Starting phenix.real_space_refine on Wed Feb 4 09:28:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k6h_62127/02_2026/9k6h_62127.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k6h_62127/02_2026/9k6h_62127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k6h_62127/02_2026/9k6h_62127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k6h_62127/02_2026/9k6h_62127.map" model { file = "/net/cci-nas-00/data/ceres_data/9k6h_62127/02_2026/9k6h_62127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k6h_62127/02_2026/9k6h_62127.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 1 7.51 5 Zn 1 6.06 5 P 57 5.49 5 S 39 5.16 5 C 6041 2.51 5 N 1651 2.21 5 O 1861 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9651 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8525 Classifications: {'peptide': 1028} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 984} Chain: "B" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 404 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "C" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "D" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 210 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "E" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'RNA': 12} Modifications used: {'rna3p_pyr': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MN': 1, ' ZN': 1, 'DTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7311 SG CYS A1130 51.993 76.145 14.243 1.00 60.51 S ATOM 7346 SG CYS A1134 52.108 75.587 10.513 1.00 72.68 S ATOM 7452 SG CYS A1147 49.786 73.386 12.649 1.00 52.84 S Time building chain proxies: 1.67, per 1000 atoms: 0.17 Number of scatterers: 9651 At special positions: 0 Unit cell: (86, 125, 114, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Mn 1 24.99 S 39 16.00 P 57 15.00 O 1861 8.00 N 1651 7.00 C 6041 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 326.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1302 " pdb="ZN ZN A1302 " - pdb=" NE2 HIS A1142 " pdb="ZN ZN A1302 " - pdb=" SG CYS A1134 " pdb="ZN ZN A1302 " - pdb=" SG CYS A1130 " pdb="ZN ZN A1302 " - pdb=" SG CYS A1147 " Number of angles added : 3 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1984 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 6 sheets defined 65.6% alpha, 6.8% beta 16 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.915A pdb=" N LEU A 257 " --> pdb=" O ASN A 253 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 258 " --> pdb=" O ASN A 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 258' Processing helix chain 'A' and resid 259 through 277 Processing helix chain 'A' and resid 283 through 311 Processing helix chain 'A' and resid 311 through 331 Processing helix chain 'A' and resid 333 through 369 removed outlier: 3.640A pdb=" N ARG A 369 " --> pdb=" O TRP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 382 Processing helix chain 'A' and resid 403 through 419 Processing helix chain 'A' and resid 425 through 436 removed outlier: 3.802A pdb=" N TYR A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 Processing helix chain 'A' and resid 454 through 465 Processing helix chain 'A' and resid 477 through 484 removed outlier: 3.854A pdb=" N TYR A 481 " --> pdb=" O THR A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 503 Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 506 through 509 Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 537 through 553 Processing helix chain 'A' and resid 554 through 559 Processing helix chain 'A' and resid 572 through 589 removed outlier: 3.667A pdb=" N ILE A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 620 Processing helix chain 'A' and resid 624 through 634 Processing helix chain 'A' and resid 663 through 682 removed outlier: 3.717A pdb=" N VAL A 674 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 730 removed outlier: 4.577A pdb=" N GLN A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 728 " --> pdb=" O ASN A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 757 Processing helix chain 'A' and resid 776 through 778 No H-bonds generated for 'chain 'A' and resid 776 through 778' Processing helix chain 'A' and resid 779 through 785 Processing helix chain 'A' and resid 785 through 800 Processing helix chain 'A' and resid 805 through 816 Processing helix chain 'A' and resid 816 through 828 removed outlier: 3.944A pdb=" N LYS A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 849 removed outlier: 3.774A pdb=" N PHE A 837 " --> pdb=" O PRO A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 862 Processing helix chain 'A' and resid 874 through 885 Processing helix chain 'A' and resid 885 through 893 removed outlier: 3.774A pdb=" N TYR A 889 " --> pdb=" O LYS A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 902 removed outlier: 3.946A pdb=" N ARG A 901 " --> pdb=" O ASP A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 915 removed outlier: 3.725A pdb=" N LEU A 915 " --> pdb=" O TYR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 947 Processing helix chain 'A' and resid 961 through 966 Processing helix chain 'A' and resid 970 through 981 removed outlier: 3.637A pdb=" N ILE A 974 " --> pdb=" O LYS A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 989 removed outlier: 3.840A pdb=" N ILE A 988 " --> pdb=" O THR A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 994 Processing helix chain 'A' and resid 998 through 1006 removed outlier: 4.206A pdb=" N MET A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA A1003 " --> pdb=" O PRO A 999 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A1006 " --> pdb=" O MET A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1021 Processing helix chain 'A' and resid 1022 through 1030 Processing helix chain 'A' and resid 1034 through 1042 removed outlier: 3.696A pdb=" N PHE A1040 " --> pdb=" O TRP A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1061 Processing helix chain 'A' and resid 1067 through 1076 removed outlier: 3.503A pdb=" N LYS A1071 " --> pdb=" O ASN A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1095 Processing helix chain 'A' and resid 1098 through 1110 Processing helix chain 'A' and resid 1115 through 1123 Processing helix chain 'A' and resid 1139 through 1145 Processing helix chain 'A' and resid 1150 through 1163 Processing helix chain 'A' and resid 1172 through 1178 Processing helix chain 'A' and resid 1189 through 1207 removed outlier: 3.653A pdb=" N THR A1207 " --> pdb=" O THR A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1215 through 1238 Processing helix chain 'A' and resid 1239 through 1257 removed outlier: 5.688A pdb=" N LYS A1249 " --> pdb=" O GLY A1245 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N LEU A1250 " --> pdb=" O THR A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1267 Processing sheet with id=AA1, first strand: chain 'A' and resid 393 through 394 removed outlier: 3.668A pdb=" N ILE A 393 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR A 401 " --> pdb=" O ILE A 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 530 through 535 removed outlier: 6.411A pdb=" N ALA A 512 " --> pdb=" O ASN A 640 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE A 642 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE A 514 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 530 through 535 removed outlier: 6.411A pdb=" N ALA A 512 " --> pdb=" O ASN A 640 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE A 642 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE A 514 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 697 through 700 Processing sheet with id=AA5, first strand: chain 'A' and resid 688 through 690 Processing sheet with id=AA6, first strand: chain 'A' and resid 765 through 768 475 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 2.07 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2374 1.33 - 1.45: 2083 1.45 - 1.57: 5341 1.57 - 1.69: 109 1.69 - 1.81: 63 Bond restraints: 9970 Sorted by residual: bond pdb=" CG1 ILE A 916 " pdb=" CD1 ILE A 916 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.31e+00 bond pdb=" CA THR A 871 " pdb=" CB THR A 871 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.69e-02 3.50e+03 9.75e-01 bond pdb=" CB LYS A 501 " pdb=" CG LYS A 501 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.42e-01 bond pdb=" CA ILE A 373 " pdb=" CB ILE A 373 " ideal model delta sigma weight residual 1.530 1.540 -0.010 1.05e-02 9.07e+03 9.09e-01 bond pdb=" CG LEU A 699 " pdb=" CD1 LEU A 699 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.57e-01 ... (remaining 9965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 13266 1.44 - 2.88: 321 2.88 - 4.32: 62 4.32 - 5.76: 20 5.76 - 7.20: 3 Bond angle restraints: 13672 Sorted by residual: angle pdb=" CA LYS A 928 " pdb=" CB LYS A 928 " pdb=" CG LYS A 928 " ideal model delta sigma weight residual 114.10 121.25 -7.15 2.00e+00 2.50e-01 1.28e+01 angle pdb=" C ILE A 870 " pdb=" N THR A 871 " pdb=" CA THR A 871 " ideal model delta sigma weight residual 121.54 127.21 -5.67 1.91e+00 2.74e-01 8.82e+00 angle pdb=" N LYS A 737 " pdb=" CA LYS A 737 " pdb=" C LYS A 737 " ideal model delta sigma weight residual 114.56 110.91 3.65 1.27e+00 6.20e-01 8.28e+00 angle pdb=" C ARG A1162 " pdb=" N ASP A1163 " pdb=" CA ASP A1163 " ideal model delta sigma weight residual 121.94 116.38 5.56 2.00e+00 2.50e-01 7.74e+00 angle pdb=" C3' DC B 15 " pdb=" C2' DC B 15 " pdb=" C1' DC B 15 " ideal model delta sigma weight residual 101.60 105.33 -3.73 1.50e+00 4.44e-01 6.19e+00 ... (remaining 13667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.71: 5236 20.71 - 41.42: 600 41.42 - 62.13: 210 62.13 - 82.84: 18 82.84 - 103.55: 5 Dihedral angle restraints: 6069 sinusoidal: 3022 harmonic: 3047 Sorted by residual: dihedral pdb=" CA PHE A 605 " pdb=" C PHE A 605 " pdb=" N ASP A 606 " pdb=" CA ASP A 606 " ideal model delta harmonic sigma weight residual 180.00 159.19 20.81 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" O4' U E 24 " pdb=" C1' U E 24 " pdb=" N1 U E 24 " pdb=" C2 U E 24 " ideal model delta sinusoidal sigma weight residual -160.00 -108.32 -51.68 1 1.50e+01 4.44e-03 1.62e+01 dihedral pdb=" CA TRP A1145 " pdb=" C TRP A1145 " pdb=" N ASP A1146 " pdb=" CA ASP A1146 " ideal model delta harmonic sigma weight residual -180.00 -160.09 -19.91 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 6066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1053 0.034 - 0.068: 325 0.068 - 0.102: 107 0.102 - 0.136: 32 0.136 - 0.170: 4 Chirality restraints: 1521 Sorted by residual: chirality pdb=" CA ILE A 407 " pdb=" N ILE A 407 " pdb=" C ILE A 407 " pdb=" CB ILE A 407 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CB ILE A 359 " pdb=" CA ILE A 359 " pdb=" CG1 ILE A 359 " pdb=" CG2 ILE A 359 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CB THR A 882 " pdb=" CA THR A 882 " pdb=" OG1 THR A 882 " pdb=" CG2 THR A 882 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 1518 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 390 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.15e+00 pdb=" C ILE A 390 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE A 390 " -0.013 2.00e-02 2.50e+03 pdb=" N ASP A 391 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 786 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A 787 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 787 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 787 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 367 " -0.013 2.00e-02 2.50e+03 1.25e-02 2.71e+00 pdb=" CG PHE A 367 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A 367 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 367 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 367 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 367 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 367 " -0.002 2.00e-02 2.50e+03 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 19 2.64 - 3.20: 8590 3.20 - 3.77: 16300 3.77 - 4.33: 22127 4.33 - 4.90: 35415 Nonbonded interactions: 82451 Sorted by model distance: nonbonded pdb=" O ASN A1066 " pdb=" OD1 ASN A1066 " model vdw 2.069 3.040 nonbonded pdb=" O ALA A 601 " pdb="MN MN A1303 " model vdw 2.129 2.320 nonbonded pdb=" OD2 ASP A 702 " pdb="MN MN A1303 " model vdw 2.171 2.320 nonbonded pdb=" O2B DTP A1301 " pdb="MN MN A1303 " model vdw 2.185 2.320 nonbonded pdb=" O1A DTP A1301 " pdb="MN MN A1303 " model vdw 2.191 2.320 ... (remaining 82446 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.210 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 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 : 0.003 0.059 9974 Z= 0.140 Angle : 0.587 7.204 13675 Z= 0.324 Chirality : 0.040 0.170 1521 Planarity : 0.004 0.041 1514 Dihedral : 18.726 103.550 4085 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.63 % Favored : 97.27 % Rotamer: Outliers : 1.06 % Allowed : 23.33 % Favored : 75.61 % 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: 1.47 (0.27), residues: 1026 helix: 1.54 (0.21), residues: 604 sheet: -1.21 (0.69), residues: 49 loop : 0.53 (0.35), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 379 TYR 0.016 0.001 TYR A1112 PHE 0.029 0.002 PHE A 367 TRP 0.012 0.001 TRP A1011 HIS 0.004 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9970) covalent geometry : angle 0.58602 (13672) hydrogen bonds : bond 0.11098 ( 501) hydrogen bonds : angle 5.59797 ( 1456) metal coordination : bond 0.00543 ( 4) metal coordination : angle 1.83819 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: A 251 LYS cc_start: 0.7547 (mttt) cc_final: 0.7274 (mtmm) REVERT: A 271 LYS cc_start: 0.7283 (tttt) cc_final: 0.6746 (tmmt) REVERT: A 474 ASP cc_start: 0.8164 (p0) cc_final: 0.7891 (p0) REVERT: A 654 LYS cc_start: 0.7898 (mtpp) cc_final: 0.7681 (mmtt) REVERT: A 732 LYS cc_start: 0.8163 (tppp) cc_final: 0.7768 (mtpt) REVERT: A 744 THR cc_start: 0.8863 (m) cc_final: 0.8359 (p) REVERT: A 800 LYS cc_start: 0.8085 (pttt) cc_final: 0.7720 (ptmm) REVERT: A 1002 MET cc_start: 0.6500 (mmp) cc_final: 0.6273 (tpp) REVERT: A 1017 LYS cc_start: 0.7314 (tttt) cc_final: 0.6996 (ttmt) REVERT: A 1026 THR cc_start: 0.8154 (m) cc_final: 0.7738 (p) REVERT: A 1044 SER cc_start: 0.8647 (p) cc_final: 0.8414 (t) REVERT: A 1171 ASP cc_start: 0.7501 (t0) cc_final: 0.7285 (m-30) REVERT: A 1210 GLN cc_start: 0.8250 (mm-40) cc_final: 0.7725 (mp10) REVERT: A 1264 THR cc_start: 0.8031 (m) cc_final: 0.7701 (p) outliers start: 10 outliers final: 6 residues processed: 137 average time/residue: 0.5257 time to fit residues: 77.0269 Evaluate side-chains 126 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 1223 MET Chi-restraints excluded: chain A residue 1235 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.0770 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN A1066 ASN A1127 ASN ** A1266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.184325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.139299 restraints weight = 10159.001| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.55 r_work: 0.3293 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 9974 Z= 0.167 Angle : 0.558 8.911 13675 Z= 0.294 Chirality : 0.041 0.149 1521 Planarity : 0.004 0.042 1514 Dihedral : 17.761 109.490 1842 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.53 % Favored : 97.37 % Rotamer: Outliers : 3.92 % Allowed : 20.57 % Favored : 75.50 % 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: 1.58 (0.27), residues: 1026 helix: 1.74 (0.21), residues: 597 sheet: -1.11 (0.72), residues: 44 loop : 0.36 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1132 TYR 0.019 0.002 TYR A1112 PHE 0.025 0.002 PHE A 605 TRP 0.011 0.001 TRP A1247 HIS 0.006 0.001 HIS A1142 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 9970) covalent geometry : angle 0.55676 (13672) hydrogen bonds : bond 0.03881 ( 501) hydrogen bonds : angle 4.40155 ( 1456) metal coordination : bond 0.00515 ( 4) metal coordination : angle 2.20430 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 251 LYS cc_start: 0.7547 (mttt) cc_final: 0.7297 (mttp) REVERT: A 271 LYS cc_start: 0.7370 (tttt) cc_final: 0.6816 (tmmt) REVERT: A 474 ASP cc_start: 0.8150 (p0) cc_final: 0.7912 (p0) REVERT: A 550 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8655 (mmm-85) REVERT: A 571 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7642 (mm-40) REVERT: A 732 LYS cc_start: 0.8137 (tppp) cc_final: 0.7707 (mtpt) REVERT: A 736 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7639 (mm110) REVERT: A 744 THR cc_start: 0.8925 (m) cc_final: 0.8630 (p) REVERT: A 800 LYS cc_start: 0.8173 (pttt) cc_final: 0.7755 (ptmm) REVERT: A 908 MET cc_start: 0.7567 (ptm) cc_final: 0.7307 (ptm) REVERT: A 975 LYS cc_start: 0.7751 (mttt) cc_final: 0.7473 (pttm) REVERT: A 995 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7182 (mmm) REVERT: A 1002 MET cc_start: 0.6752 (OUTLIER) cc_final: 0.6510 (tpp) REVERT: A 1017 LYS cc_start: 0.7356 (tttt) cc_final: 0.6972 (ttmt) REVERT: A 1026 THR cc_start: 0.8159 (m) cc_final: 0.7746 (p) REVERT: A 1044 SER cc_start: 0.8650 (p) cc_final: 0.8391 (t) REVERT: A 1155 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7747 (mttt) REVERT: A 1171 ASP cc_start: 0.7718 (t0) cc_final: 0.7451 (m-30) REVERT: A 1210 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7527 (mp-120) REVERT: A 1229 MET cc_start: 0.8778 (mmp) cc_final: 0.8473 (mmp) REVERT: A 1264 THR cc_start: 0.7989 (m) cc_final: 0.7697 (p) outliers start: 37 outliers final: 14 residues processed: 154 average time/residue: 0.4797 time to fit residues: 79.3621 Evaluate side-chains 132 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 628 LYS Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 958 LYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1066 ASN Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1155 LYS Chi-restraints excluded: chain A residue 1268 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 69 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 70 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN A 736 GLN A 900 ASN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN A1066 ASN A1127 ASN A1266 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.182617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.138461 restraints weight = 10189.080| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.47 r_work: 0.3233 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9974 Z= 0.174 Angle : 0.550 9.240 13675 Z= 0.290 Chirality : 0.041 0.151 1521 Planarity : 0.004 0.043 1514 Dihedral : 17.735 111.748 1834 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.53 % Favored : 97.37 % Rotamer: Outliers : 4.14 % Allowed : 20.78 % Favored : 75.08 % 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: 1.53 (0.27), residues: 1026 helix: 1.72 (0.21), residues: 600 sheet: -1.21 (0.71), residues: 44 loop : 0.28 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1132 TYR 0.020 0.002 TYR A1112 PHE 0.027 0.002 PHE A 605 TRP 0.009 0.001 TRP A1158 HIS 0.005 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 9970) covalent geometry : angle 0.54896 (13672) hydrogen bonds : bond 0.03876 ( 501) hydrogen bonds : angle 4.32641 ( 1456) metal coordination : bond 0.00839 ( 4) metal coordination : angle 1.77462 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 0.367 Fit side-chains REVERT: A 251 LYS cc_start: 0.7465 (mttt) cc_final: 0.7215 (mttp) REVERT: A 271 LYS cc_start: 0.7395 (tttt) cc_final: 0.6816 (tmmt) REVERT: A 474 ASP cc_start: 0.8119 (p0) cc_final: 0.7901 (p0) REVERT: A 550 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8628 (mmm-85) REVERT: A 571 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.7650 (mm-40) REVERT: A 732 LYS cc_start: 0.8167 (tppp) cc_final: 0.7686 (mtpt) REVERT: A 754 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.6971 (mpt) REVERT: A 800 LYS cc_start: 0.8167 (pttt) cc_final: 0.7757 (ptmm) REVERT: A 908 MET cc_start: 0.7601 (ptm) cc_final: 0.7308 (ptm) REVERT: A 934 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.7799 (tmtt) REVERT: A 975 LYS cc_start: 0.7745 (mttt) cc_final: 0.7471 (pttm) REVERT: A 995 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7201 (mmm) REVERT: A 1002 MET cc_start: 0.6724 (OUTLIER) cc_final: 0.6449 (tpp) REVERT: A 1026 THR cc_start: 0.8128 (m) cc_final: 0.7722 (p) REVERT: A 1044 SER cc_start: 0.8628 (p) cc_final: 0.8372 (t) REVERT: A 1092 MET cc_start: 0.8328 (ttp) cc_final: 0.7961 (ttm) REVERT: A 1122 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.8065 (mp) REVERT: A 1123 LYS cc_start: 0.7629 (mmtt) cc_final: 0.6830 (mtmp) REVERT: A 1171 ASP cc_start: 0.7723 (t0) cc_final: 0.7462 (m-30) REVERT: A 1210 GLN cc_start: 0.8331 (mm-40) cc_final: 0.7536 (mp-120) REVERT: A 1229 MET cc_start: 0.8779 (mmp) cc_final: 0.8536 (mmp) REVERT: A 1264 THR cc_start: 0.8043 (m) cc_final: 0.7742 (p) outliers start: 39 outliers final: 12 residues processed: 147 average time/residue: 0.4991 time to fit residues: 78.4454 Evaluate side-chains 133 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 958 LYS Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1122 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 40 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 82 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN A 585 HIS A 900 ASN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN A1066 ASN A1266 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.180220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.136096 restraints weight = 10144.191| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.45 r_work: 0.3187 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 9974 Z= 0.190 Angle : 0.566 9.644 13675 Z= 0.297 Chirality : 0.041 0.160 1521 Planarity : 0.004 0.043 1514 Dihedral : 17.828 122.314 1834 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.63 % Favored : 97.27 % Rotamer: Outliers : 5.09 % Allowed : 19.41 % Favored : 75.50 % 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: 1.41 (0.27), residues: 1026 helix: 1.65 (0.21), residues: 600 sheet: -1.27 (0.70), residues: 44 loop : 0.18 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1132 TYR 0.021 0.002 TYR A1112 PHE 0.029 0.002 PHE A 605 TRP 0.009 0.001 TRP A1072 HIS 0.005 0.001 HIS A1142 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 9970) covalent geometry : angle 0.56511 (13672) hydrogen bonds : bond 0.03916 ( 501) hydrogen bonds : angle 4.34184 ( 1456) metal coordination : bond 0.00951 ( 4) metal coordination : angle 2.04842 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 130 time to evaluate : 0.307 Fit side-chains REVERT: A 251 LYS cc_start: 0.7523 (mttt) cc_final: 0.7229 (mtmm) REVERT: A 271 LYS cc_start: 0.7432 (tttt) cc_final: 0.6805 (tmmt) REVERT: A 306 LYS cc_start: 0.7311 (ttpt) cc_final: 0.7109 (tttt) REVERT: A 550 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8614 (mmm-85) REVERT: A 571 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.7734 (mm-40) REVERT: A 703 ASP cc_start: 0.7679 (m-30) cc_final: 0.7411 (m-30) REVERT: A 732 LYS cc_start: 0.8200 (tppp) cc_final: 0.7696 (mtpt) REVERT: A 736 GLN cc_start: 0.8245 (pt0) cc_final: 0.7769 (mm110) REVERT: A 765 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7477 (ptm160) REVERT: A 800 LYS cc_start: 0.8144 (pttt) cc_final: 0.7736 (ptmm) REVERT: A 908 MET cc_start: 0.7596 (ptm) cc_final: 0.7258 (ptm) REVERT: A 934 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.7788 (tmtt) REVERT: A 975 LYS cc_start: 0.7772 (mttt) cc_final: 0.7426 (pttm) REVERT: A 995 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7282 (mmm) REVERT: A 1002 MET cc_start: 0.6800 (OUTLIER) cc_final: 0.6493 (tpp) REVERT: A 1026 THR cc_start: 0.8127 (m) cc_final: 0.7760 (p) REVERT: A 1044 SER cc_start: 0.8585 (p) cc_final: 0.8308 (t) REVERT: A 1078 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7531 (ptm160) REVERT: A 1092 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8100 (mtm) REVERT: A 1122 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.8030 (mp) REVERT: A 1123 LYS cc_start: 0.7628 (mmtt) cc_final: 0.6843 (mtmp) REVERT: A 1127 ASN cc_start: 0.7719 (m110) cc_final: 0.7498 (p0) REVERT: A 1171 ASP cc_start: 0.7837 (t0) cc_final: 0.7511 (m-30) REVERT: A 1210 GLN cc_start: 0.8338 (mm-40) cc_final: 0.7819 (mp-120) REVERT: A 1229 MET cc_start: 0.8783 (mmp) cc_final: 0.8495 (mmp) REVERT: A 1264 THR cc_start: 0.8013 (m) cc_final: 0.7718 (p) outliers start: 48 outliers final: 16 residues processed: 162 average time/residue: 0.5099 time to fit residues: 88.3405 Evaluate side-chains 135 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 958 LYS Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1002 MET Chi-restraints excluded: chain A residue 1078 ARG Chi-restraints excluded: chain A residue 1092 MET Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1122 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 60 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 41 optimal weight: 0.1980 chunk 90 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN A 408 GLN A 552 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN A1066 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.181700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.137387 restraints weight = 10209.846| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.47 r_work: 0.3272 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 9974 Z= 0.158 Angle : 0.540 9.285 13675 Z= 0.287 Chirality : 0.040 0.149 1521 Planarity : 0.004 0.041 1514 Dihedral : 17.800 121.276 1834 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.44 % Favored : 97.47 % Rotamer: Outliers : 4.77 % Allowed : 20.89 % Favored : 74.34 % 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: 1.41 (0.27), residues: 1026 helix: 1.68 (0.21), residues: 600 sheet: -1.30 (0.71), residues: 44 loop : 0.14 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1132 TYR 0.019 0.002 TYR A1112 PHE 0.024 0.002 PHE A 605 TRP 0.010 0.001 TRP A1158 HIS 0.004 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 9970) covalent geometry : angle 0.53948 (13672) hydrogen bonds : bond 0.03768 ( 501) hydrogen bonds : angle 4.27255 ( 1456) metal coordination : bond 0.00934 ( 4) metal coordination : angle 1.64618 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 115 time to evaluate : 0.270 Fit side-chains REVERT: A 251 LYS cc_start: 0.7537 (mttt) cc_final: 0.7257 (mtmm) REVERT: A 271 LYS cc_start: 0.7475 (tttt) cc_final: 0.6858 (tmmt) REVERT: A 550 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8635 (mmm-85) REVERT: A 571 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7700 (mm-40) REVERT: A 732 LYS cc_start: 0.8214 (tppp) cc_final: 0.7738 (mtpt) REVERT: A 736 GLN cc_start: 0.8257 (pt0) cc_final: 0.7822 (mm110) REVERT: A 800 LYS cc_start: 0.8161 (pttt) cc_final: 0.7756 (ptmm) REVERT: A 908 MET cc_start: 0.7615 (ptm) cc_final: 0.7264 (ptm) REVERT: A 934 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.7777 (tmtt) REVERT: A 975 LYS cc_start: 0.7786 (mttt) cc_final: 0.7412 (pttm) REVERT: A 995 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.7168 (mmm) REVERT: A 1026 THR cc_start: 0.8133 (m) cc_final: 0.7780 (p) REVERT: A 1044 SER cc_start: 0.8579 (p) cc_final: 0.8322 (t) REVERT: A 1092 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.7973 (ttm) REVERT: A 1122 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.8045 (mp) REVERT: A 1123 LYS cc_start: 0.7666 (mmtt) cc_final: 0.6855 (mtmp) REVERT: A 1171 ASP cc_start: 0.7796 (t0) cc_final: 0.7496 (m-30) REVERT: A 1210 GLN cc_start: 0.8392 (mm-40) cc_final: 0.7928 (mp-120) REVERT: A 1229 MET cc_start: 0.8802 (mmp) cc_final: 0.8538 (mmp) REVERT: A 1264 THR cc_start: 0.8018 (m) cc_final: 0.7726 (p) outliers start: 45 outliers final: 12 residues processed: 148 average time/residue: 0.6263 time to fit residues: 98.8465 Evaluate side-chains 129 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1092 MET Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1122 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 40 optimal weight: 0.0000 chunk 54 optimal weight: 0.5980 chunk 102 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN A 552 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 GLN A 900 ASN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN A1066 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.182986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.138949 restraints weight = 10105.018| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.47 r_work: 0.3335 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9974 Z= 0.138 Angle : 0.524 8.780 13675 Z= 0.279 Chirality : 0.039 0.139 1521 Planarity : 0.004 0.040 1514 Dihedral : 17.724 116.630 1832 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.44 % Favored : 97.47 % Rotamer: Outliers : 4.77 % Allowed : 21.42 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.27), residues: 1026 helix: 1.72 (0.21), residues: 600 sheet: -1.24 (0.72), residues: 44 loop : 0.16 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1132 TYR 0.017 0.002 TYR A1112 PHE 0.022 0.002 PHE A 605 TRP 0.010 0.001 TRP A1158 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9970) covalent geometry : angle 0.52373 (13672) hydrogen bonds : bond 0.03647 ( 501) hydrogen bonds : angle 4.22210 ( 1456) metal coordination : bond 0.00729 ( 4) metal coordination : angle 1.66930 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 116 time to evaluate : 0.437 Fit side-chains REVERT: A 251 LYS cc_start: 0.7457 (mttt) cc_final: 0.7227 (mtmm) REVERT: A 271 LYS cc_start: 0.7564 (tttt) cc_final: 0.6878 (tmmt) REVERT: A 550 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8645 (mmm-85) REVERT: A 571 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.7683 (mm-40) REVERT: A 732 LYS cc_start: 0.8208 (tppp) cc_final: 0.7747 (mtpt) REVERT: A 736 GLN cc_start: 0.8221 (pt0) cc_final: 0.7780 (mm110) REVERT: A 800 LYS cc_start: 0.8188 (pttt) cc_final: 0.7785 (ptmm) REVERT: A 908 MET cc_start: 0.7590 (ptm) cc_final: 0.7223 (ptm) REVERT: A 934 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.7794 (tmtt) REVERT: A 972 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.6789 (tppt) REVERT: A 975 LYS cc_start: 0.7786 (mttt) cc_final: 0.7247 (mmtp) REVERT: A 995 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.7094 (mmm) REVERT: A 1002 MET cc_start: 0.6688 (mmp) cc_final: 0.6386 (tpp) REVERT: A 1026 THR cc_start: 0.8112 (m) cc_final: 0.7764 (p) REVERT: A 1044 SER cc_start: 0.8636 (p) cc_final: 0.8365 (t) REVERT: A 1092 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7919 (ttm) REVERT: A 1122 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8073 (mp) REVERT: A 1123 LYS cc_start: 0.7783 (mmtt) cc_final: 0.7115 (mtmp) REVERT: A 1155 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7575 (mtmt) REVERT: A 1171 ASP cc_start: 0.7738 (t0) cc_final: 0.7456 (m-30) REVERT: A 1210 GLN cc_start: 0.8326 (mm-40) cc_final: 0.7902 (mp-120) REVERT: A 1229 MET cc_start: 0.8766 (mmp) cc_final: 0.8562 (mmp) REVERT: A 1264 THR cc_start: 0.8006 (m) cc_final: 0.7720 (p) outliers start: 45 outliers final: 14 residues processed: 149 average time/residue: 0.5993 time to fit residues: 95.2639 Evaluate side-chains 132 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 972 LYS Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1092 MET Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 97 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 77 optimal weight: 0.0070 chunk 84 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 59 optimal weight: 0.3980 chunk 90 optimal weight: 0.3980 chunk 105 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN A 552 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN A1066 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.183220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.139090 restraints weight = 10138.181| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.48 r_work: 0.3337 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9974 Z= 0.135 Angle : 0.524 8.429 13675 Z= 0.279 Chirality : 0.039 0.164 1521 Planarity : 0.004 0.040 1514 Dihedral : 17.677 111.007 1832 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.92 % Favored : 96.98 % Rotamer: Outliers : 3.50 % Allowed : 23.01 % Favored : 73.49 % 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: 1.48 (0.27), residues: 1026 helix: 1.76 (0.21), residues: 600 sheet: -1.48 (0.69), residues: 49 loop : 0.19 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1129 TYR 0.016 0.001 TYR A1112 PHE 0.022 0.001 PHE A 605 TRP 0.010 0.001 TRP A1158 HIS 0.004 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9970) covalent geometry : angle 0.52272 (13672) hydrogen bonds : bond 0.03605 ( 501) hydrogen bonds : angle 4.15273 ( 1456) metal coordination : bond 0.00952 ( 4) metal coordination : angle 2.19568 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.263 Fit side-chains REVERT: A 251 LYS cc_start: 0.7446 (mttt) cc_final: 0.7216 (mtmm) REVERT: A 271 LYS cc_start: 0.7611 (tttt) cc_final: 0.7075 (tmtp) REVERT: A 571 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.7695 (mm-40) REVERT: A 732 LYS cc_start: 0.8195 (tppp) cc_final: 0.7746 (mtpt) REVERT: A 736 GLN cc_start: 0.8219 (pt0) cc_final: 0.7773 (mm110) REVERT: A 800 LYS cc_start: 0.8176 (pttt) cc_final: 0.7777 (ptmm) REVERT: A 908 MET cc_start: 0.7603 (ptm) cc_final: 0.7309 (ptm) REVERT: A 972 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.6818 (tppt) REVERT: A 975 LYS cc_start: 0.7813 (mttt) cc_final: 0.7242 (mmtp) REVERT: A 995 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.7094 (mmm) REVERT: A 1002 MET cc_start: 0.6709 (mmp) cc_final: 0.6403 (tpp) REVERT: A 1026 THR cc_start: 0.8119 (m) cc_final: 0.7782 (p) REVERT: A 1044 SER cc_start: 0.8639 (p) cc_final: 0.8369 (t) REVERT: A 1092 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7894 (ttm) REVERT: A 1122 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.8094 (mp) REVERT: A 1123 LYS cc_start: 0.7830 (mmtt) cc_final: 0.7529 (mmpt) REVERT: A 1164 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7330 (mp) REVERT: A 1171 ASP cc_start: 0.7717 (t0) cc_final: 0.7433 (m-30) REVERT: A 1210 GLN cc_start: 0.8258 (mm-40) cc_final: 0.7851 (mp-120) REVERT: A 1264 THR cc_start: 0.8011 (m) cc_final: 0.7730 (p) outliers start: 33 outliers final: 14 residues processed: 131 average time/residue: 0.6141 time to fit residues: 86.0445 Evaluate side-chains 127 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 972 LYS Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1092 MET Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1223 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 46 optimal weight: 0.3980 chunk 98 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 76 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 48 optimal weight: 0.0870 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 0.2980 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN A1066 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.184865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.140882 restraints weight = 10150.961| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.48 r_work: 0.3416 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9974 Z= 0.122 Angle : 0.511 7.803 13675 Z= 0.272 Chirality : 0.039 0.145 1521 Planarity : 0.004 0.043 1514 Dihedral : 17.646 102.129 1832 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.92 % Favored : 96.98 % Rotamer: Outliers : 2.86 % Allowed : 23.54 % Favored : 73.59 % 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: 1.56 (0.27), residues: 1026 helix: 1.84 (0.21), residues: 600 sheet: -1.43 (0.70), residues: 49 loop : 0.18 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 375 TYR 0.015 0.001 TYR A1112 PHE 0.019 0.001 PHE A 605 TRP 0.013 0.001 TRP A1247 HIS 0.004 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9970) covalent geometry : angle 0.50980 (13672) hydrogen bonds : bond 0.03503 ( 501) hydrogen bonds : angle 4.08881 ( 1456) metal coordination : bond 0.00791 ( 4) metal coordination : angle 2.08815 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.320 Fit side-chains REVERT: A 251 LYS cc_start: 0.7448 (mttt) cc_final: 0.7246 (mtmm) REVERT: A 271 LYS cc_start: 0.7636 (tttt) cc_final: 0.7132 (tmtp) REVERT: A 571 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.7666 (mm-40) REVERT: A 732 LYS cc_start: 0.8191 (tppp) cc_final: 0.7802 (mtpt) REVERT: A 736 GLN cc_start: 0.8263 (pt0) cc_final: 0.7794 (mm110) REVERT: A 800 LYS cc_start: 0.8204 (pttt) cc_final: 0.7820 (ptmm) REVERT: A 908 MET cc_start: 0.7662 (ptm) cc_final: 0.7308 (ptm) REVERT: A 972 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.6831 (tppt) REVERT: A 975 LYS cc_start: 0.7796 (mttt) cc_final: 0.7263 (mmtp) REVERT: A 1026 THR cc_start: 0.8125 (m) cc_final: 0.7791 (p) REVERT: A 1044 SER cc_start: 0.8641 (p) cc_final: 0.8390 (t) REVERT: A 1092 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7863 (ttm) REVERT: A 1122 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8064 (mp) REVERT: A 1123 LYS cc_start: 0.7860 (mmtt) cc_final: 0.7590 (mmpt) REVERT: A 1164 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7367 (mp) REVERT: A 1171 ASP cc_start: 0.7674 (t0) cc_final: 0.7467 (m-30) REVERT: A 1210 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7869 (mp-120) REVERT: A 1232 TYR cc_start: 0.8778 (m-80) cc_final: 0.8534 (m-80) REVERT: A 1264 THR cc_start: 0.7942 (m) cc_final: 0.7668 (p) outliers start: 27 outliers final: 14 residues processed: 133 average time/residue: 0.5921 time to fit residues: 84.1529 Evaluate side-chains 128 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 965 LYS Chi-restraints excluded: chain A residue 972 LYS Chi-restraints excluded: chain A residue 1092 MET Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1223 MET Chi-restraints excluded: chain A residue 1248 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 68 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 81 optimal weight: 0.0030 chunk 4 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 84 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN A1066 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.183301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.139244 restraints weight = 10093.049| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.46 r_work: 0.3360 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9974 Z= 0.149 Angle : 0.532 8.680 13675 Z= 0.282 Chirality : 0.040 0.174 1521 Planarity : 0.004 0.043 1514 Dihedral : 17.675 103.671 1830 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.12 % Favored : 96.78 % Rotamer: Outliers : 3.18 % Allowed : 23.75 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.27), residues: 1026 helix: 1.81 (0.21), residues: 600 sheet: -1.45 (0.70), residues: 49 loop : 0.14 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1132 TYR 0.017 0.002 TYR A1112 PHE 0.025 0.002 PHE A 605 TRP 0.013 0.001 TRP A1247 HIS 0.004 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 9970) covalent geometry : angle 0.53055 (13672) hydrogen bonds : bond 0.03602 ( 501) hydrogen bonds : angle 4.12967 ( 1456) metal coordination : bond 0.00995 ( 4) metal coordination : angle 2.27978 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.363 Fit side-chains REVERT: A 251 LYS cc_start: 0.7493 (mttt) cc_final: 0.7265 (mtmm) REVERT: A 271 LYS cc_start: 0.7627 (tttt) cc_final: 0.7080 (tmtp) REVERT: A 571 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.7686 (mm-40) REVERT: A 732 LYS cc_start: 0.8191 (tppp) cc_final: 0.7767 (mtpt) REVERT: A 736 GLN cc_start: 0.8266 (pt0) cc_final: 0.7798 (mm110) REVERT: A 800 LYS cc_start: 0.8189 (pttt) cc_final: 0.7778 (ptmm) REVERT: A 908 MET cc_start: 0.7613 (ptm) cc_final: 0.7270 (ptm) REVERT: A 934 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.7821 (tmtt) REVERT: A 972 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.6863 (tppt) REVERT: A 975 LYS cc_start: 0.7804 (mttt) cc_final: 0.7260 (mmtp) REVERT: A 995 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7056 (mmm) REVERT: A 1015 LYS cc_start: 0.7101 (ttpt) cc_final: 0.6852 (ptmt) REVERT: A 1026 THR cc_start: 0.8095 (m) cc_final: 0.7742 (p) REVERT: A 1044 SER cc_start: 0.8626 (p) cc_final: 0.8358 (t) REVERT: A 1092 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7957 (ttm) REVERT: A 1122 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.8055 (mp) REVERT: A 1123 LYS cc_start: 0.7882 (mmtt) cc_final: 0.7668 (mmpt) REVERT: A 1164 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7274 (mp) REVERT: A 1171 ASP cc_start: 0.7776 (t0) cc_final: 0.7492 (m-30) REVERT: A 1210 GLN cc_start: 0.8247 (mm-40) cc_final: 0.7861 (mp-120) REVERT: A 1229 MET cc_start: 0.8794 (mmp) cc_final: 0.8554 (mmp) REVERT: A 1232 TYR cc_start: 0.8718 (m-80) cc_final: 0.8509 (m-80) REVERT: A 1264 THR cc_start: 0.7928 (m) cc_final: 0.7644 (p) outliers start: 30 outliers final: 13 residues processed: 131 average time/residue: 0.5829 time to fit residues: 81.7244 Evaluate side-chains 130 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 972 LYS Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1092 MET Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1248 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 0 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 48 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN A1066 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.182447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.139149 restraints weight = 9967.764| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.36 r_work: 0.3383 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 9974 Z= 0.157 Angle : 0.542 8.746 13675 Z= 0.288 Chirality : 0.040 0.151 1521 Planarity : 0.004 0.042 1514 Dihedral : 17.722 105.109 1830 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.22 % Favored : 96.69 % Rotamer: Outliers : 2.86 % Allowed : 24.07 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.27), residues: 1026 helix: 1.77 (0.21), residues: 600 sheet: -1.49 (0.70), residues: 49 loop : 0.15 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 522 TYR 0.018 0.002 TYR A1112 PHE 0.026 0.002 PHE A 605 TRP 0.013 0.001 TRP A1247 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 9970) covalent geometry : angle 0.54158 (13672) hydrogen bonds : bond 0.03665 ( 501) hydrogen bonds : angle 4.17555 ( 1456) metal coordination : bond 0.00932 ( 4) metal coordination : angle 2.07666 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.305 Fit side-chains REVERT: A 271 LYS cc_start: 0.7634 (tttt) cc_final: 0.7115 (tmtp) REVERT: A 571 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.7718 (mm-40) REVERT: A 732 LYS cc_start: 0.8152 (tppp) cc_final: 0.7770 (mtpt) REVERT: A 736 GLN cc_start: 0.8215 (pt0) cc_final: 0.7811 (mm110) REVERT: A 800 LYS cc_start: 0.8199 (pttt) cc_final: 0.7789 (ptmm) REVERT: A 908 MET cc_start: 0.7607 (ptm) cc_final: 0.7272 (ptm) REVERT: A 934 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.7810 (tmtt) REVERT: A 972 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.6905 (tppt) REVERT: A 975 LYS cc_start: 0.7780 (mttt) cc_final: 0.7256 (mmtp) REVERT: A 1026 THR cc_start: 0.8102 (m) cc_final: 0.7765 (p) REVERT: A 1044 SER cc_start: 0.8605 (p) cc_final: 0.8336 (t) REVERT: A 1092 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7919 (ttm) REVERT: A 1122 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8145 (mp) REVERT: A 1123 LYS cc_start: 0.7958 (mmtt) cc_final: 0.7691 (mmpt) REVERT: A 1164 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7303 (mp) REVERT: A 1171 ASP cc_start: 0.7759 (t0) cc_final: 0.7453 (m-30) REVERT: A 1210 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7927 (mp-120) REVERT: A 1229 MET cc_start: 0.8780 (mmp) cc_final: 0.8563 (mmp) REVERT: A 1232 TYR cc_start: 0.8742 (m-80) cc_final: 0.8500 (m-80) REVERT: A 1264 THR cc_start: 0.7966 (m) cc_final: 0.7707 (p) outliers start: 27 outliers final: 14 residues processed: 129 average time/residue: 0.5181 time to fit residues: 71.2737 Evaluate side-chains 127 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 815 MET Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 972 LYS Chi-restraints excluded: chain A residue 1092 MET Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1248 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 GLN A1066 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.180614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.136936 restraints weight = 10009.166| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.36 r_work: 0.3320 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 9974 Z= 0.189 Angle : 0.574 9.682 13675 Z= 0.302 Chirality : 0.041 0.162 1521 Planarity : 0.004 0.042 1514 Dihedral : 17.857 113.322 1830 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.02 % Favored : 96.88 % Rotamer: Outliers : 2.65 % Allowed : 23.86 % Favored : 73.49 % 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: 1.36 (0.27), residues: 1026 helix: 1.67 (0.21), residues: 600 sheet: -1.27 (0.73), residues: 44 loop : 0.03 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 522 TYR 0.022 0.002 TYR A1086 PHE 0.030 0.002 PHE A 605 TRP 0.012 0.001 TRP A1247 HIS 0.004 0.001 HIS A1142 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 9970) covalent geometry : angle 0.57305 (13672) hydrogen bonds : bond 0.03837 ( 501) hydrogen bonds : angle 4.26910 ( 1456) metal coordination : bond 0.01172 ( 4) metal coordination : angle 2.10910 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3276.83 seconds wall clock time: 56 minutes 36.86 seconds (3396.86 seconds total)