Starting phenix.real_space_refine on Wed Feb 4 12:10:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gkq_51433/02_2026/9gkq_51433.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gkq_51433/02_2026/9gkq_51433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gkq_51433/02_2026/9gkq_51433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gkq_51433/02_2026/9gkq_51433.map" model { file = "/net/cci-nas-00/data/ceres_data/9gkq_51433/02_2026/9gkq_51433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gkq_51433/02_2026/9gkq_51433.cif" } resolution = 2.85 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= -0.029 sd= 0.348 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: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 6581 2.51 5 N 1691 2.21 5 O 1948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 10253 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1257, 10253 Classifications: {'peptide': 1257} Link IDs: {'PTRANS': 37, 'TRANS': 1219} Chain breaks: 5 Time building chain proxies: 2.51, per 1000 atoms: 0.24 Number of scatterers: 10253 At special positions: 0 Unit cell: (78.114, 121.326, 143.763, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1948 8.00 N 1691 7.00 C 6581 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 454 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 507.5 milliseconds 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2392 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 15 sheets defined 34.3% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 53 through 57 removed outlier: 3.901A pdb=" N GLY A 57 " --> pdb=" O PRO A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 101 removed outlier: 3.789A pdb=" N THR A 101 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 114 Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 216 through 233 removed outlier: 3.609A pdb=" N THR A 220 " --> pdb=" O ASP A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 267 Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.590A pdb=" N ILE A 274 " --> pdb=" O ALA A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 299 Processing helix chain 'A' and resid 309 through 322 removed outlier: 4.053A pdb=" N MET A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 347 Processing helix chain 'A' and resid 350 through 359 Processing helix chain 'A' and resid 398 through 405 removed outlier: 3.755A pdb=" N PHE A 401 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLY A 403 " --> pdb=" O ASN A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 471 removed outlier: 3.593A pdb=" N ASN A 470 " --> pdb=" O SER A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 506 Processing helix chain 'A' and resid 549 through 557 Processing helix chain 'A' and resid 571 through 577 removed outlier: 3.511A pdb=" N LEU A 577 " --> pdb=" O ASN A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 596 Processing helix chain 'A' and resid 602 through 619 Processing helix chain 'A' and resid 634 through 636 No H-bonds generated for 'chain 'A' and resid 634 through 636' Processing helix chain 'A' and resid 637 through 642 Processing helix chain 'A' and resid 643 through 646 removed outlier: 3.970A pdb=" N MET A 646 " --> pdb=" O ILE A 643 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 643 through 646' Processing helix chain 'A' and resid 648 through 660 Processing helix chain 'A' and resid 687 through 753 removed outlier: 3.680A pdb=" N ILE A 695 " --> pdb=" O THR A 691 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR A 723 " --> pdb=" O ALA A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 766 through 800 removed outlier: 3.563A pdb=" N MET A 800 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 826 removed outlier: 3.641A pdb=" N ARG A 807 " --> pdb=" O TYR A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 829 No H-bonds generated for 'chain 'A' and resid 827 through 829' Processing helix chain 'A' and resid 833 through 847 Processing helix chain 'A' and resid 852 through 856 Processing helix chain 'A' and resid 859 through 871 Processing helix chain 'A' and resid 954 through 958 removed outlier: 3.591A pdb=" N SER A 957 " --> pdb=" O ASN A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1093 removed outlier: 3.806A pdb=" N ASN A1093 " --> pdb=" O ASP A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1215 removed outlier: 4.466A pdb=" N GLY A1215 " --> pdb=" O PRO A1212 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 148 removed outlier: 4.086A pdb=" N TYR A 21 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 38 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ILE A 42 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TRP A 43 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL A 152 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 164 " --> pdb=" O ARG A 187 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 213 through 214 removed outlier: 4.435A pdb=" N ALA A 372 " --> pdb=" O GLY A 195 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL A 373 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 324 through 325 Processing sheet with id=AA4, first strand: chain 'A' and resid 453 through 455 removed outlier: 6.882A pdb=" N CYS A 430 " --> pdb=" O LEU A 545 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 480 through 481 Processing sheet with id=AA6, first strand: chain 'A' and resid 568 through 569 Processing sheet with id=AA7, first strand: chain 'A' and resid 887 through 890 removed outlier: 3.835A pdb=" N LEU A 879 " --> pdb=" O LEU A1074 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE A1072 " --> pdb=" O LEU A 881 " (cutoff:3.500A) removed outlier: 10.299A pdb=" N TYR A 883 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 12.223A pdb=" N LYS A1070 " --> pdb=" O TYR A 883 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 887 through 890 removed outlier: 3.835A pdb=" N LEU A 879 " --> pdb=" O LEU A1074 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE A1072 " --> pdb=" O LEU A 881 " (cutoff:3.500A) removed outlier: 10.299A pdb=" N TYR A 883 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 12.223A pdb=" N LYS A1070 " --> pdb=" O TYR A 883 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N TYR A1071 " --> pdb=" O TRP A 946 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TRP A 946 " --> pdb=" O TYR A1071 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER A 942 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER A1027 " --> pdb=" O LYS A1039 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A1029 " --> pdb=" O ASP A1037 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASP A1037 " --> pdb=" O ILE A1029 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE A1031 " --> pdb=" O LEU A1035 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N LEU A1035 " --> pdb=" O ILE A1031 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 897 through 900 removed outlier: 4.091A pdb=" N LYS A 897 " --> pdb=" O ILE A 927 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A 924 " --> pdb=" O PHE A1055 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE A1055 " --> pdb=" O ILE A 924 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE A 964 " --> pdb=" O LYS A1056 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASP A1058 " --> pdb=" O TYR A 962 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N TYR A 962 " --> pdb=" O ASP A1058 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N THR A 963 " --> pdb=" O LEU A 978 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU A 978 " --> pdb=" O THR A 963 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 965 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1114 through 1115 Processing sheet with id=AB2, first strand: chain 'A' and resid 1123 through 1125 Processing sheet with id=AB3, first strand: chain 'A' and resid 1142 through 1145 Processing sheet with id=AB4, first strand: chain 'A' and resid 1159 through 1164 removed outlier: 3.712A pdb=" N LYS A1159 " --> pdb=" O VAL A1185 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ILE A1182 " --> pdb=" O LEU A1193 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A1193 " --> pdb=" O ILE A1182 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1159 through 1164 removed outlier: 3.712A pdb=" N LYS A1159 " --> pdb=" O VAL A1185 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL A1220 " --> pdb=" O GLN A1240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1203 through 1205 410 hydrogen bonds defined for protein. 1146 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.15 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3299 1.34 - 1.46: 2219 1.46 - 1.58: 4894 1.58 - 1.69: 0 1.69 - 1.81: 57 Bond restraints: 10469 Sorted by residual: bond pdb=" CG1 ILE A1036 " pdb=" CD1 ILE A1036 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.52e+00 bond pdb=" CA ILE A 801 " pdb=" CB ILE A 801 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 8.19e-01 bond pdb=" C LYS A 779 " pdb=" O LYS A 779 " ideal model delta sigma weight residual 1.236 1.246 -0.010 1.15e-02 7.56e+03 7.23e-01 bond pdb=" CG1 ILE A 634 " pdb=" CD1 ILE A 634 " ideal model delta sigma weight residual 1.513 1.480 0.033 3.90e-02 6.57e+02 7.02e-01 bond pdb=" CA ASN A 886 " pdb=" CB ASN A 886 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.54e-02 4.22e+03 6.65e-01 ... (remaining 10464 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 13685 1.16 - 2.33: 391 2.33 - 3.49: 71 3.49 - 4.65: 14 4.65 - 5.82: 8 Bond angle restraints: 14169 Sorted by residual: angle pdb=" C VAL A 607 " pdb=" N GLU A 608 " pdb=" CA GLU A 608 " ideal model delta sigma weight residual 120.31 115.57 4.74 1.52e+00 4.33e-01 9.71e+00 angle pdb=" C SER A 622 " pdb=" N THR A 623 " pdb=" CA THR A 623 " ideal model delta sigma weight residual 121.54 127.36 -5.82 1.91e+00 2.74e-01 9.27e+00 angle pdb=" N ILE A 878 " pdb=" CA ILE A 878 " pdb=" C ILE A 878 " ideal model delta sigma weight residual 113.20 110.31 2.89 9.60e-01 1.09e+00 9.07e+00 angle pdb=" N GLU A 608 " pdb=" CA GLU A 608 " pdb=" CB GLU A 608 " ideal model delta sigma weight residual 110.28 114.72 -4.44 1.55e+00 4.16e-01 8.22e+00 angle pdb=" N LYS A 301 " pdb=" CA LYS A 301 " pdb=" CB LYS A 301 " ideal model delta sigma weight residual 113.65 109.58 4.07 1.47e+00 4.63e-01 7.67e+00 ... (remaining 14164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 5650 16.81 - 33.63: 510 33.63 - 50.44: 87 50.44 - 67.25: 12 67.25 - 84.07: 13 Dihedral angle restraints: 6272 sinusoidal: 2556 harmonic: 3716 Sorted by residual: dihedral pdb=" CA HIS A1253 " pdb=" C HIS A1253 " pdb=" N GLN A1254 " pdb=" CA GLN A1254 " ideal model delta harmonic sigma weight residual -180.00 -162.48 -17.52 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA LYS A1260 " pdb=" C LYS A1260 " pdb=" N LEU A1261 " pdb=" CA LEU A1261 " ideal model delta harmonic sigma weight residual 180.00 163.36 16.64 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ILE A1258 " pdb=" C ILE A1258 " pdb=" N ALA A1259 " pdb=" CA ALA A1259 " ideal model delta harmonic sigma weight residual 180.00 163.98 16.02 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 6269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 919 0.029 - 0.058: 405 0.058 - 0.087: 128 0.087 - 0.116: 89 0.116 - 0.145: 19 Chirality restraints: 1560 Sorted by residual: chirality pdb=" CB ILE A 914 " pdb=" CA ILE A 914 " pdb=" CG1 ILE A 914 " pdb=" CG2 ILE A 914 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA ASP A1108 " pdb=" N ASP A1108 " pdb=" C ASP A1108 " pdb=" CB ASP A1108 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ASN A 886 " pdb=" N ASN A 886 " pdb=" C ASN A 886 " pdb=" CB ASN A 886 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 1557 not shown) Planarity restraints: 1821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A1109 " -0.036 5.00e-02 4.00e+02 5.54e-02 4.92e+00 pdb=" N PRO A1110 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A1110 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1110 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A1211 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO A1212 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A1212 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1212 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 907 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO A 908 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 908 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 908 " -0.024 5.00e-02 4.00e+02 ... (remaining 1818 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1000 2.75 - 3.29: 10902 3.29 - 3.82: 17589 3.82 - 4.36: 20475 4.36 - 4.90: 35264 Nonbonded interactions: 85230 Sorted by model distance: nonbonded pdb=" OG SER A 942 " pdb=" O LYS A1077 " model vdw 2.211 3.040 nonbonded pdb=" O SER A 622 " pdb=" OG1 THR A 623 " model vdw 2.220 3.040 nonbonded pdb=" OG SER A 167 " pdb=" OG SER A 182 " model vdw 2.234 3.040 nonbonded pdb=" O THR A 125 " pdb=" OG SER A 302 " model vdw 2.237 3.040 nonbonded pdb=" OH TYR A 87 " pdb=" O PHE A 188 " model vdw 2.244 3.040 ... (remaining 85225 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 3.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.730 Find NCS groups from input model: 0.050 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:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 0.048 10470 Z= 0.116 Angle : 0.495 5.817 14171 Z= 0.268 Chirality : 0.042 0.145 1560 Planarity : 0.004 0.055 1821 Dihedral : 13.195 84.065 3877 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.24), residues: 1245 helix: 1.81 (0.26), residues: 369 sheet: -0.51 (0.43), residues: 157 loop : -1.13 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1065 TYR 0.015 0.001 TYR A 636 PHE 0.017 0.001 PHE A 425 TRP 0.023 0.002 TRP A 974 HIS 0.005 0.001 HIS A1253 Details of bonding type rmsd covalent geometry : bond 0.00263 (10469) covalent geometry : angle 0.49466 (14169) SS BOND : bond 0.00055 ( 1) SS BOND : angle 0.25148 ( 2) hydrogen bonds : bond 0.18110 ( 399) hydrogen bonds : angle 6.87421 ( 1146) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.9074 (mppt) cc_final: 0.8687 (mptt) REVERT: A 272 LYS cc_start: 0.8748 (mmpt) cc_final: 0.8489 (mmpt) REVERT: A 315 ASN cc_start: 0.8561 (t0) cc_final: 0.8141 (t0) REVERT: A 483 SER cc_start: 0.9157 (p) cc_final: 0.8863 (t) REVERT: A 530 LEU cc_start: 0.9104 (tp) cc_final: 0.8877 (tm) REVERT: A 839 ASP cc_start: 0.8253 (m-30) cc_final: 0.7982 (m-30) REVERT: A 903 LYS cc_start: 0.8427 (mmpt) cc_final: 0.8018 (mmmt) REVERT: A 922 SER cc_start: 0.8637 (t) cc_final: 0.8416 (t) REVERT: A 1013 ARG cc_start: 0.7720 (mmm-85) cc_final: 0.7310 (mmm-85) REVERT: A 1014 TRP cc_start: 0.7698 (m100) cc_final: 0.7395 (m100) REVERT: A 1021 ASN cc_start: 0.8154 (m-40) cc_final: 0.7941 (m-40) REVERT: A 1214 VAL cc_start: 0.8178 (t) cc_final: 0.7961 (m) REVERT: A 1240 GLN cc_start: 0.8064 (mt0) cc_final: 0.7863 (mm-40) REVERT: A 1242 ASN cc_start: 0.7665 (t0) cc_final: 0.7464 (t0) REVERT: A 1253 HIS cc_start: 0.4522 (m90) cc_final: 0.3964 (m170) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.5781 time to fit residues: 171.4446 Evaluate side-chains 206 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.0030 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.0870 chunk 51 optimal weight: 2.9990 overall best weight: 1.0172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN A 843 ASN A 912 ASN ** A 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1177 ASN ** 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 = 0.3720 r_free = 0.3720 target = 0.084050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.075026 restraints weight = 28670.687| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.55 r_work: 0.3387 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 10470 Z= 0.213 Angle : 0.701 9.708 14171 Z= 0.371 Chirality : 0.048 0.181 1560 Planarity : 0.005 0.059 1821 Dihedral : 4.822 19.271 1365 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.45 % Allowed : 14.15 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.23), residues: 1245 helix: 1.15 (0.25), residues: 383 sheet: -0.59 (0.45), residues: 139 loop : -1.23 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 836 TYR 0.025 0.002 TYR A 250 PHE 0.018 0.002 PHE A 614 TRP 0.021 0.002 TRP A 606 HIS 0.004 0.001 HIS A1253 Details of bonding type rmsd covalent geometry : bond 0.00502 (10469) covalent geometry : angle 0.70066 (14169) SS BOND : bond 0.00732 ( 1) SS BOND : angle 2.64947 ( 2) hydrogen bonds : bond 0.05543 ( 399) hydrogen bonds : angle 5.48308 ( 1146) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.9142 (mppt) cc_final: 0.8783 (mptt) REVERT: A 272 LYS cc_start: 0.8903 (mmpt) cc_final: 0.8671 (mmpt) REVERT: A 310 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7856 (tp) REVERT: A 452 ASP cc_start: 0.7413 (t0) cc_final: 0.6811 (t0) REVERT: A 530 LEU cc_start: 0.9106 (tp) cc_final: 0.8880 (tm) REVERT: A 648 TYR cc_start: 0.7560 (m-10) cc_final: 0.7299 (m-10) REVERT: A 863 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8233 (mp) REVERT: A 903 LYS cc_start: 0.8615 (mmpt) cc_final: 0.8215 (mmmt) REVERT: A 1013 ARG cc_start: 0.7863 (mmm-85) cc_final: 0.7456 (mmm-85) REVERT: A 1067 ILE cc_start: 0.8884 (pt) cc_final: 0.8505 (pp) REVERT: A 1191 TYR cc_start: 0.7567 (m-10) cc_final: 0.7337 (m-80) REVERT: A 1242 ASN cc_start: 0.7727 (t0) cc_final: 0.7521 (t0) REVERT: A 1283 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7971 (mm-30) outliers start: 28 outliers final: 10 residues processed: 234 average time/residue: 0.5279 time to fit residues: 134.2789 Evaluate side-chains 212 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 200 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain A residue 1117 TYR Chi-restraints excluded: chain A residue 1223 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 ASN A 722 ASN ** A 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1240 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.083980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.075043 restraints weight = 28957.841| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.52 r_work: 0.3396 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10470 Z= 0.179 Angle : 0.672 11.630 14171 Z= 0.351 Chirality : 0.046 0.202 1560 Planarity : 0.004 0.059 1821 Dihedral : 4.813 18.271 1365 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.27 % Allowed : 17.47 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.23), residues: 1245 helix: 1.20 (0.25), residues: 383 sheet: -0.65 (0.41), residues: 163 loop : -1.40 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1179 TYR 0.022 0.002 TYR A 250 PHE 0.015 0.002 PHE A 679 TRP 0.023 0.002 TRP A 606 HIS 0.003 0.001 HIS A1253 Details of bonding type rmsd covalent geometry : bond 0.00424 (10469) covalent geometry : angle 0.66958 (14169) SS BOND : bond 0.01970 ( 1) SS BOND : angle 4.54800 ( 2) hydrogen bonds : bond 0.05207 ( 399) hydrogen bonds : angle 5.26794 ( 1146) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.9100 (mppt) cc_final: 0.8770 (mptt) REVERT: A 452 ASP cc_start: 0.7451 (t0) cc_final: 0.6913 (t0) REVERT: A 530 LEU cc_start: 0.9139 (tp) cc_final: 0.8897 (tm) REVERT: A 835 ASP cc_start: 0.8685 (t0) cc_final: 0.8205 (t0) REVERT: A 863 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8229 (mp) REVERT: A 903 LYS cc_start: 0.8563 (mmpt) cc_final: 0.8168 (mmpt) REVERT: A 1013 ARG cc_start: 0.7859 (mmm-85) cc_final: 0.7519 (mmm-85) REVERT: A 1165 TYR cc_start: 0.7020 (t80) cc_final: 0.6222 (t80) REVERT: A 1242 ASN cc_start: 0.7711 (t0) cc_final: 0.7484 (t0) REVERT: A 1283 GLU cc_start: 0.8222 (mm-30) cc_final: 0.8006 (mm-30) outliers start: 26 outliers final: 9 residues processed: 225 average time/residue: 0.5371 time to fit residues: 131.1746 Evaluate side-chains 207 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 197 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 TYR Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 1117 TYR Chi-restraints excluded: chain A residue 1223 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 93 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 53 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 ASN ** A 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 991 GLN ** A1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1177 ASN ** 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 = 0.3734 r_free = 0.3734 target = 0.084815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.075863 restraints weight = 28956.773| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.55 r_work: 0.3413 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10470 Z= 0.157 Angle : 0.660 8.394 14171 Z= 0.348 Chirality : 0.046 0.227 1560 Planarity : 0.004 0.056 1821 Dihedral : 4.781 19.617 1365 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.88 % Allowed : 19.30 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.23), residues: 1245 helix: 1.38 (0.26), residues: 377 sheet: -0.53 (0.42), residues: 161 loop : -1.40 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1179 TYR 0.024 0.002 TYR A 250 PHE 0.034 0.002 PHE A 679 TRP 0.022 0.001 TRP A 606 HIS 0.002 0.000 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00366 (10469) covalent geometry : angle 0.65610 (14169) SS BOND : bond 0.02517 ( 1) SS BOND : angle 6.12817 ( 2) hydrogen bonds : bond 0.04817 ( 399) hydrogen bonds : angle 5.13840 ( 1146) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 216 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.9092 (mppt) cc_final: 0.8789 (mptt) REVERT: A 452 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.6986 (t0) REVERT: A 482 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8732 (p) REVERT: A 903 LYS cc_start: 0.8568 (mmpt) cc_final: 0.8154 (mmpt) REVERT: A 1013 ARG cc_start: 0.7829 (mmm-85) cc_final: 0.7512 (mmm-85) REVERT: A 1240 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7474 (mm-40) REVERT: A 1283 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7973 (mm-30) outliers start: 33 outliers final: 10 residues processed: 230 average time/residue: 0.4922 time to fit residues: 123.4224 Evaluate side-chains 212 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 199 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 1117 TYR Chi-restraints excluded: chain A residue 1223 MET Chi-restraints excluded: chain A residue 1240 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 48 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 106 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 45 optimal weight: 0.0040 chunk 58 optimal weight: 1.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 798 ASN A 959 ASN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.085197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.076213 restraints weight = 28796.849| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.56 r_work: 0.3417 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10470 Z= 0.159 Angle : 0.689 9.943 14171 Z= 0.354 Chirality : 0.046 0.292 1560 Planarity : 0.004 0.055 1821 Dihedral : 4.766 19.755 1365 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.79 % Allowed : 20.35 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.24), residues: 1245 helix: 1.46 (0.26), residues: 377 sheet: -0.59 (0.42), residues: 163 loop : -1.35 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1179 TYR 0.029 0.002 TYR A1071 PHE 0.046 0.002 PHE A 679 TRP 0.022 0.002 TRP A 606 HIS 0.002 0.000 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00377 (10469) covalent geometry : angle 0.68315 (14169) SS BOND : bond 0.02936 ( 1) SS BOND : angle 7.62430 ( 2) hydrogen bonds : bond 0.04755 ( 399) hydrogen bonds : angle 4.98864 ( 1146) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 214 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.9075 (mppt) cc_final: 0.8774 (mptt) REVERT: A 180 TYR cc_start: 0.7024 (m-80) cc_final: 0.6817 (m-80) REVERT: A 452 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7179 (t0) REVERT: A 482 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8592 (p) REVERT: A 483 SER cc_start: 0.9128 (p) cc_final: 0.8850 (t) REVERT: A 502 TYR cc_start: 0.7521 (m-80) cc_final: 0.7241 (m-80) REVERT: A 863 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8247 (mp) REVERT: A 903 LYS cc_start: 0.8538 (mmpt) cc_final: 0.8145 (mmmt) REVERT: A 994 LYS cc_start: 0.8250 (mmmm) cc_final: 0.7932 (mmmt) REVERT: A 1013 ARG cc_start: 0.7841 (mmm-85) cc_final: 0.7558 (mmm-85) REVERT: A 1191 TYR cc_start: 0.7292 (m-10) cc_final: 0.7030 (m-10) REVERT: A 1240 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7601 (mm-40) outliers start: 32 outliers final: 10 residues processed: 225 average time/residue: 0.5136 time to fit residues: 125.7940 Evaluate side-chains 211 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 1117 TYR Chi-restraints excluded: chain A residue 1223 MET Chi-restraints excluded: chain A residue 1240 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 75 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 55 optimal weight: 0.0030 chunk 79 optimal weight: 0.6980 chunk 123 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 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 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN A 368 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 959 ASN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1091 GLN ** A1177 ASN ** 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 = 0.3735 r_free = 0.3735 target = 0.084135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.075357 restraints weight = 29263.017| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.50 r_work: 0.3429 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 10470 Z= 0.160 Angle : 0.705 11.519 14171 Z= 0.362 Chirality : 0.047 0.336 1560 Planarity : 0.004 0.055 1821 Dihedral : 4.777 19.552 1365 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.14 % Allowed : 21.22 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.24), residues: 1245 helix: 1.29 (0.26), residues: 389 sheet: -0.79 (0.39), residues: 180 loop : -1.40 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1179 TYR 0.030 0.002 TYR A 250 PHE 0.039 0.002 PHE A 679 TRP 0.022 0.001 TRP A 606 HIS 0.001 0.000 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00388 (10469) covalent geometry : angle 0.69896 (14169) SS BOND : bond 0.02730 ( 1) SS BOND : angle 8.03098 ( 2) hydrogen bonds : bond 0.04610 ( 399) hydrogen bonds : angle 4.90729 ( 1146) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 202 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.9042 (mppt) cc_final: 0.8759 (mptt) REVERT: A 256 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8413 (mt) REVERT: A 452 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7191 (t0) REVERT: A 483 SER cc_start: 0.8969 (p) cc_final: 0.8718 (t) REVERT: A 502 TYR cc_start: 0.7531 (m-80) cc_final: 0.7316 (OUTLIER) REVERT: A 758 GLU cc_start: 0.7598 (tp30) cc_final: 0.7238 (tp30) REVERT: A 903 LYS cc_start: 0.8510 (mmpt) cc_final: 0.8133 (mmmt) REVERT: A 1013 ARG cc_start: 0.7781 (mmm-85) cc_final: 0.7551 (mmm-85) REVERT: A 1054 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7475 (tmm) REVERT: A 1067 ILE cc_start: 0.8746 (pt) cc_final: 0.8331 (pp) REVERT: A 1191 TYR cc_start: 0.7232 (m-10) cc_final: 0.6977 (m-10) REVERT: A 1240 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7477 (mm110) REVERT: A 1282 TRP cc_start: 0.8582 (m100) cc_final: 0.8337 (m100) outliers start: 36 outliers final: 14 residues processed: 216 average time/residue: 0.5132 time to fit residues: 120.8086 Evaluate side-chains 210 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 193 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 1054 MET Chi-restraints excluded: chain A residue 1117 TYR Chi-restraints excluded: chain A residue 1223 MET Chi-restraints excluded: chain A residue 1240 GLN Chi-restraints excluded: chain A residue 1255 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 124 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 116 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 595 ASN A 959 ASN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1240 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.083336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.074349 restraints weight = 29062.464| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.55 r_work: 0.3378 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 10470 Z= 0.211 Angle : 0.739 11.291 14171 Z= 0.383 Chirality : 0.048 0.278 1560 Planarity : 0.004 0.059 1821 Dihedral : 4.958 18.856 1365 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.41 % Allowed : 22.36 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.23), residues: 1245 helix: 1.02 (0.25), residues: 389 sheet: -0.82 (0.39), residues: 180 loop : -1.45 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1175 TYR 0.035 0.002 TYR A 250 PHE 0.034 0.002 PHE A 679 TRP 0.025 0.002 TRP A 606 HIS 0.002 0.001 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00508 (10469) covalent geometry : angle 0.73613 (14169) SS BOND : bond 0.01901 ( 1) SS BOND : angle 5.85132 ( 2) hydrogen bonds : bond 0.05173 ( 399) hydrogen bonds : angle 4.97297 ( 1146) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 205 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.9137 (mppt) cc_final: 0.8819 (mptt) REVERT: A 180 TYR cc_start: 0.7022 (m-80) cc_final: 0.6730 (m-80) REVERT: A 452 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7203 (t0) REVERT: A 483 SER cc_start: 0.8892 (p) cc_final: 0.8678 (t) REVERT: A 863 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8294 (mp) REVERT: A 903 LYS cc_start: 0.8596 (mmpt) cc_final: 0.8203 (mmmt) REVERT: A 994 LYS cc_start: 0.8302 (mmmm) cc_final: 0.8042 (mmmt) REVERT: A 1013 ARG cc_start: 0.7839 (mmm-85) cc_final: 0.7579 (mmm-85) REVERT: A 1067 ILE cc_start: 0.8845 (pt) cc_final: 0.8424 (pp) REVERT: A 1191 TYR cc_start: 0.7261 (m-10) cc_final: 0.7023 (m-10) REVERT: A 1203 GLU cc_start: 0.8259 (pp20) cc_final: 0.8041 (pp20) REVERT: A 1240 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7570 (mm110) REVERT: A 1242 ASN cc_start: 0.7564 (t0) cc_final: 0.7301 (t0) REVERT: A 1282 TRP cc_start: 0.8616 (m100) cc_final: 0.8356 (m100) outliers start: 39 outliers final: 18 residues processed: 223 average time/residue: 0.5026 time to fit residues: 122.3549 Evaluate side-chains 220 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 502 TYR Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 1223 MET Chi-restraints excluded: chain A residue 1240 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 16 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 108 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 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 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.082532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.073800 restraints weight = 29260.488| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.50 r_work: 0.3384 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 10470 Z= 0.184 Angle : 0.770 16.105 14171 Z= 0.394 Chirality : 0.049 0.330 1560 Planarity : 0.004 0.066 1821 Dihedral : 4.972 19.645 1365 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.45 % Allowed : 23.58 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.23), residues: 1245 helix: 1.06 (0.25), residues: 389 sheet: -0.85 (0.39), residues: 180 loop : -1.46 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1179 TYR 0.042 0.002 TYR A 250 PHE 0.039 0.002 PHE A 679 TRP 0.025 0.002 TRP A 606 HIS 0.002 0.000 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00442 (10469) covalent geometry : angle 0.76558 (14169) SS BOND : bond 0.02733 ( 1) SS BOND : angle 6.84449 ( 2) hydrogen bonds : bond 0.04924 ( 399) hydrogen bonds : angle 4.97577 ( 1146) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.9100 (mppt) cc_final: 0.8798 (mptt) REVERT: A 452 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7334 (t0) REVERT: A 483 SER cc_start: 0.8758 (p) cc_final: 0.8550 (t) REVERT: A 554 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7875 (tt) REVERT: A 756 GLU cc_start: 0.8017 (tp30) cc_final: 0.7817 (tp30) REVERT: A 758 GLU cc_start: 0.7595 (tp30) cc_final: 0.7252 (tp30) REVERT: A 781 MET cc_start: 0.8761 (mmm) cc_final: 0.8120 (mmm) REVERT: A 903 LYS cc_start: 0.8408 (mmpt) cc_final: 0.8005 (mmmt) REVERT: A 922 SER cc_start: 0.8436 (t) cc_final: 0.8231 (t) REVERT: A 995 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8297 (tm-30) REVERT: A 1013 ARG cc_start: 0.7805 (mmm-85) cc_final: 0.7588 (mmm-85) REVERT: A 1054 MET cc_start: 0.8152 (tpp) cc_final: 0.7833 (tpp) REVERT: A 1067 ILE cc_start: 0.8801 (pt) cc_final: 0.8380 (pp) REVERT: A 1083 GLU cc_start: 0.8422 (tp30) cc_final: 0.8202 (tp30) REVERT: A 1191 TYR cc_start: 0.7192 (m-10) cc_final: 0.6959 (m-10) REVERT: A 1240 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7536 (mm-40) REVERT: A 1242 ASN cc_start: 0.7475 (t0) cc_final: 0.7195 (t0) REVERT: A 1282 TRP cc_start: 0.8596 (m100) cc_final: 0.8358 (m100) outliers start: 28 outliers final: 14 residues processed: 221 average time/residue: 0.4891 time to fit residues: 118.0550 Evaluate side-chains 224 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 206 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 968 MET Chi-restraints excluded: chain A residue 995 GLN Chi-restraints excluded: chain A residue 1117 TYR Chi-restraints excluded: chain A residue 1223 MET Chi-restraints excluded: chain A residue 1240 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 60 optimal weight: 0.0770 chunk 27 optimal weight: 0.0170 chunk 69 optimal weight: 0.4980 chunk 120 optimal weight: 0.4980 chunk 112 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 396 ASN ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 ASN A 722 ASN A 959 ASN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.086090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.077147 restraints weight = 29017.378| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.57 r_work: 0.3440 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10470 Z= 0.157 Angle : 0.786 14.643 14171 Z= 0.398 Chirality : 0.047 0.270 1560 Planarity : 0.004 0.066 1821 Dihedral : 4.933 20.122 1365 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.71 % Allowed : 24.45 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.24), residues: 1245 helix: 1.31 (0.26), residues: 389 sheet: -0.62 (0.41), residues: 169 loop : -1.46 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1179 TYR 0.046 0.002 TYR A 250 PHE 0.046 0.002 PHE A 679 TRP 0.025 0.001 TRP A 606 HIS 0.003 0.001 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00380 (10469) covalent geometry : angle 0.78330 (14169) SS BOND : bond 0.02062 ( 1) SS BOND : angle 5.48267 ( 2) hydrogen bonds : bond 0.04530 ( 399) hydrogen bonds : angle 4.90195 ( 1146) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.9051 (mppt) cc_final: 0.8745 (mptt) REVERT: A 30 MET cc_start: 0.5711 (ppp) cc_final: 0.5310 (pp-130) REVERT: A 452 ASP cc_start: 0.7598 (t0) cc_final: 0.7317 (t0) REVERT: A 554 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7853 (tt) REVERT: A 903 LYS cc_start: 0.8257 (mmpt) cc_final: 0.7821 (mmmt) REVERT: A 1067 ILE cc_start: 0.8738 (pt) cc_final: 0.8308 (pp) REVERT: A 1191 TYR cc_start: 0.7214 (m-10) cc_final: 0.6947 (m-10) REVERT: A 1240 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7569 (mm110) REVERT: A 1242 ASN cc_start: 0.7524 (t0) cc_final: 0.7197 (t0) REVERT: A 1282 TRP cc_start: 0.8593 (m100) cc_final: 0.8208 (m100) outliers start: 31 outliers final: 13 residues processed: 217 average time/residue: 0.4626 time to fit residues: 109.3801 Evaluate side-chains 214 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 199 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 1117 TYR Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1240 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 57 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 108 optimal weight: 0.0050 chunk 40 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 519 ASN ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1003 GLN ** A1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1091 GLN ** 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 = 0.3728 r_free = 0.3728 target = 0.084040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.075241 restraints weight = 28838.737| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.49 r_work: 0.3414 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10470 Z= 0.178 Angle : 0.834 14.179 14171 Z= 0.422 Chirality : 0.049 0.265 1560 Planarity : 0.004 0.064 1821 Dihedral : 5.071 23.832 1365 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.31 % Allowed : 26.46 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.23), residues: 1245 helix: 1.22 (0.26), residues: 389 sheet: -0.74 (0.39), residues: 182 loop : -1.50 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1179 TYR 0.049 0.002 TYR A 250 PHE 0.027 0.002 PHE A 941 TRP 0.035 0.002 TRP A 606 HIS 0.001 0.000 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00438 (10469) covalent geometry : angle 0.83162 (14169) SS BOND : bond 0.01977 ( 1) SS BOND : angle 4.98981 ( 2) hydrogen bonds : bond 0.04738 ( 399) hydrogen bonds : angle 4.89176 ( 1146) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.9040 (mppt) cc_final: 0.8754 (mptt) REVERT: A 30 MET cc_start: 0.5491 (ppp) cc_final: 0.5063 (pp-130) REVERT: A 256 LEU cc_start: 0.8500 (mm) cc_final: 0.8277 (mm) REVERT: A 390 PHE cc_start: 0.5252 (m-80) cc_final: 0.5012 (m-10) REVERT: A 413 PHE cc_start: 0.6536 (m-10) cc_final: 0.6234 (m-10) REVERT: A 452 ASP cc_start: 0.7615 (t0) cc_final: 0.7330 (t0) REVERT: A 554 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7907 (tt) REVERT: A 903 LYS cc_start: 0.8248 (mmpt) cc_final: 0.7801 (mmmt) REVERT: A 1067 ILE cc_start: 0.8712 (pt) cc_final: 0.8299 (pp) REVERT: A 1087 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8862 (tt) REVERT: A 1191 TYR cc_start: 0.7294 (m-10) cc_final: 0.7091 (m-10) REVERT: A 1240 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7514 (mm110) REVERT: A 1242 ASN cc_start: 0.7594 (t0) cc_final: 0.7268 (t0) REVERT: A 1282 TRP cc_start: 0.8532 (m100) cc_final: 0.8280 (m100) outliers start: 15 outliers final: 12 residues processed: 211 average time/residue: 0.4528 time to fit residues: 104.2804 Evaluate side-chains 212 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 197 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 368 ASN Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 608 GLU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1117 TYR Chi-restraints excluded: chain A residue 1240 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 88 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 24 optimal weight: 0.0670 chunk 19 optimal weight: 0.8980 chunk 65 optimal weight: 0.0970 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 ASN A 368 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1240 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.084636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.075843 restraints weight = 29197.640| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.52 r_work: 0.3428 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10470 Z= 0.170 Angle : 0.833 15.909 14171 Z= 0.421 Chirality : 0.048 0.261 1560 Planarity : 0.004 0.067 1821 Dihedral : 5.129 31.938 1365 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.75 % Allowed : 26.29 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.24), residues: 1245 helix: 1.29 (0.26), residues: 389 sheet: -0.83 (0.38), residues: 193 loop : -1.51 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1179 TYR 0.046 0.002 TYR A1071 PHE 0.028 0.002 PHE A 941 TRP 0.036 0.002 TRP A 606 HIS 0.001 0.000 HIS A 223 Details of bonding type rmsd covalent geometry : bond 0.00413 (10469) covalent geometry : angle 0.83075 (14169) SS BOND : bond 0.01871 ( 1) SS BOND : angle 4.74366 ( 2) hydrogen bonds : bond 0.04674 ( 399) hydrogen bonds : angle 4.93114 ( 1146) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3395.10 seconds wall clock time: 59 minutes 1.03 seconds (3541.03 seconds total)