain g residue 87 SER Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 96 SER Chi-restraints excluded: chain h residue 117 VAL Chi-restraints excluded: chain h residue 118 THR Chi-restraints excluded: chain h residue 134 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 52 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 27 GLN i 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.196336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.164306 restraints weight = 14785.976| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 0.85 r_work: 0.3414 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14761 Z= 0.155 Angle : 0.565 10.204 21035 Z= 0.328 Chirality : 0.036 0.155 2368 Planarity : 0.004 0.044 1755 Dihedral : 29.421 178.496 4036 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.07 % Allowed : 12.96 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.26), residues: 1052 helix: 1.17 (0.21), residues: 651 sheet: -0.66 (0.79), residues: 47 loop : -1.47 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG g 79 TYR 0.011 0.001 TYR b 57 PHE 0.014 0.001 PHE a 476 TRP 0.008 0.001 TRP a 363 HIS 0.003 0.001 HIS i 75 Details of bonding type rmsd covalent geometry : bond 0.00346 (14759) covalent geometry : angle 0.56495 (21033) SS BOND : bond 0.00624 ( 1) SS BOND : angle 1.54105 ( 2) hydrogen bonds : bond 0.03922 ( 688) hydrogen bonds : angle 3.61232 ( 1796) metal coordination : bond 0.00109 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 449 PHE cc_start: 0.4891 (OUTLIER) cc_final: 0.4547 (m-80) REVERT: b 71 ARG cc_start: 0.8143 (mtp-110) cc_final: 0.7794 (ttm-80) REVERT: c 67 ASN cc_start: 0.8901 (m-40) cc_final: 0.8472 (m110) REVERT: d 56 LYS cc_start: 0.8280 (ttpp) cc_final: 0.8038 (ttpt) REVERT: d 133 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.6587 (mt-10) REVERT: e 92 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7897 (ttp80) REVERT: h 123 ASP cc_start: 0.8031 (p0) cc_final: 0.7796 (p0) outliers start: 19 outliers final: 14 residues processed: 131 average time/residue: 0.1615 time to fit residues: 28.2056 Evaluate side-chains 132 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 204 VAL Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain a residue 223 ILE Chi-restraints excluded: chain a residue 297 LEU Chi-restraints excluded: chain a residue 322 THR Chi-restraints excluded: chain a residue 445 LEU Chi-restraints excluded: chain a residue 449 PHE Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain d residue 133 GLU Chi-restraints excluded: chain e residue 92 ARG Chi-restraints excluded: chain g residue 87 SER Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 96 SER Chi-restraints excluded: chain h residue 117 VAL Chi-restraints excluded: chain h residue 118 THR Chi-restraints excluded: chain h residue 134 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 102 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 92 optimal weight: 0.0470 chunk 54 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 27 GLN i 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.194959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.162259 restraints weight = 14900.173| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 0.87 r_work: 0.3374 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14761 Z= 0.163 Angle : 0.560 10.397 21035 Z= 0.325 Chirality : 0.036 0.152 2368 Planarity : 0.004 0.044 1755 Dihedral : 29.368 178.063 4036 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.07 % Allowed : 13.40 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.26), residues: 1052 helix: 1.23 (0.21), residues: 651 sheet: -0.65 (0.80), residues: 47 loop : -1.46 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG g 79 TYR 0.010 0.001 TYR b 57 PHE 0.014 0.001 PHE a 476 TRP 0.008 0.001 TRP a 363 HIS 0.003 0.001 HIS h 113 Details of bonding type rmsd covalent geometry : bond 0.00366 (14759) covalent geometry : angle 0.56034 (21033) SS BOND : bond 0.00601 ( 1) SS BOND : angle 1.40084 ( 2) hydrogen bonds : bond 0.03890 ( 688) hydrogen bonds : angle 3.58033 ( 1796) metal coordination : bond 0.00086 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 449 PHE cc_start: 0.4789 (OUTLIER) cc_final: 0.4524 (m-80) REVERT: b 71 ARG cc_start: 0.8167 (mtp-110) cc_final: 0.7792 (ttm-80) REVERT: c 67 ASN cc_start: 0.8954 (m-40) cc_final: 0.8519 (m110) REVERT: d 56 LYS cc_start: 0.8286 (ttpp) cc_final: 0.8064 (ttpt) REVERT: d 133 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.6585 (mt-10) REVERT: e 92 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7910 (ttp80) REVERT: h 123 ASP cc_start: 0.8021 (p0) cc_final: 0.7778 (p0) outliers start: 19 outliers final: 13 residues processed: 140 average time/residue: 0.1496 time to fit residues: 28.5626 Evaluate side-chains 139 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 204 VAL Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain a residue 297 LEU Chi-restraints excluded: chain a residue 322 THR Chi-restraints excluded: chain a residue 445 LEU Chi-restraints excluded: chain a residue 449 PHE Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain d residue 133 GLU Chi-restraints excluded: chain e residue 92 ARG Chi-restraints excluded: chain g residue 87 SER Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 96 SER Chi-restraints excluded: chain h residue 117 VAL Chi-restraints excluded: chain h residue 118 THR Chi-restraints excluded: chain h residue 134 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 15 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 27 GLN i 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.187118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.146162 restraints weight = 14850.566| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 0.90 r_work: 0.3303 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 14761 Z= 0.267 Angle : 0.652 10.176 21035 Z= 0.369 Chirality : 0.041 0.162 2368 Planarity : 0.005 0.057 1755 Dihedral : 29.669 179.257 4036 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.96 % Allowed : 13.40 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.25), residues: 1052 helix: 0.75 (0.20), residues: 650 sheet: -0.79 (0.80), residues: 47 loop : -1.62 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG e 45 TYR 0.017 0.002 TYR a 235 PHE 0.023 0.002 PHE a 476 TRP 0.012 0.002 TRP a 431 HIS 0.005 0.001 HIS h 113 Details of bonding type rmsd covalent geometry : bond 0.00621 (14759) covalent geometry : angle 0.65214 (21033) SS BOND : bond 0.00710 ( 1) SS BOND : angle 1.62124 ( 2) hydrogen bonds : bond 0.04864 ( 688) hydrogen bonds : angle 3.83722 ( 1796) metal coordination : bond 0.00082 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 307 ASP cc_start: 0.6454 (p0) cc_final: 0.6225 (p0) REVERT: a 449 PHE cc_start: 0.4698 (OUTLIER) cc_final: 0.4270 (m-80) REVERT: b 71 ARG cc_start: 0.8169 (mtp-110) cc_final: 0.7778 (ttm-80) REVERT: c 67 ASN cc_start: 0.8989 (m-40) cc_final: 0.8543 (m110) REVERT: d 56 LYS cc_start: 0.8258 (ttpp) cc_final: 0.8030 (ttpt) REVERT: d 133 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.6938 (mt-10) REVERT: e 92 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7885 (ttp80) REVERT: h 123 ASP cc_start: 0.8246 (p0) cc_final: 0.7991 (p0) outliers start: 18 outliers final: 14 residues processed: 141 average time/residue: 0.1584 time to fit residues: 30.1443 Evaluate side-chains 142 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 204 VAL Chi-restraints excluded: chain a residue 214 VAL Chi-restraints excluded: chain a residue 223 ILE Chi-restraints excluded: chain a residue 297 LEU Chi-restraints excluded: chain a residue 322 THR Chi-restraints excluded: chain a residue 445 LEU Chi-restraints excluded: chain a residue 449 PHE Chi-restraints excluded: chain b residue 18 SER Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain d residue 133 GLU Chi-restraints excluded: chain e residue 92 ARG Chi-restraints excluded: chain g residue 87 SER Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 96 SER Chi-restraints excluded: chain h residue 117 VAL Chi-restraints excluded: chain h residue 118 THR Chi-restraints excluded: chain h residue 134 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 63 optimal weight: 0.5980 chunk 97 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 74 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 27 GLN i 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.194849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.161564 restraints weight = 14866.073| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 0.80 r_work: 0.3382 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14761 Z= 0.164 Angle : 0.589 10.517 21035 Z= 0.340 Chirality : 0.037 0.155 2368 Planarity : 0.004 0.042 1755 Dihedral : 29.586 178.815 4036 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.07 % Allowed : 12.85 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.25), residues: 1052 helix: 0.99 (0.20), residues: 651 sheet: -0.71 (0.79), residues: 47 loop : -1.52 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG g 79 TYR 0.012 0.001 TYR a 235 PHE 0.016 0.001 PHE a 476 TRP 0.012 0.002 TRP a 363 HIS 0.003 0.001 HIS h 113 Details of bonding type rmsd covalent geometry : bond 0.00363 (14759) covalent geometry : angle 0.58861 (21033) SS BOND : bond 0.00649 ( 1) SS BOND : angle 1.54178 ( 2) hydrogen bonds : bond 0.04166 ( 688) hydrogen bonds : angle 3.69038 ( 1796) metal coordination : bond 0.00077 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3510.92 seconds wall clock time: 60 minutes 28.32 seconds (3628.32 seconds total)