Starting phenix.real_space_refine on Thu Jul 31 11:06:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a08_11601/07_2025/7a08_11601.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a08_11601/07_2025/7a08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7a08_11601/07_2025/7a08_11601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a08_11601/07_2025/7a08_11601.map" model { file = "/net/cci-nas-00/data/ceres_data/7a08_11601/07_2025/7a08_11601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a08_11601/07_2025/7a08_11601.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.34, per 1000 atoms: 0.60 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: 3.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 5.95 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: 5.75 Time building geometry restraints manager: 3.81 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 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: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 39.320 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.710 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.002 TRP a 363 HIS 0.005 0.001 HIS c 82 PHE 0.033 0.002 PHE a 449 TYR 0.013 0.002 TYR b 57 ARG 0.014 0.001 ARG c 86 Details of bonding type rmsd hydrogen bonds : bond 0.22776 ( 688) hydrogen bonds : angle 8.08322 ( 1796) metal coordination : bond 0.00261 ( 1) SS BOND : bond 0.01012 ( 1) SS BOND : angle 1.95129 ( 2) covalent geometry : bond 0.00585 (14759) covalent geometry : angle 0.66975 (21033) *********************** 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 : 1.238 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: 0.3855 time to fit residues: 82.4864 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 : 1.145 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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 = 0.195207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.161867 restraints weight = 14720.015| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 0.83 r_work: 0.3403 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1518 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= 0.162 Angle : 0.614 10.234 21035 Z= 0.355 Chirality : 0.038 0.199 2368 Planarity : 0.005 0.043 1755 Dihedral : 29.480 178.180 4039 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.42 % Allowed : 6.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.25), residues: 1052 helix: 0.06 (0.20), residues: 658 sheet: -1.07 (0.78), residues: 45 loop : -2.02 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP a 363 HIS 0.005 0.001 HIS a 369 PHE 0.018 0.001 PHE h 67 TYR 0.015 0.001 TYR a 346 ARG 0.006 0.000 ARG i 45 Details of bonding type rmsd hydrogen bonds : bond 0.04602 ( 688) hydrogen bonds : angle 3.97094 ( 1796) metal coordination : bond 0.00060 ( 1) SS BOND : bond 0.01684 ( 1) SS BOND : angle 1.94531 ( 2) covalent geometry : bond 0.00347 (14759) covalent geometry : angle 0.61360 (21033) *********************** 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 151 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: a 449 PHE cc_start: 0.4974 (OUTLIER) cc_final: 0.4402 (m-80) REVERT: a 462 THR cc_start: 0.7690 (p) cc_final: 0.7410 (p) REVERT: b 71 ARG cc_start: 0.8087 (mtp-110) cc_final: 0.7791 (ttm-80) REVERT: d 56 LYS cc_start: 0.8317 (ttpp) cc_final: 0.7951 (ttpp) outliers start: 13 outliers final: 6 residues processed: 144 average time/residue: 0.3708 time to fit residues: 72.8904 Evaluate side-chains 127 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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 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 38 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 h 113 HIS i 25 ASN i 27 GLN i 75 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.196604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.164372 restraints weight = 14752.178| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 0.87 r_work: 0.3389 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1923 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= 0.155 Angle : 0.562 9.750 21035 Z= 0.327 Chirality : 0.036 0.141 2368 Planarity : 0.004 0.043 1755 Dihedral : 29.369 179.097 4036 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.85 % Allowed : 9.26 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.26), residues: 1052 helix: 0.69 (0.21), residues: 658 sheet: -0.81 (0.79), residues: 45 loop : -1.75 (0.29), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 363 HIS 0.003 0.001 HIS h 113 PHE 0.012 0.001 PHE h 67 TYR 0.013 0.001 TYR e 72 ARG 0.004 0.000 ARG i 45 Details of bonding type rmsd hydrogen bonds : bond 0.04319 ( 688) hydrogen bonds : angle 3.66335 ( 1796) metal coordination : bond 0.00152 ( 1) SS BOND : bond 0.00885 ( 1) SS BOND : angle 1.41680 ( 2) covalent geometry : bond 0.00344 (14759) covalent geometry : angle 0.56139 (21033) *********************** 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: 17 poor density : 134 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 449 PHE cc_start: 0.4785 (OUTLIER) cc_final: 0.4279 (m-80) REVERT: b 71 ARG cc_start: 0.8104 (mtp-110) cc_final: 0.7774 (ttm-80) REVERT: h 57 SER cc_start: 0.3754 (m) cc_final: 0.3379 (p) REVERT: h 123 ASP cc_start: 0.7937 (p0) cc_final: 0.7651 (p0) REVERT: i 78 ARG cc_start: 0.8051 (mtm-85) cc_final: 0.7712 (mtm-85) outliers start: 17 outliers final: 9 residues processed: 144 average time/residue: 0.4660 time to fit residues: 92.1718 Evaluate side-chains 128 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 445 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 101 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 121 optimal weight: 0.0870 chunk 124 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 overall best weight: 2.1762 ------------------------------------------------------------------------------- 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 = 0.4139 r_free = 0.4139 target = 0.194407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.161522 restraints weight = 14732.242| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 0.82 r_work: 0.3364 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14761 Z= 0.208 Angle : 0.601 9.382 21035 Z= 0.345 Chirality : 0.038 0.141 2368 Planarity : 0.004 0.045 1755 Dihedral : 29.530 178.447 4036 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.07 % Allowed : 10.68 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.26), residues: 1052 helix: 0.70 (0.21), residues: 654 sheet: -1.07 (0.80), residues: 47 loop : -1.68 (0.29), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 363 HIS 0.005 0.001 HIS h 113 PHE 0.018 0.002 PHE a 476 TYR 0.013 0.001 TYR b 57 ARG 0.005 0.000 ARG e 39 Details of bonding type rmsd hydrogen bonds : bond 0.04507 ( 688) hydrogen bonds : angle 3.74772 ( 1796) metal coordination : bond 0.00189 ( 1) SS BOND : bond 0.00707 ( 1) SS BOND : angle 1.54993 ( 2) covalent geometry : bond 0.00479 (14759) covalent geometry : angle 0.60066 (21033) *********************** 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 145 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 449 PHE cc_start: 0.4895 (OUTLIER) cc_final: 0.4436 (m-80) REVERT: b 71 ARG cc_start: 0.8140 (mtp-110) cc_final: 0.7789 (ttm-80) REVERT: d 79 LYS cc_start: 0.8368 (ttpt) cc_final: 0.8150 (ttpt) REVERT: i 78 ARG cc_start: 0.8121 (mtm-85) cc_final: 0.7556 (mtm180) outliers start: 19 outliers final: 13 residues processed: 136 average time/residue: 0.3843 time to fit residues: 71.4466 Evaluate side-chains 137 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 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 76 GLN 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 46 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 359 GLN ** a 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 27 GLN h 113 HIS i 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.187097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.149599 restraints weight = 15001.409| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 0.93 r_work: 0.3278 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 14761 Z= 0.277 Angle : 0.656 9.772 21035 Z= 0.373 Chirality : 0.041 0.170 2368 Planarity : 0.005 0.061 1755 Dihedral : 29.757 179.053 4036 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.40 % Allowed : 12.20 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.25), residues: 1052 helix: 0.37 (0.20), residues: 655 sheet: -1.02 (0.81), residues: 47 loop : -1.77 (0.29), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP a 363 HIS 0.007 0.001 HIS h 113 PHE 0.023 0.002 PHE a 476 TYR 0.013 0.002 TYR b 57 ARG 0.007 0.001 ARG e 45 Details of bonding type rmsd hydrogen bonds : bond 0.05128 ( 688) hydrogen bonds : angle 3.94348 ( 1796) metal coordination : bond 0.00244 ( 1) SS BOND : bond 0.00771 ( 1) SS BOND : angle 1.71635 ( 2) covalent geometry : bond 0.00646 (14759) covalent geometry : angle 0.65589 (21033) *********************** 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 149 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 407 GLN cc_start: 0.5412 (tp-100) cc_final: 0.5208 (tp40) REVERT: a 449 PHE cc_start: 0.4918 (OUTLIER) cc_final: 0.4291 (m-80) REVERT: b 71 ARG cc_start: 0.8208 (mtp-110) cc_final: 0.7836 (ttm-80) outliers start: 22 outliers final: 15 residues processed: 141 average time/residue: 0.3711 time to fit residues: 72.6882 Evaluate side-chains 138 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 1.186 ------------------------------------------------------------------------------- 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 g residue 113 GLU Chi-restraints excluded: chain h residue 76 GLN 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 5 optimal weight: 0.0970 chunk 0 optimal weight: 20.0000 chunk 97 optimal weight: 0.1980 chunk 62 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 359 GLN a 407 GLN e 27 GLN h 113 HIS i 25 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.195613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.162930 restraints weight = 14975.590| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 0.87 r_work: 0.3441 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14761 Z= 0.143 Angle : 0.553 10.120 21035 Z= 0.323 Chirality : 0.035 0.153 2368 Planarity : 0.004 0.045 1755 Dihedral : 29.368 177.023 4036 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.26), residues: 1052 helix: 1.02 (0.21), residues: 650 sheet: -0.94 (0.80), residues: 47 loop : -1.52 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 363 HIS 0.003 0.001 HIS i 75 PHE 0.017 0.001 PHE h 67 TYR 0.012 0.001 TYR a 346 ARG 0.004 0.000 ARG e 40 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 688) hydrogen bonds : angle 3.59925 ( 1796) metal coordination : bond 0.00116 ( 1) SS BOND : bond 0.00564 ( 1) SS BOND : angle 1.42390 ( 2) covalent geometry : bond 0.00313 (14759) covalent geometry : angle 0.55291 (21033) *********************** 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 149 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 449 PHE cc_start: 0.4773 (OUTLIER) cc_final: 0.4513 (m-80) REVERT: b 71 ARG cc_start: 0.8137 (mtp-110) cc_final: 0.7808 (ttm-80) REVERT: c 67 ASN cc_start: 0.8839 (m-40) cc_final: 0.8450 (m-40) REVERT: e 92 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7893 (ttp80) REVERT: i 95 ARG cc_start: 0.8349 (mtt90) cc_final: 0.7987 (mtp85) outliers start: 19 outliers final: 13 residues processed: 142 average time/residue: 0.3547 time to fit residues: 67.4431 Evaluate side-chains 135 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 1.497 ------------------------------------------------------------------------------- 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 a residue 503 ILE Chi-restraints excluded: chain c residue 39 VAL Chi-restraints excluded: chain e residue 92 ARG Chi-restraints excluded: chain g residue 64 SER Chi-restraints excluded: chain g residue 87 SER Chi-restraints excluded: chain h residue 76 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.189871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.152658 restraints weight = 14994.893| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 0.82 r_work: 0.3348 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14761 Z= 0.193 Angle : 0.584 9.901 21035 Z= 0.337 Chirality : 0.037 0.158 2368 Planarity : 0.004 0.044 1755 Dihedral : 29.480 179.047 4036 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.18 % Allowed : 12.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.25), residues: 1052 helix: 0.94 (0.21), residues: 651 sheet: -0.91 (0.80), residues: 47 loop : -1.55 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 363 HIS 0.004 0.001 HIS h 113 PHE 0.017 0.002 PHE a 476 TYR 0.012 0.001 TYR b 57 ARG 0.008 0.000 ARG g 79 Details of bonding type rmsd hydrogen bonds : bond 0.04194 ( 688) hydrogen bonds : angle 3.69391 ( 1796) metal coordination : bond 0.00224 ( 1) SS BOND : bond 0.00625 ( 1) SS BOND : angle 1.44242 ( 2) covalent geometry : bond 0.00444 (14759) covalent geometry : angle 0.58343 (21033) *********************** 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 148 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 332 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7946 (mm) REVERT: a 449 PHE cc_start: 0.4847 (OUTLIER) cc_final: 0.4492 (m-80) REVERT: b 71 ARG cc_start: 0.8150 (mtp-110) cc_final: 0.7775 (ttm-80) REVERT: c 67 ASN cc_start: 0.8914 (m-40) cc_final: 0.8481 (m110) REVERT: c 93 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7593 (mt-10) REVERT: d 133 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.6745 (mt-10) REVERT: e 92 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7886 (ttp80) outliers start: 20 outliers final: 13 residues processed: 142 average time/residue: 0.3629 time to fit residues: 69.4571 Evaluate side-chains 139 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 332 LEU 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 d residue 133 GLU Chi-restraints excluded: chain e residue 92 ARG Chi-restraints excluded: chain g residue 64 SER Chi-restraints excluded: chain g residue 87 SER Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 76 GLN 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 13 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.194873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.161253 restraints weight = 14841.269| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 0.74 r_work: 0.3403 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2254 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= 0.159 Angle : 0.570 10.287 21035 Z= 0.331 Chirality : 0.036 0.157 2368 Planarity : 0.004 0.055 1755 Dihedral : 29.464 178.983 4036 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.29 % Allowed : 13.40 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.26), residues: 1052 helix: 1.04 (0.21), residues: 653 sheet: -0.87 (0.79), residues: 47 loop : -1.48 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 363 HIS 0.004 0.001 HIS h 113 PHE 0.029 0.002 PHE a 358 TYR 0.012 0.001 TYR b 57 ARG 0.006 0.000 ARG g 79 Details of bonding type rmsd hydrogen bonds : bond 0.03967 ( 688) hydrogen bonds : angle 3.65627 ( 1796) metal coordination : bond 0.00271 ( 1) SS BOND : bond 0.00575 ( 1) SS BOND : angle 1.47631 ( 2) covalent geometry : bond 0.00355 (14759) covalent geometry : angle 0.56952 (21033) *********************** 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 141 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 429 HIS cc_start: 0.7229 (OUTLIER) cc_final: 0.6651 (m-70) REVERT: a 449 PHE cc_start: 0.4871 (OUTLIER) cc_final: 0.4524 (m-80) REVERT: b 71 ARG cc_start: 0.8142 (mtp-110) cc_final: 0.7786 (ttm-80) REVERT: c 67 ASN cc_start: 0.8870 (m-40) cc_final: 0.8448 (m110) REVERT: c 93 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7465 (mt-10) REVERT: d 133 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.6664 (mt-10) REVERT: e 40 ARG cc_start: 0.7586 (ttt180) cc_final: 0.7372 (ttt180) REVERT: e 92 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7843 (ttp80) outliers start: 21 outliers final: 15 residues processed: 135 average time/residue: 0.3281 time to fit residues: 60.2749 Evaluate side-chains 137 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 429 HIS 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 64 SER Chi-restraints excluded: chain g residue 87 SER Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 76 GLN 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 90 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 77 optimal weight: 0.4980 chunk 118 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 27 GLN h 93 GLN h 113 HIS i 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.186739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.149271 restraints weight = 14986.649| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 0.86 r_work: 0.3298 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 14761 Z= 0.283 Angle : 0.663 10.295 21035 Z= 0.375 Chirality : 0.042 0.164 2368 Planarity : 0.005 0.061 1755 Dihedral : 29.769 179.621 4036 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.40 % Allowed : 13.40 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.25), residues: 1052 helix: 0.59 (0.20), residues: 651 sheet: -1.04 (0.79), residues: 47 loop : -1.71 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP a 363 HIS 0.006 0.001 HIS h 113 PHE 0.024 0.002 PHE a 476 TYR 0.016 0.002 TYR a 235 ARG 0.007 0.001 ARG e 45 Details of bonding type rmsd hydrogen bonds : bond 0.05065 ( 688) hydrogen bonds : angle 3.92214 ( 1796) metal coordination : bond 0.00268 ( 1) SS BOND : bond 0.00754 ( 1) SS BOND : angle 1.64104 ( 2) covalent geometry : bond 0.00662 (14759) covalent geometry : angle 0.66284 (21033) *********************** 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 148 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 429 HIS cc_start: 0.7304 (OUTLIER) cc_final: 0.6678 (m-70) REVERT: a 449 PHE cc_start: 0.4870 (OUTLIER) cc_final: 0.4385 (m-80) REVERT: b 71 ARG cc_start: 0.8199 (mtp-110) cc_final: 0.7816 (ttm-80) REVERT: d 133 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.6985 (mt-10) REVERT: e 92 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7946 (ttp80) outliers start: 22 outliers final: 16 residues processed: 142 average time/residue: 0.3334 time to fit residues: 64.0589 Evaluate side-chains 144 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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 304 ILE Chi-restraints excluded: chain a residue 322 THR Chi-restraints excluded: chain a residue 429 HIS 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 64 SER Chi-restraints excluded: chain g residue 87 SER Chi-restraints excluded: chain g residue 113 GLU Chi-restraints excluded: chain h residue 76 GLN 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 24 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 63 optimal weight: 0.0980 chunk 119 optimal weight: 0.5980 chunk 105 optimal weight: 0.0980 chunk 121 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 96 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 27 GLN h 93 GLN h 113 HIS i 25 ASN i 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.196597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.163503 restraints weight = 14758.850| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 0.74 r_work: 0.3426 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14761 Z= 0.151 Angle : 0.603 10.901 21035 Z= 0.348 Chirality : 0.038 0.156 2368 Planarity : 0.004 0.042 1755 Dihedral : 29.666 179.494 4036 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.52 % Favored : 96.39 % Rotamer: Outliers : 1.96 % Allowed : 13.94 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1052 helix: 1.01 (0.21), residues: 651 sheet: -1.05 (0.78), residues: 47 loop : -1.53 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP a 331 HIS 0.005 0.001 HIS a 369 PHE 0.024 0.002 PHE h 67 TYR 0.016 0.001 TYR a 346 ARG 0.006 0.001 ARG g 79 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 688) hydrogen bonds : angle 3.71081 ( 1796) metal coordination : bond 0.00093 ( 1) SS BOND : bond 0.00687 ( 1) SS BOND : angle 1.47431 ( 2) covalent geometry : bond 0.00326 (14759) covalent geometry : angle 0.60249 (21033) ********************** 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 146 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 307 ASP cc_start: 0.6819 (p0) cc_final: 0.6114 (p0) REVERT: a 429 HIS cc_start: 0.7273 (OUTLIER) cc_final: 0.6637 (m-70) REVERT: a 449 PHE cc_start: 0.4824 (OUTLIER) cc_final: 0.4410 (m-80) REVERT: b 71 ARG cc_start: 0.8131 (mtp-110) cc_final: 0.7771 (ttm-80) REVERT: c 67 ASN cc_start: 0.8811 (m-40) cc_final: 0.8416 (m-40) REVERT: d 133 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7043 (mt-10) REVERT: e 92 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7805 (ttp80) REVERT: i 95 ARG cc_start: 0.8431 (mtt90) cc_final: 0.8055 (mtp85) outliers start: 18 outliers final: 11 residues processed: 141 average time/residue: 0.3813 time to fit residues: 71.7329 Evaluate side-chains 140 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 429 HIS 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 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 76 GLN 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 12 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 17 optimal weight: 0.0970 chunk 38 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 overall best weight: 1.0980 ------------------------------------------------------------------------------- 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 i 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.195344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.162715 restraints weight = 14929.617| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 0.82 r_work: 0.3429 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2369 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= 0.158 Angle : 0.570 10.148 21035 Z= 0.330 Chirality : 0.036 0.149 2368 Planarity : 0.004 0.044 1755 Dihedral : 29.439 177.383 4036 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.23 % Favored : 96.67 % Rotamer: Outliers : 1.96 % Allowed : 14.38 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.26), residues: 1052 helix: 1.15 (0.20), residues: 658 sheet: -1.03 (0.77), residues: 47 loop : -1.49 (0.30), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 331 HIS 0.004 0.001 HIS h 113 PHE 0.016 0.001 PHE h 67 TYR 0.021 0.001 TYR a 373 ARG 0.005 0.000 ARG g 79 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 688) hydrogen bonds : angle 3.63033 ( 1796) metal coordination : bond 0.00082 ( 1) SS BOND : bond 0.00559 ( 1) SS BOND : angle 1.42770 ( 2) covalent geometry : bond 0.00356 (14759) covalent geometry : angle 0.57013 (21033) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7981.27 seconds wall clock time: 140 minutes 32.23 seconds (8432.23 seconds total)