Starting phenix.real_space_refine on Thu Feb 13 05:02:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cr8_45854/02_2025/9cr8_45854.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cr8_45854/02_2025/9cr8_45854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cr8_45854/02_2025/9cr8_45854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cr8_45854/02_2025/9cr8_45854.map" model { file = "/net/cci-nas-00/data/ceres_data/9cr8_45854/02_2025/9cr8_45854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cr8_45854/02_2025/9cr8_45854.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 32 5.16 5 C 5675 2.51 5 N 1426 2.21 5 O 1531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8664 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8430 Classifications: {'peptide': 1087} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 27, 'TRANS': 1059} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 234 Unusual residues: {'UPL': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 289 Unresolved non-hydrogen dihedrals: 302 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 5.19, per 1000 atoms: 0.60 Number of scatterers: 8664 At special positions: 0 Unit cell: (98.604, 119.52, 114.54, 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 32 16.00 O 1531 8.00 N 1426 7.00 C 5675 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: 2.79 Conformation dependent library (CDL) restraints added in 1.5 seconds 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2002 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 4 sheets defined 66.1% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 44 through 63 Processing helix chain 'A' and resid 64 through 81 removed outlier: 3.518A pdb=" N ASN A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 156 removed outlier: 3.521A pdb=" N VAL A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TRP A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.667A pdb=" N PHE A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP A 164 " --> pdb=" O ILE A 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 159 through 164' Processing helix chain 'A' and resid 167 through 186 removed outlier: 4.383A pdb=" N VAL A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N SER A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 210 removed outlier: 3.884A pdb=" N THR A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 222 removed outlier: 3.992A pdb=" N THR A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 241 removed outlier: 3.699A pdb=" N LEU A 227 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASP A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 260 Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 269 through 315 Processing helix chain 'A' and resid 329 through 345 removed outlier: 4.161A pdb=" N VAL A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 371 removed outlier: 3.946A pdb=" N GLU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 441 removed outlier: 3.669A pdb=" N GLN A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 467 Processing helix chain 'A' and resid 468 through 470 No H-bonds generated for 'chain 'A' and resid 468 through 470' Processing helix chain 'A' and resid 483 through 490 Processing helix chain 'A' and resid 496 through 506 removed outlier: 3.526A pdb=" N ILE A 500 " --> pdb=" O THR A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 516 Processing helix chain 'A' and resid 532 through 548 Processing helix chain 'A' and resid 565 through 578 removed outlier: 3.554A pdb=" N VAL A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS A 578 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 707 through 736 removed outlier: 3.633A pdb=" N PHE A 711 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN A 725 " --> pdb=" O ASN A 721 " (cutoff:3.500A) Proline residue: A 726 - end of helix removed outlier: 3.813A pdb=" N ALA A 729 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 730 " --> pdb=" O PRO A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 739 No H-bonds generated for 'chain 'A' and resid 737 through 739' Processing helix chain 'A' and resid 752 through 799 Processing helix chain 'A' and resid 800 through 806 removed outlier: 3.952A pdb=" N PHE A 804 " --> pdb=" O ASP A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 820 Processing helix chain 'A' and resid 825 through 854 removed outlier: 4.229A pdb=" N LEU A 833 " --> pdb=" O ILE A 829 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ALA A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR A 845 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY A 846 " --> pdb=" O ASN A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 890 Proline residue: A 866 - end of helix removed outlier: 3.683A pdb=" N GLN A 882 " --> pdb=" O MET A 878 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LYS A 887 " --> pdb=" O ALA A 883 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 903 Processing helix chain 'A' and resid 903 through 911 Processing helix chain 'A' and resid 912 through 965 removed outlier: 3.619A pdb=" N PHE A 916 " --> pdb=" O GLN A 912 " (cutoff:3.500A) Proline residue: A 927 - end of helix removed outlier: 3.603A pdb=" N ALA A 935 " --> pdb=" O SER A 931 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N HIS A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE A 937 " --> pdb=" O ARG A 933 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR A 953 " --> pdb=" O MET A 949 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 954 " --> pdb=" O TYR A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 994 removed outlier: 3.915A pdb=" N PHE A 983 " --> pdb=" O SER A 979 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 987 " --> pdb=" O PHE A 983 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 993 " --> pdb=" O GLY A 989 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A 994 " --> pdb=" O GLN A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1012 removed outlier: 3.825A pdb=" N ILE A1003 " --> pdb=" O ALA A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1084 Processing helix chain 'A' and resid 1105 through 1111 Processing helix chain 'A' and resid 1126 through 1133 Processing helix chain 'A' and resid 1141 through 1152 removed outlier: 3.799A pdb=" N ILE A1145 " --> pdb=" O SER A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1161 Processing helix chain 'A' and resid 1177 through 1193 removed outlier: 3.951A pdb=" N ARG A1192 " --> pdb=" O ARG A1188 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN A1193 " --> pdb=" O ALA A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1222 removed outlier: 3.572A pdb=" N VAL A1214 " --> pdb=" O SER A1210 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 408 through 416 removed outlier: 6.868A pdb=" N ILE A 409 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N SER A 400 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LYS A 411 " --> pdb=" O HIS A 398 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HIS A 398 " --> pdb=" O LYS A 411 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LEU A 413 " --> pdb=" O ASN A 396 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER A 452 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 551 through 552 removed outlier: 3.751A pdb=" N ALA A 599 " --> pdb=" O ALA A 424 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1035 through 1041 removed outlier: 5.524A pdb=" N PHE A1037 " --> pdb=" O LEU A1095 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU A1095 " --> pdb=" O PHE A1037 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLU A1039 " --> pdb=" O LYS A1093 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LYS A1093 " --> pdb=" O GLU A1039 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1065 through 1067 removed outlier: 6.358A pdb=" N LEU A1066 " --> pdb=" O VAL A1229 " (cutoff:3.500A) 521 hydrogen bonds defined for protein. 1539 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: 3.62 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2715 1.34 - 1.46: 1818 1.46 - 1.58: 4216 1.58 - 1.69: 0 1.69 - 1.81: 57 Bond restraints: 8806 Sorted by residual: bond pdb=" N VAL A 71 " pdb=" CA VAL A 71 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.47e+00 bond pdb=" N ILE A 78 " pdb=" CA ILE A 78 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.05e+00 bond pdb=" N GLU A 74 " pdb=" CA GLU A 74 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.20e+00 bond pdb=" N ASP A 188 " pdb=" CA ASP A 188 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.31e-02 5.83e+03 6.18e+00 bond pdb=" N THR A 76 " pdb=" CA THR A 76 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.06e+00 ... (remaining 8801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 11492 1.27 - 2.54: 253 2.54 - 3.82: 59 3.82 - 5.09: 10 5.09 - 6.36: 2 Bond angle restraints: 11816 Sorted by residual: angle pdb=" C ALA A 246 " pdb=" N TYR A 247 " pdb=" CA TYR A 247 " ideal model delta sigma weight residual 120.72 114.62 6.10 1.67e+00 3.59e-01 1.33e+01 angle pdb=" CA VAL A 71 " pdb=" C VAL A 71 " pdb=" O VAL A 71 " ideal model delta sigma weight residual 120.85 117.14 3.71 1.06e+00 8.90e-01 1.23e+01 angle pdb=" CA ILE A 78 " pdb=" C ILE A 78 " pdb=" O ILE A 78 " ideal model delta sigma weight residual 120.95 117.86 3.09 1.04e+00 9.25e-01 8.80e+00 angle pdb=" CA GLY A 73 " pdb=" C GLY A 73 " pdb=" O GLY A 73 " ideal model delta sigma weight residual 120.75 117.69 3.06 1.03e+00 9.43e-01 8.80e+00 angle pdb=" CA MET A 75 " pdb=" C MET A 75 " pdb=" O MET A 75 " ideal model delta sigma weight residual 120.55 117.42 3.13 1.06e+00 8.90e-01 8.70e+00 ... (remaining 11811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 4867 17.31 - 34.62: 331 34.62 - 51.94: 86 51.94 - 69.25: 15 69.25 - 86.56: 4 Dihedral angle restraints: 5303 sinusoidal: 2184 harmonic: 3119 Sorted by residual: dihedral pdb=" CA ASP A 821 " pdb=" C ASP A 821 " pdb=" N ALA A 822 " pdb=" CA ALA A 822 " ideal model delta harmonic sigma weight residual 180.00 162.19 17.81 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA PHE A 983 " pdb=" C PHE A 983 " pdb=" N GLY A 984 " pdb=" CA GLY A 984 " ideal model delta harmonic sigma weight residual 180.00 162.28 17.72 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA PHE A 697 " pdb=" C PHE A 697 " pdb=" N TRP A 698 " pdb=" CA TRP A 698 " ideal model delta harmonic sigma weight residual 180.00 163.21 16.79 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 5300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 940 0.035 - 0.070: 301 0.070 - 0.104: 72 0.104 - 0.139: 31 0.139 - 0.174: 4 Chirality restraints: 1348 Sorted by residual: chirality pdb=" CB VAL A 71 " pdb=" CA VAL A 71 " pdb=" CG1 VAL A 71 " pdb=" CG2 VAL A 71 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.55e-01 chirality pdb=" CA ILE A 78 " pdb=" N ILE A 78 " pdb=" C ILE A 78 " pdb=" CB ILE A 78 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.00e-01 chirality pdb=" CA LEU A 70 " pdb=" N LEU A 70 " pdb=" C LEU A 70 " pdb=" CB LEU A 70 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.23e-01 ... (remaining 1345 not shown) Planarity restraints: 1465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 980 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C ALA A 980 " -0.030 2.00e-02 2.50e+03 pdb=" O ALA A 980 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL A 981 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 222 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO A 223 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 223 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 223 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 203 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C GLY A 203 " -0.029 2.00e-02 2.50e+03 pdb=" O GLY A 203 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE A 204 " 0.010 2.00e-02 2.50e+03 ... (remaining 1462 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1235 2.76 - 3.29: 8760 3.29 - 3.83: 13591 3.83 - 4.36: 15059 4.36 - 4.90: 26804 Nonbonded interactions: 65449 Sorted by model distance: nonbonded pdb=" O HIS A 398 " pdb=" OG1 THR A 447 " model vdw 2.219 3.040 nonbonded pdb=" O LEU A 216 " pdb=" OH TYR A 310 " model vdw 2.222 3.040 nonbonded pdb=" O ASP A 805 " pdb=" OD1 ASP A 805 " model vdw 2.259 3.040 nonbonded pdb=" NH1 ARG A 588 " pdb=" OG SER A 590 " model vdw 2.274 3.120 nonbonded pdb=" OE2 GLU A 273 " pdb=" OH TYR A1133 " model vdw 2.280 3.040 ... (remaining 65444 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.220 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 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 0.035 8806 Z= 0.174 Angle : 0.494 6.359 11816 Z= 0.295 Chirality : 0.039 0.174 1348 Planarity : 0.004 0.042 1465 Dihedral : 12.788 86.561 3301 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.22 % Allowed : 9.43 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.26), residues: 1081 helix: 1.47 (0.20), residues: 678 sheet: -0.80 (0.82), residues: 52 loop : -1.85 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 698 HIS 0.002 0.001 HIS A1007 PHE 0.011 0.001 PHE A 72 TYR 0.021 0.001 TYR A 247 ARG 0.002 0.000 ARG A 699 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 167 time to evaluate : 0.968 Fit side-chains REVERT: A 75 MET cc_start: 0.6481 (ttt) cc_final: 0.5567 (mtp) REVERT: A 380 LYS cc_start: 0.7684 (ptpp) cc_final: 0.6619 (ttpt) REVERT: A 450 MET cc_start: 0.7276 (ptp) cc_final: 0.6916 (ptp) REVERT: A 460 THR cc_start: 0.7788 (p) cc_final: 0.7358 (p) REVERT: A 502 LYS cc_start: 0.8239 (mtpp) cc_final: 0.7907 (ttmm) REVERT: A 925 GLN cc_start: 0.7926 (tm-30) cc_final: 0.7178 (tt0) REVERT: A 950 TYR cc_start: 0.7373 (t80) cc_final: 0.7171 (t80) REVERT: A 951 PHE cc_start: 0.7243 (t80) cc_final: 0.6832 (t80) REVERT: A 974 VAL cc_start: 0.8699 (t) cc_final: 0.8364 (t) REVERT: A 1062 LYS cc_start: 0.6913 (tptt) cc_final: 0.6088 (tttt) REVERT: A 1172 LYS cc_start: 0.6659 (pttt) cc_final: 0.6425 (pttp) outliers start: 2 outliers final: 1 residues processed: 168 average time/residue: 0.2138 time to fit residues: 49.5045 Evaluate side-chains 123 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 0.0470 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 84 optimal weight: 0.0270 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 GLN A 487 ASN A 530 GLN A 535 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.177256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.149446 restraints weight = 12369.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.147054 restraints weight = 14923.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.148732 restraints weight = 15438.254| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8806 Z= 0.167 Angle : 0.504 6.496 11816 Z= 0.274 Chirality : 0.039 0.149 1348 Planarity : 0.003 0.040 1465 Dihedral : 7.393 58.673 1364 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.58 % Allowed : 14.14 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.26), residues: 1081 helix: 1.90 (0.20), residues: 684 sheet: -1.19 (0.73), residues: 62 loop : -1.80 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 698 HIS 0.002 0.001 HIS A 153 PHE 0.019 0.001 PHE A 72 TYR 0.043 0.002 TYR A 998 ARG 0.003 0.000 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.895 Fit side-chains REVERT: A 380 LYS cc_start: 0.7560 (ptpp) cc_final: 0.6754 (ttpt) REVERT: A 925 GLN cc_start: 0.7636 (tm-30) cc_final: 0.7022 (tt0) REVERT: A 951 PHE cc_start: 0.7087 (t80) cc_final: 0.6752 (t80) REVERT: A 1062 LYS cc_start: 0.6734 (tptt) cc_final: 0.6209 (tttt) outliers start: 23 outliers final: 16 residues processed: 148 average time/residue: 0.1926 time to fit residues: 40.8291 Evaluate side-chains 131 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 971 PHE Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1121 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 84 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 GLN A 587 HIS A 750 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.175809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.150071 restraints weight = 12765.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.147627 restraints weight = 17758.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.149435 restraints weight = 18149.053| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8806 Z= 0.265 Angle : 0.566 6.244 11816 Z= 0.306 Chirality : 0.040 0.150 1348 Planarity : 0.004 0.039 1465 Dihedral : 8.033 57.453 1364 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.82 % Allowed : 13.69 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.26), residues: 1081 helix: 1.66 (0.20), residues: 686 sheet: -1.31 (0.72), residues: 62 loop : -1.85 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 315 HIS 0.003 0.001 HIS A 518 PHE 0.013 0.001 PHE A 200 TYR 0.033 0.002 TYR A 998 ARG 0.008 0.000 ARG A1147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 1.007 Fit side-chains REVERT: A 934 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7557 (tttm) REVERT: A 1061 LYS cc_start: 0.7858 (mtmm) cc_final: 0.6895 (ttpp) REVERT: A 1062 LYS cc_start: 0.6825 (tptt) cc_final: 0.6109 (tttt) outliers start: 34 outliers final: 27 residues processed: 135 average time/residue: 0.2028 time to fit residues: 39.4186 Evaluate side-chains 131 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 856 GLN Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 918 HIS Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 971 PHE Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1230 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 61 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.174243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.146573 restraints weight = 12637.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.144154 restraints weight = 17194.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.145997 restraints weight = 17366.517| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8806 Z= 0.298 Angle : 0.587 7.732 11816 Z= 0.317 Chirality : 0.041 0.156 1348 Planarity : 0.004 0.041 1465 Dihedral : 8.434 59.512 1364 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 5.27 % Allowed : 14.81 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.26), residues: 1081 helix: 1.48 (0.19), residues: 686 sheet: -1.41 (0.71), residues: 62 loop : -1.91 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 315 HIS 0.004 0.001 HIS A 518 PHE 0.015 0.002 PHE A1157 TYR 0.033 0.003 TYR A 247 ARG 0.004 0.000 ARG A1147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 111 time to evaluate : 0.939 Fit side-chains REVERT: A 736 ILE cc_start: 0.8539 (tp) cc_final: 0.8312 (tp) REVERT: A 851 PHE cc_start: 0.6176 (OUTLIER) cc_final: 0.5906 (m-10) REVERT: A 925 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7368 (tt0) REVERT: A 934 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7693 (tttm) REVERT: A 1061 LYS cc_start: 0.7818 (mtmm) cc_final: 0.6855 (ttpp) REVERT: A 1062 LYS cc_start: 0.6865 (tptt) cc_final: 0.6082 (tttt) REVERT: A 1167 THR cc_start: 0.8009 (OUTLIER) cc_final: 0.7798 (t) outliers start: 47 outliers final: 30 residues processed: 146 average time/residue: 0.1978 time to fit residues: 41.3773 Evaluate side-chains 136 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 856 GLN Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 918 HIS Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 971 PHE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1230 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 chunk 54 optimal weight: 20.0000 chunk 4 optimal weight: 6.9990 chunk 12 optimal weight: 0.0870 chunk 100 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.176574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.149070 restraints weight = 12579.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.146312 restraints weight = 15132.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.147524 restraints weight = 17380.760| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8806 Z= 0.202 Angle : 0.527 8.068 11816 Z= 0.285 Chirality : 0.039 0.147 1348 Planarity : 0.003 0.041 1465 Dihedral : 8.118 58.512 1364 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.93 % Allowed : 17.28 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.26), residues: 1081 helix: 1.69 (0.19), residues: 685 sheet: -1.31 (0.71), residues: 62 loop : -1.94 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 315 HIS 0.002 0.001 HIS A 518 PHE 0.014 0.001 PHE A1157 TYR 0.028 0.002 TYR A 247 ARG 0.005 0.000 ARG A1147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.879 Fit side-chains REVERT: A 851 PHE cc_start: 0.5855 (OUTLIER) cc_final: 0.5608 (m-10) REVERT: A 925 GLN cc_start: 0.7977 (tm-30) cc_final: 0.7408 (tt0) REVERT: A 934 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7570 (tttm) REVERT: A 986 MET cc_start: 0.7543 (mtp) cc_final: 0.7268 (mtm) REVERT: A 1061 LYS cc_start: 0.7775 (mtmm) cc_final: 0.6786 (ttpp) REVERT: A 1062 LYS cc_start: 0.6804 (tptt) cc_final: 0.5968 (tttt) outliers start: 35 outliers final: 28 residues processed: 137 average time/residue: 0.1946 time to fit residues: 38.0525 Evaluate side-chains 134 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 856 GLN Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 918 HIS Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 971 PHE Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1230 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.175906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.147807 restraints weight = 12249.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.147086 restraints weight = 14022.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.148189 restraints weight = 14647.919| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8806 Z= 0.241 Angle : 0.551 9.000 11816 Z= 0.298 Chirality : 0.040 0.148 1348 Planarity : 0.004 0.041 1465 Dihedral : 8.212 57.649 1364 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 4.83 % Allowed : 17.96 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.26), residues: 1081 helix: 1.61 (0.19), residues: 692 sheet: -1.32 (0.69), residues: 62 loop : -2.08 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 803 HIS 0.003 0.001 HIS A 518 PHE 0.019 0.002 PHE A1157 TYR 0.032 0.002 TYR A 247 ARG 0.002 0.000 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 111 time to evaluate : 0.876 Fit side-chains REVERT: A 736 ILE cc_start: 0.8506 (tp) cc_final: 0.8185 (tp) REVERT: A 851 PHE cc_start: 0.5908 (OUTLIER) cc_final: 0.5616 (m-10) REVERT: A 925 GLN cc_start: 0.7977 (tm-30) cc_final: 0.7427 (tt0) REVERT: A 934 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7589 (tttm) REVERT: A 1061 LYS cc_start: 0.7750 (mtmm) cc_final: 0.6851 (ttpp) REVERT: A 1062 LYS cc_start: 0.6850 (tptt) cc_final: 0.6112 (tttt) outliers start: 43 outliers final: 31 residues processed: 142 average time/residue: 0.1875 time to fit residues: 38.7024 Evaluate side-chains 141 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 856 GLN Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 918 HIS Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 971 PHE Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1230 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 90 optimal weight: 0.0040 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.178383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.152869 restraints weight = 12701.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.150426 restraints weight = 17148.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.152584 restraints weight = 16652.992| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8806 Z= 0.162 Angle : 0.509 10.365 11816 Z= 0.274 Chirality : 0.039 0.143 1348 Planarity : 0.003 0.041 1465 Dihedral : 7.788 56.632 1364 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.26 % Allowed : 18.52 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.26), residues: 1081 helix: 1.90 (0.20), residues: 685 sheet: -0.69 (0.75), residues: 52 loop : -2.02 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 315 HIS 0.001 0.000 HIS A 166 PHE 0.024 0.001 PHE A1157 TYR 0.026 0.002 TYR A 247 ARG 0.002 0.000 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 119 time to evaluate : 0.922 Fit side-chains REVERT: A 736 ILE cc_start: 0.8432 (tp) cc_final: 0.8141 (tp) REVERT: A 738 VAL cc_start: 0.7859 (OUTLIER) cc_final: 0.7625 (t) REVERT: A 851 PHE cc_start: 0.5823 (OUTLIER) cc_final: 0.5588 (m-10) REVERT: A 925 GLN cc_start: 0.7829 (tm-30) cc_final: 0.7283 (tt0) REVERT: A 934 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7539 (tttm) REVERT: A 1061 LYS cc_start: 0.7712 (mtmm) cc_final: 0.6852 (ttpp) REVERT: A 1062 LYS cc_start: 0.6729 (tptt) cc_final: 0.5970 (tttt) outliers start: 38 outliers final: 25 residues processed: 145 average time/residue: 0.1875 time to fit residues: 39.2202 Evaluate side-chains 139 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 490 TYR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 856 GLN Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1230 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.177194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.153349 restraints weight = 12751.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.151835 restraints weight = 19367.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.152593 restraints weight = 17516.565| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8806 Z= 0.199 Angle : 0.532 11.450 11816 Z= 0.287 Chirality : 0.039 0.162 1348 Planarity : 0.003 0.039 1465 Dihedral : 7.767 55.021 1364 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 4.04 % Allowed : 18.86 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1081 helix: 1.75 (0.19), residues: 692 sheet: -1.21 (0.68), residues: 62 loop : -2.04 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 315 HIS 0.002 0.001 HIS A 518 PHE 0.020 0.001 PHE A1157 TYR 0.030 0.002 TYR A 247 ARG 0.002 0.000 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 0.907 Fit side-chains REVERT: A 736 ILE cc_start: 0.8432 (tp) cc_final: 0.8171 (tp) REVERT: A 738 VAL cc_start: 0.7884 (OUTLIER) cc_final: 0.7645 (t) REVERT: A 851 PHE cc_start: 0.5898 (OUTLIER) cc_final: 0.5610 (m-10) REVERT: A 925 GLN cc_start: 0.7871 (tm-30) cc_final: 0.7320 (tt0) REVERT: A 934 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7523 (tttm) REVERT: A 1061 LYS cc_start: 0.7660 (mtmm) cc_final: 0.6742 (ttpp) REVERT: A 1062 LYS cc_start: 0.6677 (tptt) cc_final: 0.6171 (tttt) outliers start: 36 outliers final: 30 residues processed: 141 average time/residue: 0.1782 time to fit residues: 36.7391 Evaluate side-chains 145 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 490 TYR Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 856 GLN Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 918 HIS Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1065 THR Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1190 LEU Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1230 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 64 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 104 optimal weight: 0.1980 chunk 36 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 68 optimal weight: 0.2980 chunk 65 optimal weight: 0.7980 chunk 98 optimal weight: 0.0970 chunk 92 optimal weight: 9.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.181444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.158585 restraints weight = 12593.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.154011 restraints weight = 19793.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.153390 restraints weight = 14820.960| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8806 Z= 0.144 Angle : 0.502 10.461 11816 Z= 0.271 Chirality : 0.039 0.194 1348 Planarity : 0.003 0.040 1465 Dihedral : 7.251 58.792 1364 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.25 % Allowed : 20.65 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.26), residues: 1081 helix: 1.97 (0.20), residues: 694 sheet: -1.10 (0.69), residues: 62 loop : -2.01 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 803 HIS 0.002 0.000 HIS A 166 PHE 0.022 0.001 PHE A1157 TYR 0.024 0.001 TYR A 247 ARG 0.002 0.000 ARG A1085 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.887 Fit side-chains REVERT: A 75 MET cc_start: 0.6413 (ttt) cc_final: 0.5643 (mtp) REVERT: A 117 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.6528 (t80) REVERT: A 315 TRP cc_start: 0.6949 (OUTLIER) cc_final: 0.6241 (t60) REVERT: A 736 ILE cc_start: 0.8339 (tp) cc_final: 0.8093 (tp) REVERT: A 851 PHE cc_start: 0.5776 (OUTLIER) cc_final: 0.5563 (m-10) REVERT: A 925 GLN cc_start: 0.7781 (tm-30) cc_final: 0.7167 (tt0) REVERT: A 934 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7405 (tttm) REVERT: A 1062 LYS cc_start: 0.6658 (tptt) cc_final: 0.5915 (tttt) outliers start: 29 outliers final: 19 residues processed: 145 average time/residue: 0.2022 time to fit residues: 43.1455 Evaluate side-chains 135 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 490 TYR Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 856 GLN Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1230 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 60 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 94 optimal weight: 0.3980 chunk 47 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 chunk 4 optimal weight: 0.4980 chunk 68 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.180400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.157881 restraints weight = 12587.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.152436 restraints weight = 20683.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.151266 restraints weight = 15502.856| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8806 Z= 0.166 Angle : 0.545 12.689 11816 Z= 0.287 Chirality : 0.040 0.217 1348 Planarity : 0.003 0.038 1465 Dihedral : 7.127 56.813 1364 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.03 % Allowed : 21.44 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.26), residues: 1081 helix: 1.87 (0.20), residues: 696 sheet: -0.85 (0.77), residues: 52 loop : -1.99 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 212 HIS 0.001 0.000 HIS A 166 PHE 0.024 0.002 PHE A 767 TYR 0.028 0.001 TYR A 247 ARG 0.002 0.000 ARG A 467 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 1.020 Fit side-chains REVERT: A 75 MET cc_start: 0.6441 (ttt) cc_final: 0.5654 (mtp) REVERT: A 117 TYR cc_start: 0.7971 (OUTLIER) cc_final: 0.6541 (t80) REVERT: A 297 ILE cc_start: 0.8369 (tp) cc_final: 0.8123 (mt) REVERT: A 736 ILE cc_start: 0.8307 (tp) cc_final: 0.8062 (tp) REVERT: A 851 PHE cc_start: 0.5841 (OUTLIER) cc_final: 0.5541 (m-10) REVERT: A 925 GLN cc_start: 0.7648 (tm-30) cc_final: 0.6994 (tt0) REVERT: A 934 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7414 (tttm) REVERT: A 1062 LYS cc_start: 0.6652 (tptt) cc_final: 0.5931 (tttt) outliers start: 27 outliers final: 23 residues processed: 134 average time/residue: 0.1862 time to fit residues: 36.2753 Evaluate side-chains 138 residues out of total 896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 490 TYR Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 913 GLU Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 1010 MET Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1121 ILE Chi-restraints excluded: chain A residue 1166 SER Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1230 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 104 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.178997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.156744 restraints weight = 12606.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.154555 restraints weight = 18567.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.152249 restraints weight = 13446.050| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8806 Z= 0.198 Angle : 0.558 12.257 11816 Z= 0.296 Chirality : 0.040 0.245 1348 Planarity : 0.003 0.037 1465 Dihedral : 7.310 54.093 1364 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.20 % Favored : 93.71 % Rotamer: Outliers : 3.37 % Allowed : 21.66 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.26), residues: 1081 helix: 1.76 (0.20), residues: 696 sheet: -0.89 (0.76), residues: 52 loop : -1.99 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 803 HIS 0.002 0.001 HIS A 518 PHE 0.023 0.002 PHE A 767 TYR 0.042 0.002 TYR A 998 ARG 0.002 0.000 ARG A 467 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2411.98 seconds wall clock time: 44 minutes 18.08 seconds (2658.08 seconds total)