Starting phenix.real_space_refine on Wed Sep 17 12:51:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nfi_49366/09_2025/9nfi_49366_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nfi_49366/09_2025/9nfi_49366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nfi_49366/09_2025/9nfi_49366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nfi_49366/09_2025/9nfi_49366.map" model { file = "/net/cci-nas-00/data/ceres_data/9nfi_49366/09_2025/9nfi_49366_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nfi_49366/09_2025/9nfi_49366_neut.cif" } resolution = 3.79 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= 0.044 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 49 5.16 5 C 5550 2.51 5 N 1468 2.21 5 O 1597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8664 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 8664 Classifications: {'peptide': 1116} Link IDs: {'PTRANS': 32, 'TRANS': 1083} Chain breaks: 5 Time building chain proxies: 2.21, per 1000 atoms: 0.26 Number of scatterers: 8664 At special positions: 0 Unit cell: (82.28, 99.11, 142.12, 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 49 16.00 O 1597 8.00 N 1468 7.00 C 5550 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: 0.85 Conformation dependent library (CDL) restraints added in 366.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 5 sheets defined 65.9% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 47 through 52 removed outlier: 3.592A pdb=" N PHE A 52 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 96 Proline residue: A 78 - end of helix removed outlier: 4.166A pdb=" N CYS A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET A 96 " --> pdb=" O ILE A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 170 Processing helix chain 'A' and resid 171 through 177 removed outlier: 3.908A pdb=" N PHE A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 222 removed outlier: 3.974A pdb=" N ASP A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL A 202 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 256 through 272 removed outlier: 5.515A pdb=" N LYS A 261 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ALA A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 281 through 336 Processing helix chain 'A' and resid 341 through 382 removed outlier: 4.192A pdb=" N SER A 361 " --> pdb=" O MET A 357 " (cutoff:3.500A) Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 445 through 453 removed outlier: 4.130A pdb=" N ILE A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 481 Processing helix chain 'A' and resid 495 through 502 removed outlier: 3.551A pdb=" N TYR A 502 " --> pdb=" O GLU A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 520 Processing helix chain 'A' and resid 544 through 559 removed outlier: 4.122A pdb=" N ARG A 559 " --> pdb=" O ARG A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 589 removed outlier: 4.101A pdb=" N ILE A 580 " --> pdb=" O GLU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 630 removed outlier: 3.584A pdb=" N LYS A 630 " --> pdb=" O LEU A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 723 Processing helix chain 'A' and resid 725 through 756 Proline residue: A 744 - end of helix Processing helix chain 'A' and resid 762 through 816 Processing helix chain 'A' and resid 818 through 823 removed outlier: 3.743A pdb=" N ASP A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASN A 823 " --> pdb=" O GLY A 819 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 818 through 823' Processing helix chain 'A' and resid 824 through 826 No H-bonds generated for 'chain 'A' and resid 824 through 826' Processing helix chain 'A' and resid 827 through 871 removed outlier: 4.429A pdb=" N ALA A 839 " --> pdb=" O LEU A 835 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA A 840 " --> pdb=" O ALA A 836 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY A 847 " --> pdb=" O GLN A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 880 Processing helix chain 'A' and resid 883 through 891 removed outlier: 4.322A pdb=" N VAL A 887 " --> pdb=" O PRO A 883 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A 888 " --> pdb=" O ILE A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 920 removed outlier: 3.761A pdb=" N ALA A 910 " --> pdb=" O GLU A 906 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE A 913 " --> pdb=" O LYS A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 927 Processing helix chain 'A' and resid 929 through 984 removed outlier: 4.156A pdb=" N VAL A 943 " --> pdb=" O GLU A 939 " (cutoff:3.500A) Proline residue: A 944 - end of helix removed outlier: 3.975A pdb=" N ILE A 966 " --> pdb=" O SER A 962 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR A 967 " --> pdb=" O GLN A 963 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE A 974 " --> pdb=" O TYR A 970 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A 975 " --> pdb=" O ALA A 971 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE A 976 " --> pdb=" O GLY A 972 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TRP A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1002 Processing helix chain 'A' and resid 1014 through 1029 Processing helix chain 'A' and resid 1094 through 1101 Processing helix chain 'A' and resid 1122 through 1129 Processing helix chain 'A' and resid 1143 through 1150 Processing helix chain 'A' and resid 1158 through 1168 removed outlier: 3.859A pdb=" N ILE A1162 " --> pdb=" O THR A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1176 Processing helix chain 'A' and resid 1180 through 1184 removed outlier: 3.669A pdb=" N ASP A1183 " --> pdb=" O GLN A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1208 Processing helix chain 'A' and resid 1224 through 1239 removed outlier: 4.370A pdb=" N LYS A1229 " --> pdb=" O THR A1225 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL A1230 " --> pdb=" O GLU A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1256 removed outlier: 4.012A pdb=" N ILE A1254 " --> pdb=" O ARG A1250 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN A1256 " --> pdb=" O SER A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1273 through 1280 Processing helix chain 'A' and resid 1282 through 1288 removed outlier: 4.209A pdb=" N MET A1286 " --> pdb=" O GLY A1282 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 422 through 429 removed outlier: 5.394A pdb=" N ASN A 423 " --> pdb=" O PHE A 411 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N PHE A 411 " --> pdb=" O ASN A 423 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N LEU A 427 " --> pdb=" O ARG A 407 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ARG A 407 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N VAL A 429 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N GLU A 405 " --> pdb=" O VAL A 429 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE A 409 " --> pdb=" O GLU A 460 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLU A 460 " --> pdb=" O ILE A 409 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 482 through 486 removed outlier: 3.586A pdb=" N VAL A 596 " --> pdb=" O ILE A 435 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA A 436 " --> pdb=" O ALA A 611 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N PHE A 613 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL A 438 " --> pdb=" O PHE A 613 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE A 610 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU A 621 " --> pdb=" O ILE A 610 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLY A 612 " --> pdb=" O ILE A 619 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1076 through 1077 Processing sheet with id=AA4, first strand: chain 'A' and resid 1130 through 1133 removed outlier: 6.113A pdb=" N GLY A1131 " --> pdb=" O LEU A1215 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A1083 " --> pdb=" O CYS A1244 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A1246 " --> pdb=" O LEU A1083 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N THR A1082 " --> pdb=" O ARG A1259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1263 through 1264 554 hydrogen bonds defined for protein. 1632 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: 1.62 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2820 1.34 - 1.46: 1671 1.46 - 1.58: 4240 1.58 - 1.69: 0 1.69 - 1.81: 89 Bond restraints: 8820 Sorted by residual: bond pdb=" C ALA A 50 " pdb=" N LEU A 51 " ideal model delta sigma weight residual 1.332 1.308 0.025 1.40e-02 5.10e+03 3.07e+00 bond pdb=" CB GLN A 542 " pdb=" CG GLN A 542 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.17e+00 bond pdb=" CA GLU A1101 " pdb=" C GLU A1101 " ideal model delta sigma weight residual 1.522 1.504 0.018 1.72e-02 3.38e+03 1.06e+00 bond pdb=" CA GLN A 743 " pdb=" C GLN A 743 " ideal model delta sigma weight residual 1.521 1.533 -0.011 1.17e-02 7.31e+03 9.15e-01 bond pdb=" C GLU A 902 " pdb=" O GLU A 902 " ideal model delta sigma weight residual 1.231 1.250 -0.019 2.00e-02 2.50e+03 8.64e-01 ... (remaining 8815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 11811 2.56 - 5.13: 89 5.13 - 7.69: 8 7.69 - 10.26: 2 10.26 - 12.82: 1 Bond angle restraints: 11911 Sorted by residual: angle pdb=" C TRP A 224 " pdb=" N LYS A 225 " pdb=" CA LYS A 225 " ideal model delta sigma weight residual 122.40 135.22 -12.82 1.45e+00 4.76e-01 7.82e+01 angle pdb=" C THR A 846 " pdb=" N GLY A 847 " pdb=" CA GLY A 847 " ideal model delta sigma weight residual 120.00 127.21 -7.21 1.10e+00 8.26e-01 4.30e+01 angle pdb=" CA MET A 885 " pdb=" CB MET A 885 " pdb=" CG MET A 885 " ideal model delta sigma weight residual 114.10 121.44 -7.34 2.00e+00 2.50e-01 1.35e+01 angle pdb=" CB MET A 168 " pdb=" CG MET A 168 " pdb=" SD MET A 168 " ideal model delta sigma weight residual 112.70 121.50 -8.80 3.00e+00 1.11e-01 8.61e+00 angle pdb=" N VAL A 891 " pdb=" CA VAL A 891 " pdb=" C VAL A 891 " ideal model delta sigma weight residual 112.98 109.36 3.62 1.25e+00 6.40e-01 8.38e+00 ... (remaining 11906 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 4600 17.83 - 35.67: 535 35.67 - 53.50: 124 53.50 - 71.34: 17 71.34 - 89.17: 14 Dihedral angle restraints: 5290 sinusoidal: 2083 harmonic: 3207 Sorted by residual: dihedral pdb=" CA GLU A 902 " pdb=" C GLU A 902 " pdb=" N ASP A 903 " pdb=" CA ASP A 903 " ideal model delta harmonic sigma weight residual 180.00 157.81 22.19 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA PRO A 883 " pdb=" C PRO A 883 " pdb=" N ILE A 884 " pdb=" CA ILE A 884 " ideal model delta harmonic sigma weight residual 180.00 158.10 21.90 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA GLN A1271 " pdb=" C GLN A1271 " pdb=" N GLY A1272 " pdb=" CA GLY A1272 " ideal model delta harmonic sigma weight residual -180.00 -161.24 -18.76 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 5287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1266 0.072 - 0.144: 98 0.144 - 0.216: 1 0.216 - 0.289: 0 0.289 - 0.361: 2 Chirality restraints: 1367 Sorted by residual: chirality pdb=" CA PHE A 976 " pdb=" N PHE A 976 " pdb=" C PHE A 976 " pdb=" CB PHE A 976 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA ARG A 975 " pdb=" N ARG A 975 " pdb=" C ARG A 975 " pdb=" CB ARG A 975 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CB ILE A 753 " pdb=" CA ILE A 753 " pdb=" CG1 ILE A 753 " pdb=" CG2 ILE A 753 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.96e-01 ... (remaining 1364 not shown) Planarity restraints: 1517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 77 " -0.043 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO A 78 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 78 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 78 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A1074 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.39e+00 pdb=" C ASN A1074 " -0.027 2.00e-02 2.50e+03 pdb=" O ASN A1074 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU A1075 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 560 " 0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO A 561 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 561 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 561 " 0.021 5.00e-02 4.00e+02 ... (remaining 1514 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 154 2.62 - 3.19: 8824 3.19 - 3.76: 13801 3.76 - 4.33: 17644 4.33 - 4.90: 29316 Nonbonded interactions: 69739 Sorted by model distance: nonbonded pdb=" O TRP A 872 " pdb=" OG1 THR A 875 " model vdw 2.046 3.040 nonbonded pdb=" ND2 ASN A 184 " pdb=" OG1 THR A 915 " model vdw 2.091 3.120 nonbonded pdb=" O TRP A 820 " pdb=" ND2 ASN A 826 " model vdw 2.099 3.120 nonbonded pdb=" OG SER A 724 " pdb=" OE1 GLU A 725 " model vdw 2.100 3.040 nonbonded pdb=" OG SER A 335 " pdb=" OE2 GLU A 337 " model vdw 2.100 3.040 ... (remaining 69734 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.270 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 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 0.039 8820 Z= 0.151 Angle : 0.620 12.819 11911 Z= 0.346 Chirality : 0.039 0.361 1367 Planarity : 0.004 0.065 1517 Dihedral : 16.380 89.171 3226 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.19 % Allowed : 19.09 % Favored : 79.72 % 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 aren not related in a simple way. whole: 0.44 (0.25), residues: 1104 helix: 1.58 (0.19), residues: 680 sheet: -0.73 (0.66), residues: 59 loop : -2.12 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 407 TYR 0.014 0.001 TYR A 322 PHE 0.014 0.001 PHE A 212 TRP 0.020 0.002 TRP A1125 HIS 0.005 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8820) covalent geometry : angle 0.61953 (11911) hydrogen bonds : bond 0.10929 ( 554) hydrogen bonds : angle 4.86920 ( 1632) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 PHE cc_start: 0.7570 (m-10) cc_final: 0.7287 (t80) REVERT: A 80 MET cc_start: 0.7381 (tpt) cc_final: 0.5339 (ptt) REVERT: A 135 PHE cc_start: 0.7921 (t80) cc_final: 0.7660 (t80) REVERT: A 168 MET cc_start: 0.9012 (mmm) cc_final: 0.8311 (mmm) REVERT: A 174 TRP cc_start: 0.8604 (t60) cc_final: 0.8320 (t60) REVERT: A 267 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6968 (tp30) REVERT: A 334 MET cc_start: 0.5235 (mmt) cc_final: 0.4166 (ttt) REVERT: A 723 LEU cc_start: 0.8944 (mt) cc_final: 0.8550 (tt) REVERT: A 734 PHE cc_start: 0.7612 (t80) cc_final: 0.7142 (t80) REVERT: A 737 ILE cc_start: 0.8509 (mm) cc_final: 0.8230 (tt) REVERT: A 742 MET cc_start: 0.6933 (tpt) cc_final: 0.6336 (mtm) REVERT: A 873 GLU cc_start: 0.8455 (mp0) cc_final: 0.8034 (mt-10) REVERT: A 939 GLU cc_start: 0.8199 (tp30) cc_final: 0.7953 (tm-30) REVERT: A 1047 LYS cc_start: 0.8021 (tmtt) cc_final: 0.7670 (tptt) REVERT: A 1101 GLU cc_start: 0.8732 (mm-30) cc_final: 0.7886 (tp30) outliers start: 11 outliers final: 4 residues processed: 178 average time/residue: 0.0913 time to fit residues: 23.0355 Evaluate side-chains 140 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 136 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain A residue 1081 GLU Chi-restraints excluded: chain A residue 1114 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 ASN A 195 GLN A 292 ASN A 423 ASN ** A 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 GLN A 920 ASN A1051 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.136421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.116941 restraints weight = 23232.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.120127 restraints weight = 13184.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.122278 restraints weight = 9004.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.123724 restraints weight = 6955.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.124625 restraints weight = 5797.280| |-----------------------------------------------------------------------------| r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 8820 Z= 0.212 Angle : 0.658 12.898 11911 Z= 0.347 Chirality : 0.041 0.182 1367 Planarity : 0.004 0.045 1517 Dihedral : 4.988 40.369 1203 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.24 % Allowed : 18.66 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.25), residues: 1104 helix: 1.40 (0.19), residues: 679 sheet: -0.51 (0.67), residues: 63 loop : -1.94 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 186 TYR 0.021 0.002 TYR A 289 PHE 0.018 0.002 PHE A 715 TRP 0.015 0.002 TRP A1125 HIS 0.007 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 8820) covalent geometry : angle 0.65820 (11911) hydrogen bonds : bond 0.04532 ( 554) hydrogen bonds : angle 4.57027 ( 1632) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 PHE cc_start: 0.7854 (m-10) cc_final: 0.7310 (t80) REVERT: A 80 MET cc_start: 0.6822 (tpt) cc_final: 0.5814 (ptt) REVERT: A 130 TYR cc_start: 0.5721 (m-80) cc_final: 0.4970 (m-80) REVERT: A 142 TYR cc_start: 0.8739 (t80) cc_final: 0.8273 (t80) REVERT: A 168 MET cc_start: 0.9363 (mmm) cc_final: 0.8649 (mmm) REVERT: A 267 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7584 (tp30) REVERT: A 293 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8490 (mm) REVERT: A 308 ASN cc_start: 0.8329 (m-40) cc_final: 0.8121 (m-40) REVERT: A 334 MET cc_start: 0.4930 (mmt) cc_final: 0.4205 (ttp) REVERT: A 496 ILE cc_start: 0.5981 (OUTLIER) cc_final: 0.5779 (mp) REVERT: A 500 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.8900 (tt) REVERT: A 637 LEU cc_start: 0.7935 (pp) cc_final: 0.7266 (mm) REVERT: A 723 LEU cc_start: 0.8968 (mt) cc_final: 0.8571 (tt) REVERT: A 734 PHE cc_start: 0.8058 (t80) cc_final: 0.7414 (t80) REVERT: A 737 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8276 (tt) REVERT: A 742 MET cc_start: 0.6301 (tpt) cc_final: 0.5857 (mtm) REVERT: A 790 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7467 (tm-30) REVERT: A 814 MET cc_start: 0.8179 (mmp) cc_final: 0.7761 (mmp) REVERT: A 873 GLU cc_start: 0.8701 (mp0) cc_final: 0.8394 (mt-10) REVERT: A 909 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.7891 (tppt) REVERT: A 939 GLU cc_start: 0.8506 (tp30) cc_final: 0.8103 (tm-30) REVERT: A 986 MET cc_start: 0.5306 (ppp) cc_final: 0.5005 (ppp) REVERT: A 992 TYR cc_start: 0.7350 (OUTLIER) cc_final: 0.4142 (m-80) REVERT: A 1020 MET cc_start: 0.8513 (tpt) cc_final: 0.8269 (tpt) REVERT: A 1047 LYS cc_start: 0.8074 (tmtt) cc_final: 0.7787 (tptt) REVERT: A 1074 ASN cc_start: 0.7632 (m-40) cc_final: 0.7379 (t0) REVERT: A 1077 VAL cc_start: 0.6112 (OUTLIER) cc_final: 0.5829 (m) REVERT: A 1101 GLU cc_start: 0.9345 (mm-30) cc_final: 0.8043 (tp30) REVERT: A 1240 ARG cc_start: 0.7645 (mmt90) cc_final: 0.6929 (mmt90) outliers start: 30 outliers final: 16 residues processed: 172 average time/residue: 0.0835 time to fit residues: 20.8152 Evaluate side-chains 154 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 726 TRP Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 909 LYS Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 1051 ASN Chi-restraints excluded: chain A residue 1071 ARG Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1244 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 ASN A 410 HIS A 547 GLN ** A 816 GLN ** 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 = 0.4192 r_free = 0.4192 target = 0.138459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.118857 restraints weight = 22912.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.122128 restraints weight = 13031.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.124302 restraints weight = 8910.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.125748 restraints weight = 6855.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.126752 restraints weight = 5728.597| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8820 Z= 0.142 Angle : 0.601 11.115 11911 Z= 0.312 Chirality : 0.040 0.196 1367 Planarity : 0.004 0.041 1517 Dihedral : 4.268 29.752 1195 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.24 % Allowed : 19.74 % Favored : 77.02 % 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 aren not related in a simple way. whole: 0.50 (0.25), residues: 1104 helix: 1.53 (0.19), residues: 677 sheet: -0.46 (0.68), residues: 63 loop : -1.87 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1240 TYR 0.016 0.002 TYR A 130 PHE 0.017 0.001 PHE A 715 TRP 0.017 0.002 TRP A1125 HIS 0.006 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8820) covalent geometry : angle 0.60125 (11911) hydrogen bonds : bond 0.03992 ( 554) hydrogen bonds : angle 4.29103 ( 1632) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 PHE cc_start: 0.7769 (m-10) cc_final: 0.7302 (t80) REVERT: A 123 MET cc_start: 0.6459 (mmm) cc_final: 0.6255 (mmm) REVERT: A 142 TYR cc_start: 0.8753 (t80) cc_final: 0.8341 (t80) REVERT: A 168 MET cc_start: 0.9373 (mmm) cc_final: 0.9012 (mmm) REVERT: A 267 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7353 (tp30) REVERT: A 308 ASN cc_start: 0.8556 (m-40) cc_final: 0.8349 (m-40) REVERT: A 334 MET cc_start: 0.4825 (mmt) cc_final: 0.4135 (ttm) REVERT: A 355 PHE cc_start: 0.7180 (OUTLIER) cc_final: 0.6328 (m-80) REVERT: A 723 LEU cc_start: 0.8933 (mt) cc_final: 0.8508 (tt) REVERT: A 734 PHE cc_start: 0.8038 (t80) cc_final: 0.7394 (t80) REVERT: A 737 ILE cc_start: 0.8547 (mm) cc_final: 0.8289 (tt) REVERT: A 742 MET cc_start: 0.6274 (tpt) cc_final: 0.5991 (mtm) REVERT: A 790 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.6927 (tm-30) REVERT: A 814 MET cc_start: 0.8468 (mmp) cc_final: 0.8122 (mmp) REVERT: A 873 GLU cc_start: 0.8595 (mp0) cc_final: 0.8306 (mt-10) REVERT: A 974 PHE cc_start: 0.5661 (m-10) cc_final: 0.5391 (m-10) REVERT: A 986 MET cc_start: 0.5357 (ppp) cc_final: 0.5080 (ppp) REVERT: A 1047 LYS cc_start: 0.8190 (tmtt) cc_final: 0.7844 (tptt) REVERT: A 1074 ASN cc_start: 0.7684 (m-40) cc_final: 0.7292 (t0) REVERT: A 1077 VAL cc_start: 0.5937 (OUTLIER) cc_final: 0.5673 (m) REVERT: A 1101 GLU cc_start: 0.9399 (mm-30) cc_final: 0.7937 (tp30) REVERT: A 1112 GLU cc_start: 0.4995 (tm-30) cc_final: 0.4499 (tm-30) REVERT: A 1207 ILE cc_start: 0.8901 (tp) cc_final: 0.8608 (pt) REVERT: A 1223 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6247 (mp) outliers start: 30 outliers final: 15 residues processed: 162 average time/residue: 0.0850 time to fit residues: 20.0765 Evaluate side-chains 152 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 726 TRP Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 1051 ASN Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1223 LEU Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1244 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 69 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 97 optimal weight: 0.0050 chunk 53 optimal weight: 3.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 ASN A1051 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.135342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.114509 restraints weight = 24108.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.117682 restraints weight = 13916.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.119864 restraints weight = 9681.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.121333 restraints weight = 7549.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.122303 restraints weight = 6335.475| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8820 Z= 0.148 Angle : 0.584 9.419 11911 Z= 0.305 Chirality : 0.039 0.209 1367 Planarity : 0.003 0.042 1517 Dihedral : 4.175 29.230 1195 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.53 % Allowed : 19.96 % Favored : 75.51 % 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 aren not related in a simple way. whole: 0.55 (0.25), residues: 1104 helix: 1.56 (0.20), residues: 679 sheet: -0.59 (0.67), residues: 63 loop : -1.82 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 539 TYR 0.011 0.001 TYR A 322 PHE 0.018 0.001 PHE A 715 TRP 0.034 0.002 TRP A1125 HIS 0.007 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8820) covalent geometry : angle 0.58410 (11911) hydrogen bonds : bond 0.03894 ( 554) hydrogen bonds : angle 4.24927 ( 1632) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 144 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7351 (mp) REVERT: A 64 PHE cc_start: 0.7957 (m-10) cc_final: 0.7236 (t80) REVERT: A 133 MET cc_start: 0.8093 (ptt) cc_final: 0.7313 (ptt) REVERT: A 142 TYR cc_start: 0.8806 (t80) cc_final: 0.8388 (t80) REVERT: A 168 MET cc_start: 0.9046 (mmm) cc_final: 0.8554 (mmm) REVERT: A 190 ASP cc_start: 0.8997 (m-30) cc_final: 0.8610 (m-30) REVERT: A 267 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7430 (tp30) REVERT: A 293 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8397 (mm) REVERT: A 326 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7779 (m-80) REVERT: A 334 MET cc_start: 0.4843 (mmt) cc_final: 0.4158 (ttm) REVERT: A 355 PHE cc_start: 0.7360 (OUTLIER) cc_final: 0.6468 (m-80) REVERT: A 496 ILE cc_start: 0.6273 (OUTLIER) cc_final: 0.6052 (mp) REVERT: A 543 MET cc_start: 0.7277 (tmm) cc_final: 0.6997 (tmm) REVERT: A 637 LEU cc_start: 0.7907 (pp) cc_final: 0.7253 (mm) REVERT: A 734 PHE cc_start: 0.8111 (t80) cc_final: 0.7450 (t80) REVERT: A 742 MET cc_start: 0.6390 (tpt) cc_final: 0.6150 (mtm) REVERT: A 790 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.6689 (tm-30) REVERT: A 814 MET cc_start: 0.8374 (mmp) cc_final: 0.7913 (mmp) REVERT: A 873 GLU cc_start: 0.8719 (mp0) cc_final: 0.8347 (mt-10) REVERT: A 986 MET cc_start: 0.5596 (ppp) cc_final: 0.5098 (ppp) REVERT: A 992 TYR cc_start: 0.7513 (OUTLIER) cc_final: 0.4287 (m-80) REVERT: A 1020 MET cc_start: 0.8683 (tpt) cc_final: 0.8381 (tpt) REVERT: A 1047 LYS cc_start: 0.8103 (tmtt) cc_final: 0.7771 (tptt) REVERT: A 1074 ASN cc_start: 0.7314 (m-40) cc_final: 0.7059 (t0) REVERT: A 1077 VAL cc_start: 0.6235 (OUTLIER) cc_final: 0.5944 (m) REVERT: A 1101 GLU cc_start: 0.8960 (mm-30) cc_final: 0.7557 (tp30) REVERT: A 1112 GLU cc_start: 0.4891 (tm-30) cc_final: 0.4447 (tm-30) REVERT: A 1223 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.6295 (mp) REVERT: A 1258 ASP cc_start: 0.8407 (t70) cc_final: 0.8199 (m-30) outliers start: 42 outliers final: 25 residues processed: 171 average time/residue: 0.0758 time to fit residues: 19.5793 Evaluate side-chains 163 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 726 TRP Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 1051 ASN Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1223 LEU Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1244 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.136357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.115336 restraints weight = 24305.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.118584 restraints weight = 14014.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.120773 restraints weight = 9750.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.122232 restraints weight = 7592.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.123067 restraints weight = 6396.493| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8820 Z= 0.131 Angle : 0.578 8.557 11911 Z= 0.300 Chirality : 0.039 0.224 1367 Planarity : 0.003 0.043 1517 Dihedral : 4.060 26.741 1195 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.10 % Allowed : 21.57 % Favored : 74.33 % 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 aren not related in a simple way. whole: 0.68 (0.25), residues: 1104 helix: 1.67 (0.20), residues: 679 sheet: -0.67 (0.66), residues: 63 loop : -1.75 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1240 TYR 0.010 0.001 TYR A 322 PHE 0.016 0.001 PHE A 715 TRP 0.031 0.002 TRP A1125 HIS 0.006 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8820) covalent geometry : angle 0.57769 (11911) hydrogen bonds : bond 0.03751 ( 554) hydrogen bonds : angle 4.15448 ( 1632) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7302 (mp) REVERT: A 64 PHE cc_start: 0.7906 (m-10) cc_final: 0.7334 (t80) REVERT: A 142 TYR cc_start: 0.8747 (t80) cc_final: 0.8395 (t80) REVERT: A 144 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8302 (pp30) REVERT: A 168 MET cc_start: 0.8927 (mmm) cc_final: 0.8092 (mmm) REVERT: A 190 ASP cc_start: 0.8968 (m-30) cc_final: 0.8581 (m-30) REVERT: A 267 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7401 (tp30) REVERT: A 293 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8362 (mm) REVERT: A 311 MET cc_start: 0.7626 (mtt) cc_final: 0.7315 (mtm) REVERT: A 326 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7807 (m-80) REVERT: A 334 MET cc_start: 0.4826 (mmt) cc_final: 0.4135 (ttm) REVERT: A 355 PHE cc_start: 0.7047 (OUTLIER) cc_final: 0.6530 (m-80) REVERT: A 543 MET cc_start: 0.7470 (tmm) cc_final: 0.7071 (tmm) REVERT: A 637 LEU cc_start: 0.7917 (pp) cc_final: 0.7305 (mm) REVERT: A 734 PHE cc_start: 0.7999 (t80) cc_final: 0.7436 (t80) REVERT: A 742 MET cc_start: 0.6472 (tpt) cc_final: 0.6195 (mtm) REVERT: A 790 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.6902 (tm-30) REVERT: A 814 MET cc_start: 0.8115 (mmp) cc_final: 0.7482 (mmp) REVERT: A 873 GLU cc_start: 0.8692 (mp0) cc_final: 0.8357 (mt-10) REVERT: A 968 PHE cc_start: 0.8236 (m-80) cc_final: 0.7982 (m-80) REVERT: A 986 MET cc_start: 0.5783 (ppp) cc_final: 0.5267 (ppp) REVERT: A 992 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.4240 (m-80) REVERT: A 1047 LYS cc_start: 0.8110 (tmtt) cc_final: 0.7769 (tptt) REVERT: A 1074 ASN cc_start: 0.7326 (m-40) cc_final: 0.7057 (t0) REVERT: A 1077 VAL cc_start: 0.6137 (OUTLIER) cc_final: 0.5888 (m) REVERT: A 1101 GLU cc_start: 0.8020 (mm-30) cc_final: 0.6531 (tp30) REVERT: A 1112 GLU cc_start: 0.4845 (tm-30) cc_final: 0.4376 (tm-30) REVERT: A 1223 LEU cc_start: 0.6581 (OUTLIER) cc_final: 0.6295 (mp) outliers start: 38 outliers final: 21 residues processed: 161 average time/residue: 0.0773 time to fit residues: 18.5460 Evaluate side-chains 153 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 726 TRP Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 1051 ASN Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1223 LEU Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1244 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 48 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 ASN ** A1147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.134406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.113457 restraints weight = 23966.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.116661 restraints weight = 13821.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.118822 restraints weight = 9609.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.120063 restraints weight = 7508.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.121087 restraints weight = 6421.832| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8820 Z= 0.162 Angle : 0.609 13.186 11911 Z= 0.312 Chirality : 0.040 0.238 1367 Planarity : 0.003 0.043 1517 Dihedral : 4.077 18.230 1193 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.10 % Allowed : 22.22 % Favored : 73.68 % 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 aren not related in a simple way. whole: 0.65 (0.26), residues: 1104 helix: 1.63 (0.20), residues: 677 sheet: -0.65 (0.67), residues: 63 loop : -1.73 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1205 TYR 0.012 0.002 TYR A 992 PHE 0.030 0.002 PHE A 532 TRP 0.023 0.002 TRP A1125 HIS 0.007 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8820) covalent geometry : angle 0.60892 (11911) hydrogen bonds : bond 0.03906 ( 554) hydrogen bonds : angle 4.26618 ( 1632) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7443 (mp) REVERT: A 64 PHE cc_start: 0.7841 (m-10) cc_final: 0.7361 (t80) REVERT: A 80 MET cc_start: 0.5928 (ptt) cc_final: 0.5247 (tpt) REVERT: A 142 TYR cc_start: 0.8748 (t80) cc_final: 0.8333 (t80) REVERT: A 168 MET cc_start: 0.8940 (mmm) cc_final: 0.8353 (mmm) REVERT: A 190 ASP cc_start: 0.9011 (m-30) cc_final: 0.8601 (m-30) REVERT: A 267 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7442 (tp30) REVERT: A 282 GLN cc_start: 0.7552 (mm-40) cc_final: 0.7135 (mm-40) REVERT: A 293 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8387 (mm) REVERT: A 326 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.7786 (m-80) REVERT: A 334 MET cc_start: 0.4892 (mmt) cc_final: 0.4326 (ttt) REVERT: A 355 PHE cc_start: 0.6812 (OUTLIER) cc_final: 0.6487 (m-80) REVERT: A 487 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7823 (pm20) REVERT: A 543 MET cc_start: 0.7493 (tmm) cc_final: 0.7089 (tmm) REVERT: A 717 LYS cc_start: 0.8544 (pttp) cc_final: 0.8166 (ptmm) REVERT: A 734 PHE cc_start: 0.8018 (t80) cc_final: 0.7459 (t80) REVERT: A 742 MET cc_start: 0.6421 (tpt) cc_final: 0.6213 (mtm) REVERT: A 790 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.6971 (tm-30) REVERT: A 814 MET cc_start: 0.8035 (mmp) cc_final: 0.7207 (mmp) REVERT: A 968 PHE cc_start: 0.8340 (m-80) cc_final: 0.8022 (m-80) REVERT: A 992 TYR cc_start: 0.7579 (OUTLIER) cc_final: 0.4255 (m-80) REVERT: A 1047 LYS cc_start: 0.8182 (tmtt) cc_final: 0.7850 (tptt) REVERT: A 1074 ASN cc_start: 0.7334 (m-40) cc_final: 0.7107 (t0) REVERT: A 1077 VAL cc_start: 0.6267 (OUTLIER) cc_final: 0.5987 (m) REVERT: A 1101 GLU cc_start: 0.8907 (mm-30) cc_final: 0.7565 (tp30) REVERT: A 1217 ASP cc_start: 0.5623 (p0) cc_final: 0.5408 (p0) REVERT: A 1223 LEU cc_start: 0.6255 (OUTLIER) cc_final: 0.6007 (mp) outliers start: 38 outliers final: 28 residues processed: 157 average time/residue: 0.0762 time to fit residues: 17.8725 Evaluate side-chains 162 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 726 TRP Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 1051 ASN Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1223 LEU Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1244 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 18 optimal weight: 0.8980 chunk 91 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.134694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.113821 restraints weight = 23963.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.117070 restraints weight = 13696.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.119222 restraints weight = 9445.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.120645 restraints weight = 7346.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.121635 restraints weight = 6186.621| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8820 Z= 0.144 Angle : 0.623 11.138 11911 Z= 0.313 Chirality : 0.040 0.183 1367 Planarity : 0.003 0.042 1517 Dihedral : 4.021 17.322 1193 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.31 % Allowed : 22.55 % Favored : 73.14 % 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 aren not related in a simple way. whole: 0.68 (0.26), residues: 1104 helix: 1.61 (0.20), residues: 681 sheet: -0.62 (0.68), residues: 61 loop : -1.65 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1240 TYR 0.010 0.001 TYR A 992 PHE 0.026 0.001 PHE A 532 TRP 0.023 0.002 TRP A1125 HIS 0.007 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8820) covalent geometry : angle 0.62343 (11911) hydrogen bonds : bond 0.03800 ( 554) hydrogen bonds : angle 4.19894 ( 1632) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 131 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7564 (mp) REVERT: A 64 PHE cc_start: 0.7848 (m-10) cc_final: 0.7422 (t80) REVERT: A 80 MET cc_start: 0.6917 (ptt) cc_final: 0.5168 (tpt) REVERT: A 142 TYR cc_start: 0.8798 (t80) cc_final: 0.8358 (t80) REVERT: A 168 MET cc_start: 0.8934 (mmm) cc_final: 0.8340 (mmm) REVERT: A 190 ASP cc_start: 0.9009 (m-30) cc_final: 0.8605 (m-30) REVERT: A 267 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7509 (tp30) REVERT: A 282 GLN cc_start: 0.7265 (mm-40) cc_final: 0.6866 (mm-40) REVERT: A 293 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8369 (mm) REVERT: A 326 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7876 (m-80) REVERT: A 334 MET cc_start: 0.4485 (mmt) cc_final: 0.3953 (ttt) REVERT: A 355 PHE cc_start: 0.7160 (OUTLIER) cc_final: 0.6762 (m-80) REVERT: A 487 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7886 (pm20) REVERT: A 543 MET cc_start: 0.7480 (tmm) cc_final: 0.7095 (tmm) REVERT: A 637 LEU cc_start: 0.7728 (pp) cc_final: 0.7349 (mm) REVERT: A 717 LYS cc_start: 0.8564 (pttp) cc_final: 0.8188 (ptmm) REVERT: A 734 PHE cc_start: 0.7954 (t80) cc_final: 0.7443 (t80) REVERT: A 790 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.7205 (tm-30) REVERT: A 814 MET cc_start: 0.7993 (mmp) cc_final: 0.7167 (mmp) REVERT: A 968 PHE cc_start: 0.8345 (m-80) cc_final: 0.8015 (m-80) REVERT: A 992 TYR cc_start: 0.7594 (OUTLIER) cc_final: 0.4378 (m-80) REVERT: A 1047 LYS cc_start: 0.8222 (tmtt) cc_final: 0.7940 (tptt) REVERT: A 1074 ASN cc_start: 0.7343 (m-40) cc_final: 0.7103 (t0) REVERT: A 1077 VAL cc_start: 0.6218 (OUTLIER) cc_final: 0.5960 (m) REVERT: A 1150 TYR cc_start: 0.8223 (t80) cc_final: 0.8009 (t80) REVERT: A 1217 ASP cc_start: 0.5189 (p0) cc_final: 0.4388 (p0) REVERT: A 1223 LEU cc_start: 0.5953 (OUTLIER) cc_final: 0.5715 (mp) outliers start: 40 outliers final: 27 residues processed: 158 average time/residue: 0.0759 time to fit residues: 18.0082 Evaluate side-chains 161 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 726 TRP Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 908 GLU Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 1051 ASN Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1223 LEU Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1244 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 110 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 43 optimal weight: 0.3980 chunk 95 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 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 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 ASN ** A1147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.135863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.115143 restraints weight = 23731.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.118376 restraints weight = 13562.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.120586 restraints weight = 9368.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.122025 restraints weight = 7277.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.122876 restraints weight = 6125.766| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8820 Z= 0.123 Angle : 0.610 9.422 11911 Z= 0.308 Chirality : 0.040 0.275 1367 Planarity : 0.003 0.042 1517 Dihedral : 3.932 16.213 1193 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.88 % Allowed : 23.41 % Favored : 72.71 % 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 aren not related in a simple way. whole: 0.77 (0.25), residues: 1104 helix: 1.65 (0.20), residues: 684 sheet: 0.22 (0.76), residues: 48 loop : -1.68 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 539 TYR 0.019 0.001 TYR A1284 PHE 0.023 0.001 PHE A 532 TRP 0.048 0.002 TRP A1125 HIS 0.007 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8820) covalent geometry : angle 0.60999 (11911) hydrogen bonds : bond 0.03640 ( 554) hydrogen bonds : angle 4.10863 ( 1632) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 PHE cc_start: 0.7809 (m-10) cc_final: 0.7398 (t80) REVERT: A 80 MET cc_start: 0.7512 (ptt) cc_final: 0.5723 (tpt) REVERT: A 142 TYR cc_start: 0.8773 (t80) cc_final: 0.8362 (t80) REVERT: A 168 MET cc_start: 0.8928 (mmm) cc_final: 0.8350 (mmm) REVERT: A 190 ASP cc_start: 0.8991 (m-30) cc_final: 0.8612 (m-30) REVERT: A 267 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7496 (tp30) REVERT: A 282 GLN cc_start: 0.7859 (mm-40) cc_final: 0.7264 (mm-40) REVERT: A 293 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8337 (mm) REVERT: A 326 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7630 (m-80) REVERT: A 334 MET cc_start: 0.4491 (mmt) cc_final: 0.3961 (ttt) REVERT: A 355 PHE cc_start: 0.6912 (OUTLIER) cc_final: 0.6643 (m-80) REVERT: A 365 GLN cc_start: 0.8408 (tm-30) cc_final: 0.7796 (mt0) REVERT: A 425 MET cc_start: 0.7350 (tmm) cc_final: 0.6551 (ppp) REVERT: A 487 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7859 (pm20) REVERT: A 543 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.7081 (tmm) REVERT: A 637 LEU cc_start: 0.7745 (pp) cc_final: 0.7365 (mm) REVERT: A 734 PHE cc_start: 0.7933 (t80) cc_final: 0.7544 (t80) REVERT: A 790 GLN cc_start: 0.7280 (OUTLIER) cc_final: 0.6621 (tm-30) REVERT: A 814 MET cc_start: 0.7899 (mmp) cc_final: 0.7127 (mmp) REVERT: A 968 PHE cc_start: 0.8315 (m-80) cc_final: 0.7963 (m-80) REVERT: A 992 TYR cc_start: 0.7497 (OUTLIER) cc_final: 0.4318 (m-80) REVERT: A 1020 MET cc_start: 0.8680 (tpt) cc_final: 0.8419 (tpt) REVERT: A 1047 LYS cc_start: 0.8220 (tmtt) cc_final: 0.7870 (tptt) REVERT: A 1074 ASN cc_start: 0.7326 (m-40) cc_final: 0.7071 (t0) REVERT: A 1150 TYR cc_start: 0.8171 (t80) cc_final: 0.7967 (t80) REVERT: A 1217 ASP cc_start: 0.4393 (p0) cc_final: 0.4067 (p0) REVERT: A 1223 LEU cc_start: 0.6281 (OUTLIER) cc_final: 0.6019 (mp) REVERT: A 1235 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8532 (mt) outliers start: 36 outliers final: 24 residues processed: 153 average time/residue: 0.0722 time to fit residues: 16.5301 Evaluate side-chains 159 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 726 TRP Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 933 PHE Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 1051 ASN Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1223 LEU Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1244 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 12 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 34 optimal weight: 0.0970 chunk 55 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 76 optimal weight: 0.0570 chunk 13 optimal weight: 0.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.135856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.114667 restraints weight = 23896.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.117981 restraints weight = 13508.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.120230 restraints weight = 9293.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.121693 restraints weight = 7211.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.122551 restraints weight = 6068.739| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8820 Z= 0.129 Angle : 0.620 9.244 11911 Z= 0.313 Chirality : 0.040 0.241 1367 Planarity : 0.003 0.044 1517 Dihedral : 3.889 15.753 1193 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.42 % Allowed : 23.84 % Favored : 71.74 % 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 aren not related in a simple way. whole: 0.71 (0.25), residues: 1104 helix: 1.55 (0.20), residues: 686 sheet: 0.24 (0.76), residues: 48 loop : -1.61 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 539 TYR 0.014 0.001 TYR A1284 PHE 0.019 0.001 PHE A 532 TRP 0.042 0.002 TRP A1125 HIS 0.007 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8820) covalent geometry : angle 0.61975 (11911) hydrogen bonds : bond 0.03660 ( 554) hydrogen bonds : angle 4.11977 ( 1632) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 PHE cc_start: 0.7801 (m-10) cc_final: 0.7405 (t80) REVERT: A 80 MET cc_start: 0.7475 (ptt) cc_final: 0.5696 (tpt) REVERT: A 142 TYR cc_start: 0.8764 (t80) cc_final: 0.8369 (t80) REVERT: A 143 MET cc_start: 0.8236 (mtp) cc_final: 0.7823 (mtp) REVERT: A 168 MET cc_start: 0.8939 (mmm) cc_final: 0.8369 (mmm) REVERT: A 190 ASP cc_start: 0.8998 (m-30) cc_final: 0.8628 (m-30) REVERT: A 293 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8343 (mm) REVERT: A 326 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.7845 (m-80) REVERT: A 334 MET cc_start: 0.4509 (mmt) cc_final: 0.3953 (ttt) REVERT: A 355 PHE cc_start: 0.6985 (OUTLIER) cc_final: 0.6690 (m-10) REVERT: A 365 GLN cc_start: 0.8395 (tm-30) cc_final: 0.7813 (mt0) REVERT: A 487 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.7972 (pm20) REVERT: A 543 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7385 (tmm) REVERT: A 557 LEU cc_start: 0.8300 (mt) cc_final: 0.8090 (tt) REVERT: A 637 LEU cc_start: 0.7804 (pp) cc_final: 0.7382 (mm) REVERT: A 734 PHE cc_start: 0.7977 (t80) cc_final: 0.7559 (t80) REVERT: A 790 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6632 (tm-30) REVERT: A 814 MET cc_start: 0.7910 (mmp) cc_final: 0.7119 (mmp) REVERT: A 968 PHE cc_start: 0.8243 (m-80) cc_final: 0.8012 (m-80) REVERT: A 992 TYR cc_start: 0.7593 (OUTLIER) cc_final: 0.4320 (m-80) REVERT: A 1020 MET cc_start: 0.8695 (tpt) cc_final: 0.8391 (tpt) REVERT: A 1047 LYS cc_start: 0.8252 (tmtt) cc_final: 0.7970 (tptt) REVERT: A 1074 ASN cc_start: 0.7321 (m-40) cc_final: 0.7048 (t0) REVERT: A 1150 TYR cc_start: 0.8121 (t80) cc_final: 0.7868 (t80) REVERT: A 1217 ASP cc_start: 0.4339 (p0) cc_final: 0.3936 (p0) REVERT: A 1223 LEU cc_start: 0.6277 (OUTLIER) cc_final: 0.6040 (mp) REVERT: A 1235 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8606 (mt) REVERT: A 1259 ARG cc_start: 0.8297 (ptm-80) cc_final: 0.7370 (ptt-90) outliers start: 41 outliers final: 28 residues processed: 157 average time/residue: 0.0805 time to fit residues: 18.7232 Evaluate side-chains 160 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 726 TRP Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 933 PHE Chi-restraints excluded: chain A residue 992 TYR Chi-restraints excluded: chain A residue 1051 ASN Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1223 LEU Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1244 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 57 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 93 optimal weight: 0.0070 chunk 41 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 89 optimal weight: 0.4980 chunk 50 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 ASN ** A1147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.136730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.115985 restraints weight = 23743.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.119277 restraints weight = 13609.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.121462 restraints weight = 9386.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.122936 restraints weight = 7286.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.123928 restraints weight = 6109.374| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8820 Z= 0.122 Angle : 0.638 9.676 11911 Z= 0.321 Chirality : 0.040 0.229 1367 Planarity : 0.003 0.043 1517 Dihedral : 3.889 18.441 1193 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.56 % Allowed : 25.35 % Favored : 71.09 % 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 aren not related in a simple way. whole: 0.74 (0.26), residues: 1104 helix: 1.56 (0.20), residues: 686 sheet: 0.19 (0.76), residues: 48 loop : -1.55 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 539 TYR 0.019 0.001 TYR A1061 PHE 0.018 0.001 PHE A 532 TRP 0.043 0.002 TRP A1125 HIS 0.007 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8820) covalent geometry : angle 0.63849 (11911) hydrogen bonds : bond 0.03585 ( 554) hydrogen bonds : angle 4.06364 ( 1632) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 PHE cc_start: 0.7777 (m-10) cc_final: 0.7393 (t80) REVERT: A 80 MET cc_start: 0.7453 (ptt) cc_final: 0.5704 (tpt) REVERT: A 123 MET cc_start: 0.7966 (mmm) cc_final: 0.7675 (mmm) REVERT: A 142 TYR cc_start: 0.8740 (t80) cc_final: 0.8371 (t80) REVERT: A 143 MET cc_start: 0.8249 (mtp) cc_final: 0.7711 (mtp) REVERT: A 168 MET cc_start: 0.8943 (mmm) cc_final: 0.8362 (mmm) REVERT: A 190 ASP cc_start: 0.8992 (m-30) cc_final: 0.8634 (m-30) REVERT: A 293 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8350 (mm) REVERT: A 326 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7856 (m-80) REVERT: A 334 MET cc_start: 0.4508 (mmt) cc_final: 0.3924 (ttt) REVERT: A 355 PHE cc_start: 0.7004 (OUTLIER) cc_final: 0.6682 (m-10) REVERT: A 365 GLN cc_start: 0.8362 (tm-30) cc_final: 0.7802 (mt0) REVERT: A 487 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7899 (pm20) REVERT: A 557 LEU cc_start: 0.8303 (mt) cc_final: 0.8095 (tt) REVERT: A 637 LEU cc_start: 0.7694 (pp) cc_final: 0.7359 (mm) REVERT: A 734 PHE cc_start: 0.7926 (t80) cc_final: 0.7415 (t80) REVERT: A 790 GLN cc_start: 0.7123 (OUTLIER) cc_final: 0.6607 (tm-30) REVERT: A 814 MET cc_start: 0.8606 (mmp) cc_final: 0.7305 (mmm) REVERT: A 912 LYS cc_start: 0.8604 (ptpt) cc_final: 0.8216 (pttm) REVERT: A 968 PHE cc_start: 0.8276 (m-80) cc_final: 0.8006 (m-80) REVERT: A 1020 MET cc_start: 0.8671 (tpt) cc_final: 0.8355 (tpt) REVERT: A 1047 LYS cc_start: 0.8261 (tmtt) cc_final: 0.7977 (tptt) REVERT: A 1074 ASN cc_start: 0.7364 (m-40) cc_final: 0.7110 (t0) REVERT: A 1150 TYR cc_start: 0.8016 (t80) cc_final: 0.7730 (t80) REVERT: A 1217 ASP cc_start: 0.4322 (p0) cc_final: 0.3930 (p0) REVERT: A 1235 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8549 (mt) REVERT: A 1259 ARG cc_start: 0.8011 (ptm-80) cc_final: 0.7184 (ptt-90) outliers start: 33 outliers final: 25 residues processed: 155 average time/residue: 0.0802 time to fit residues: 18.0563 Evaluate side-chains 158 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 155 GLN Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 613 PHE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 933 PHE Chi-restraints excluded: chain A residue 1051 ASN Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1223 LEU Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1244 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 95 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.136202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.115542 restraints weight = 23560.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.118801 restraints weight = 13545.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.120977 restraints weight = 9360.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.122400 restraints weight = 7281.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.123255 restraints weight = 6125.282| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8820 Z= 0.129 Angle : 0.653 10.559 11911 Z= 0.327 Chirality : 0.041 0.294 1367 Planarity : 0.004 0.044 1517 Dihedral : 3.889 18.886 1193 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.67 % Allowed : 25.78 % Favored : 70.55 % 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 aren not related in a simple way. whole: 0.77 (0.26), residues: 1104 helix: 1.53 (0.20), residues: 693 sheet: 0.16 (0.76), residues: 50 loop : -1.47 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1240 TYR 0.018 0.001 TYR A1061 PHE 0.017 0.001 PHE A 532 TRP 0.047 0.002 TRP A1125 HIS 0.007 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8820) covalent geometry : angle 0.65284 (11911) hydrogen bonds : bond 0.03596 ( 554) hydrogen bonds : angle 4.07625 ( 1632) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1482.00 seconds wall clock time: 26 minutes 29.58 seconds (1589.58 seconds total)