Starting phenix.real_space_refine on Sat Aug 23 09:26:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8att_15662/08_2025/8att_15662.cif Found real_map, /net/cci-nas-00/data/ceres_data/8att_15662/08_2025/8att_15662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8att_15662/08_2025/8att_15662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8att_15662/08_2025/8att_15662.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8att_15662/08_2025/8att_15662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8att_15662/08_2025/8att_15662.map" } resolution = 3.44 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= 0.001 sd= 0.011 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: 5 Type Number sf(0) Gaussians P 59 5.49 5 S 36 5.16 5 C 6931 2.51 5 N 1921 2.21 5 O 2177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11124 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2785 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 320} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 7184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 7184 Classifications: {'peptide': 906} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 43, 'TRANS': 862} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "N" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 553 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DA:plan': 1, ' DA:plan2': 1} Unresolved non-hydrogen planarities: 12 Chain: "T" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 505 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {' DG:plan': 1, ' DG:plan2': 1, ' DC:plan': 1, ' DC:plan2': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.34, per 1000 atoms: 0.21 Number of scatterers: 11124 At special positions: 0 Unit cell: (104.76, 109.61, 119.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 59 15.00 O 2177 8.00 N 1921 7.00 C 6931 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 465.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2354 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 12 sheets defined 58.9% alpha, 9.4% beta 22 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'B' and resid 7 through 14 removed outlier: 3.801A pdb=" N LEU B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 37 Processing helix chain 'B' and resid 37 through 42 removed outlier: 4.173A pdb=" N THR B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 69 Processing helix chain 'B' and resid 79 through 90 Processing helix chain 'B' and resid 104 through 113 removed outlier: 3.711A pdb=" N TYR B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 157 removed outlier: 3.987A pdb=" N ILE B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.704A pdb=" N PHE B 163 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 181 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 209 through 215 removed outlier: 3.828A pdb=" N LYS B 214 " --> pdb=" O ASN B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 230 through 234 removed outlier: 3.574A pdb=" N ILE B 234 " --> pdb=" O ALA B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 267 Processing helix chain 'B' and resid 268 through 270 No H-bonds generated for 'chain 'B' and resid 268 through 270' Processing helix chain 'B' and resid 273 through 278 removed outlier: 4.048A pdb=" N MET B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 297 through 301 removed outlier: 4.011A pdb=" N LYS B 300 " --> pdb=" O ASP B 297 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS B 301 " --> pdb=" O LEU B 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 297 through 301' Processing helix chain 'B' and resid 307 through 321 Processing helix chain 'A' and resid 408 through 420 removed outlier: 3.706A pdb=" N ARG A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 442 removed outlier: 3.618A pdb=" N TRP A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU A 437 " --> pdb=" O HIS A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 477 Proline residue: A 463 - end of helix removed outlier: 3.510A pdb=" N SER A 477 " --> pdb=" O ARG A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 501 removed outlier: 3.840A pdb=" N LEU A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 495 " --> pdb=" O THR A 491 " (cutoff:3.500A) Proline residue: A 498 - end of helix removed outlier: 3.563A pdb=" N THR A 501 " --> pdb=" O GLY A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 519 Processing helix chain 'A' and resid 531 through 558 Processing helix chain 'A' and resid 593 through 610 Processing helix chain 'A' and resid 652 through 660 removed outlier: 3.739A pdb=" N GLN A 658 " --> pdb=" O THR A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 703 through 717 removed outlier: 4.245A pdb=" N VAL A 707 " --> pdb=" O SER A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 731 Processing helix chain 'A' and resid 737 through 751 removed outlier: 3.535A pdb=" N GLY A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 813 Processing helix chain 'A' and resid 842 through 848 Processing helix chain 'A' and resid 857 through 872 removed outlier: 4.657A pdb=" N LEU A 862 " --> pdb=" O GLY A 858 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LYS A 863 " --> pdb=" O PRO A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 890 removed outlier: 3.909A pdb=" N HIS A 890 " --> pdb=" O PHE A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 900 Processing helix chain 'A' and resid 913 through 930 Processing helix chain 'A' and resid 932 through 935 removed outlier: 3.515A pdb=" N GLU A 935 " --> pdb=" O ASN A 932 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 932 through 935' Processing helix chain 'A' and resid 948 through 959 Processing helix chain 'A' and resid 960 through 967 Processing helix chain 'A' and resid 977 through 994 Processing helix chain 'A' and resid 995 through 997 No H-bonds generated for 'chain 'A' and resid 995 through 997' Processing helix chain 'A' and resid 998 through 1005 Processing helix chain 'A' and resid 1009 through 1021 removed outlier: 4.053A pdb=" N THR A1019 " --> pdb=" O GLN A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1038 Processing helix chain 'A' and resid 1047 through 1066 removed outlier: 3.720A pdb=" N TYR A1053 " --> pdb=" O ASP A1049 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU A1064 " --> pdb=" O SER A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1085 Processing helix chain 'A' and resid 1149 through 1181 Proline residue: A1158 - end of helix Processing helix chain 'A' and resid 1197 through 1214 Processing helix chain 'A' and resid 1216 through 1229 Processing helix chain 'A' and resid 1242 through 1260 removed outlier: 3.630A pdb=" N LYS A1247 " --> pdb=" O ASP A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1281 Processing helix chain 'A' and resid 1283 through 1293 Processing helix chain 'A' and resid 1295 through 1303 Processing helix chain 'A' and resid 1305 through 1310 Processing helix chain 'A' and resid 1339 through 1346 removed outlier: 3.658A pdb=" N VAL A1342 " --> pdb=" O ASP A1339 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A1343 " --> pdb=" O VAL A1340 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 98 through 99 removed outlier: 6.614A pdb=" N VAL B 50 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N LEU B 76 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASP B 52 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS B 49 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 133 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LYS B 167 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 9.642A pdb=" N LYS B 131 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 13.433A pdb=" N LEU B 169 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 10.225A pdb=" N LEU B 133 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 12.416A pdb=" N TRP B 171 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N VAL B 135 " --> pdb=" O TRP B 171 " (cutoff:3.500A) removed outlier: 11.565A pdb=" N ASN B 137 " --> pdb=" O PRO B 173 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL B 166 " --> pdb=" O PRO B 249 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE B 242 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE B 207 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU B 244 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N ILE B 227 " --> pdb=" O LYS B 203 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ILE B 205 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 528 through 530 Processing sheet with id=AA3, first strand: chain 'A' and resid 613 through 620 removed outlier: 3.685A pdb=" N ALA A 625 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 680 through 684 removed outlier: 7.599A pdb=" N TRP A 682 " --> pdb=" O GLY A 689 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N GLY A 689 " --> pdb=" O TRP A 682 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN A 684 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 817 through 819 Processing sheet with id=AA6, first strand: chain 'A' and resid 822 through 824 Processing sheet with id=AA7, first strand: chain 'A' and resid 855 through 856 removed outlier: 3.516A pdb=" N LYS A 855 " --> pdb=" O SER A 938 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 938 " --> pdb=" O LYS A 855 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 942 through 945 removed outlier: 3.667A pdb=" N THR A1193 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A1185 " --> pdb=" O TRP A1192 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1086 through 1088 Processing sheet with id=AB1, first strand: chain 'A' and resid 1109 through 1111 Processing sheet with id=AB2, first strand: chain 'A' and resid 1127 through 1131 removed outlier: 3.511A pdb=" N ILE A1139 " --> pdb=" O LYS A1128 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1236 through 1238 531 hydrogen bonds defined for protein. 1551 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 1.91 Time building geometry restraints manager: 1.24 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: 3347 1.34 - 1.46: 2025 1.46 - 1.57: 5952 1.57 - 1.69: 108 1.69 - 1.81: 61 Bond restraints: 11493 Sorted by residual: bond pdb=" O3' DG N 126 " pdb=" P DA N 127 " ideal model delta sigma weight residual 1.607 1.475 0.132 1.50e-02 4.44e+03 7.76e+01 bond pdb=" O3' DA N 129 " pdb=" P DA N 130 " ideal model delta sigma weight residual 1.607 1.504 0.103 1.50e-02 4.44e+03 4.75e+01 bond pdb=" C4' DG N 108 " pdb=" O4' DG N 108 " ideal model delta sigma weight residual 1.450 1.552 -0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" O3' DT N 128 " pdb=" P DA N 129 " ideal model delta sigma weight residual 1.607 1.678 -0.071 1.50e-02 4.44e+03 2.21e+01 bond pdb=" O3' DA N 125 " pdb=" P DG N 126 " ideal model delta sigma weight residual 1.607 1.677 -0.070 1.50e-02 4.44e+03 2.18e+01 ... (remaining 11488 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 15677 3.54 - 7.08: 102 7.08 - 10.62: 11 10.62 - 14.16: 3 14.16 - 17.70: 2 Bond angle restraints: 15795 Sorted by residual: angle pdb=" C5' DG N 108 " pdb=" C4' DG N 108 " pdb=" O4' DG N 108 " ideal model delta sigma weight residual 109.40 127.10 -17.70 1.50e+00 4.44e-01 1.39e+02 angle pdb=" C3' DG N 126 " pdb=" O3' DG N 126 " pdb=" P DA N 127 " ideal model delta sigma weight residual 120.20 107.37 12.83 1.50e+00 4.44e-01 7.31e+01 angle pdb=" C5' DT T 16 " pdb=" C4' DT T 16 " pdb=" O4' DT T 16 " ideal model delta sigma weight residual 109.40 121.15 -11.75 1.50e+00 4.44e-01 6.13e+01 angle pdb=" C4' DA T 19 " pdb=" C3' DA T 19 " pdb=" O3' DA T 19 " ideal model delta sigma weight residual 110.00 120.31 -10.31 1.50e+00 4.44e-01 4.72e+01 angle pdb=" CA PRO A 621 " pdb=" N PRO A 621 " pdb=" CD PRO A 621 " ideal model delta sigma weight residual 112.00 102.99 9.01 1.40e+00 5.10e-01 4.14e+01 ... (remaining 15790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.43: 6258 26.43 - 52.87: 483 52.87 - 79.30: 82 79.30 - 105.73: 5 105.73 - 132.17: 1 Dihedral angle restraints: 6829 sinusoidal: 3194 harmonic: 3635 Sorted by residual: dihedral pdb=" C4' GTP C 201 " pdb=" C5' GTP C 201 " pdb=" O5' GTP C 201 " pdb=" PA GTP C 201 " ideal model delta sinusoidal sigma weight residual 260.87 128.71 132.17 1 2.00e+01 2.50e-03 4.01e+01 dihedral pdb=" C8 GTP C 201 " pdb=" C1' GTP C 201 " pdb=" N9 GTP C 201 " pdb=" O4' GTP C 201 " ideal model delta sinusoidal sigma weight residual 104.59 3.46 101.14 1 2.00e+01 2.50e-03 2.86e+01 dihedral pdb=" C5' GTP C 201 " pdb=" O5' GTP C 201 " pdb=" PA GTP C 201 " pdb=" O3A GTP C 201 " ideal model delta sinusoidal sigma weight residual 69.27 5.26 64.01 1 2.00e+01 2.50e-03 1.35e+01 ... (remaining 6826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1697 0.127 - 0.254: 28 0.254 - 0.381: 2 0.381 - 0.508: 8 0.508 - 0.635: 10 Chirality restraints: 1745 Sorted by residual: chirality pdb=" P DC T 24 " pdb=" OP1 DC T 24 " pdb=" OP2 DC T 24 " pdb=" O5' DC T 24 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.63 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" P DA N 122 " pdb=" OP1 DA N 122 " pdb=" OP2 DA N 122 " pdb=" O5' DA N 122 " both_signs ideal model delta sigma weight residual True 2.35 -2.93 -0.58 2.00e-01 2.50e+01 8.52e+00 chirality pdb=" P DG T 22 " pdb=" OP1 DG T 22 " pdb=" OP2 DG T 22 " pdb=" O5' DG T 22 " both_signs ideal model delta sigma weight residual True 2.35 -2.91 -0.57 2.00e-01 2.50e+01 8.03e+00 ... (remaining 1742 not shown) Planarity restraints: 1822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 620 " 0.068 5.00e-02 4.00e+02 9.69e-02 1.50e+01 pdb=" N PRO A 621 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 621 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 621 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 431 " -0.018 2.00e-02 2.50e+03 1.38e-02 4.74e+00 pdb=" CG TRP A 431 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 431 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 431 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 431 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 431 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 431 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 431 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 431 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 431 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A1019 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.56e+00 pdb=" C THR A1019 " -0.033 2.00e-02 2.50e+03 pdb=" O THR A1019 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN A1020 " 0.011 2.00e-02 2.50e+03 ... (remaining 1819 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 254 2.68 - 3.24: 10708 3.24 - 3.79: 17891 3.79 - 4.35: 23515 4.35 - 4.90: 37602 Nonbonded interactions: 89970 Sorted by model distance: nonbonded pdb=" OG SER A1186 " pdb=" O SER A1190 " model vdw 2.127 3.040 nonbonded pdb=" OG1 THR A1132 " pdb=" O GLN A1135 " model vdw 2.134 3.040 nonbonded pdb=" OG1 THR B 307 " pdb=" OE1 GLU B 310 " model vdw 2.210 3.040 nonbonded pdb=" NZ LYS B 21 " pdb=" O LYS B 240 " model vdw 2.227 3.120 nonbonded pdb=" OG SER A 703 " pdb=" OE1 GLN A 706 " model vdw 2.232 3.040 ... (remaining 89965 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.870 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 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 : 0.005 0.132 11494 Z= 0.268 Angle : 0.806 17.700 15795 Z= 0.451 Chirality : 0.070 0.635 1745 Planarity : 0.005 0.097 1822 Dihedral : 17.712 132.167 4475 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.18 % Allowed : 0.18 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.24), residues: 1238 helix: 1.64 (0.21), residues: 685 sheet: -0.20 (0.50), residues: 106 loop : -0.88 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1063 TYR 0.012 0.001 TYR A 496 PHE 0.024 0.001 PHE A1338 TRP 0.037 0.001 TRP A 431 HIS 0.005 0.001 HIS A1213 Details of bonding type rmsd covalent geometry : bond 0.00493 (11493) covalent geometry : angle 0.80598 (15795) hydrogen bonds : bond 0.14420 ( 580) hydrogen bonds : angle 5.88031 ( 1649) Misc. bond : bond 0.09185 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 166 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 ASN cc_start: 0.8252 (p0) cc_final: 0.7887 (p0) REVERT: A 544 MET cc_start: 0.7622 (mmt) cc_final: 0.7396 (mmt) REVERT: A 657 ARG cc_start: 0.8021 (ttm-80) cc_final: 0.7801 (ptm160) REVERT: A 763 GLU cc_start: 0.6832 (pt0) cc_final: 0.6549 (pt0) REVERT: A 976 GLN cc_start: 0.6396 (mt0) cc_final: 0.5625 (tp-100) REVERT: A 1157 LEU cc_start: 0.6675 (tp) cc_final: 0.6426 (tp) outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.0806 time to fit residues: 19.8078 Evaluate side-chains 131 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.0770 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 overall best weight: 4.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 HIS ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.172344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.127894 restraints weight = 16533.079| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.70 r_work: 0.3510 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11494 Z= 0.175 Angle : 0.609 8.686 15795 Z= 0.326 Chirality : 0.042 0.158 1745 Planarity : 0.004 0.041 1822 Dihedral : 19.387 127.724 2005 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.56 % Allowed : 7.64 % Favored : 90.80 % 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: 0.90 (0.24), residues: 1238 helix: 1.61 (0.20), residues: 691 sheet: -0.01 (0.50), residues: 96 loop : -0.84 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 797 TYR 0.033 0.002 TYR B 161 PHE 0.012 0.001 PHE A1041 TRP 0.020 0.002 TRP A 431 HIS 0.005 0.001 HIS A1213 Details of bonding type rmsd covalent geometry : bond 0.00400 (11493) covalent geometry : angle 0.60883 (15795) hydrogen bonds : bond 0.04784 ( 580) hydrogen bonds : angle 4.67845 ( 1649) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 ILE cc_start: 0.8618 (mp) cc_final: 0.8355 (mm) REVERT: B 334 MET cc_start: 0.6509 (mmt) cc_final: 0.6207 (mmm) REVERT: A 544 MET cc_start: 0.7862 (mmt) cc_final: 0.7620 (mmt) REVERT: A 553 LYS cc_start: 0.6172 (pptt) cc_final: 0.5816 (pptt) REVERT: A 1070 HIS cc_start: 0.7168 (t-90) cc_final: 0.6865 (t70) REVERT: A 1300 PHE cc_start: 0.7153 (m-80) cc_final: 0.6225 (m-80) outliers start: 17 outliers final: 12 residues processed: 157 average time/residue: 0.0794 time to fit residues: 18.4363 Evaluate side-chains 149 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1132 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 35 optimal weight: 0.2980 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 HIS A 660 ASN ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 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 = 0.4219 r_free = 0.4219 target = 0.173501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.129226 restraints weight = 16604.860| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.73 r_work: 0.3519 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11494 Z= 0.134 Angle : 0.555 7.779 15795 Z= 0.297 Chirality : 0.040 0.150 1745 Planarity : 0.004 0.040 1822 Dihedral : 19.323 125.638 2005 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.21 % Allowed : 10.58 % Favored : 87.21 % 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: 1.06 (0.25), residues: 1238 helix: 1.77 (0.20), residues: 689 sheet: -0.45 (0.48), residues: 110 loop : -0.66 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 827 TYR 0.021 0.002 TYR B 83 PHE 0.018 0.001 PHE A1338 TRP 0.015 0.001 TRP A 431 HIS 0.004 0.001 HIS A1213 Details of bonding type rmsd covalent geometry : bond 0.00298 (11493) covalent geometry : angle 0.55513 (15795) hydrogen bonds : bond 0.04202 ( 580) hydrogen bonds : angle 4.42442 ( 1649) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 334 MET cc_start: 0.6639 (mmt) cc_final: 0.6293 (mmm) REVERT: A 544 MET cc_start: 0.7866 (mmt) cc_final: 0.7638 (mmt) REVERT: A 553 LYS cc_start: 0.6174 (pptt) cc_final: 0.5878 (pptt) REVERT: A 675 MET cc_start: 0.7998 (mtp) cc_final: 0.7780 (mtm) REVERT: A 1300 PHE cc_start: 0.7092 (m-80) cc_final: 0.6084 (m-80) outliers start: 24 outliers final: 16 residues processed: 157 average time/residue: 0.0784 time to fit residues: 18.3600 Evaluate side-chains 151 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 660 ASN Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1327 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 14 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 113 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 ASN ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.168662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.127448 restraints weight = 16824.280| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.64 r_work: 0.3442 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11494 Z= 0.229 Angle : 0.625 7.934 15795 Z= 0.331 Chirality : 0.043 0.163 1745 Planarity : 0.004 0.043 1822 Dihedral : 19.450 123.511 2005 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.76 % Allowed : 12.88 % Favored : 84.36 % 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: 0.80 (0.24), residues: 1238 helix: 1.59 (0.20), residues: 683 sheet: -0.48 (0.49), residues: 104 loop : -0.86 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 827 TYR 0.034 0.002 TYR B 161 PHE 0.019 0.002 PHE A1338 TRP 0.021 0.002 TRP A 431 HIS 0.007 0.001 HIS A 652 Details of bonding type rmsd covalent geometry : bond 0.00531 (11493) covalent geometry : angle 0.62476 (15795) hydrogen bonds : bond 0.04747 ( 580) hydrogen bonds : angle 4.57767 ( 1649) Misc. bond : bond 0.00069 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.7883 (mmt) cc_final: 0.7665 (mmt) REVERT: A 553 LYS cc_start: 0.6189 (pptt) cc_final: 0.5883 (pptt) REVERT: A 1070 HIS cc_start: 0.7626 (t-90) cc_final: 0.7323 (t70) REVERT: A 1201 MET cc_start: 0.7292 (ttp) cc_final: 0.7077 (ttp) REVERT: A 1300 PHE cc_start: 0.6952 (m-80) cc_final: 0.5920 (m-80) outliers start: 30 outliers final: 21 residues processed: 165 average time/residue: 0.0871 time to fit residues: 21.0338 Evaluate side-chains 157 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 10 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 ASN ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.169184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.128193 restraints weight = 16714.405| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.61 r_work: 0.3450 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11494 Z= 0.195 Angle : 0.617 7.943 15795 Z= 0.323 Chirality : 0.042 0.174 1745 Planarity : 0.004 0.042 1822 Dihedral : 19.354 121.856 2005 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.22 % Allowed : 14.17 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.24), residues: 1238 helix: 1.61 (0.20), residues: 683 sheet: -0.40 (0.48), residues: 106 loop : -0.86 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1250 TYR 0.043 0.002 TYR B 161 PHE 0.022 0.002 PHE A1338 TRP 0.018 0.002 TRP A 431 HIS 0.005 0.001 HIS A 652 Details of bonding type rmsd covalent geometry : bond 0.00454 (11493) covalent geometry : angle 0.61688 (15795) hydrogen bonds : bond 0.04455 ( 580) hydrogen bonds : angle 4.52080 ( 1649) Misc. bond : bond 0.00065 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.7931 (mmt) cc_final: 0.7705 (mmt) REVERT: A 553 LYS cc_start: 0.6195 (pptt) cc_final: 0.5950 (pptt) REVERT: A 1070 HIS cc_start: 0.7658 (t-90) cc_final: 0.7384 (t70) REVERT: A 1201 MET cc_start: 0.7212 (ttp) cc_final: 0.6960 (ttp) REVERT: A 1250 ARG cc_start: 0.8717 (mmm160) cc_final: 0.8042 (tpp80) REVERT: A 1300 PHE cc_start: 0.7023 (m-80) cc_final: 0.5915 (m-80) outliers start: 35 outliers final: 27 residues processed: 164 average time/residue: 0.0794 time to fit residues: 19.5669 Evaluate side-chains 158 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 106 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 59 optimal weight: 50.0000 chunk 86 optimal weight: 20.0000 chunk 42 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A1129 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 = 0.4169 r_free = 0.4169 target = 0.169611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.128635 restraints weight = 16821.610| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.61 r_work: 0.3458 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11494 Z= 0.176 Angle : 0.603 8.297 15795 Z= 0.316 Chirality : 0.041 0.154 1745 Planarity : 0.004 0.041 1822 Dihedral : 19.254 120.824 2005 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.85 % Allowed : 14.90 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.24), residues: 1238 helix: 1.67 (0.20), residues: 684 sheet: -0.31 (0.49), residues: 106 loop : -0.83 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 797 TYR 0.023 0.002 TYR B 161 PHE 0.022 0.001 PHE A1338 TRP 0.016 0.001 TRP A 431 HIS 0.004 0.001 HIS B 265 Details of bonding type rmsd covalent geometry : bond 0.00408 (11493) covalent geometry : angle 0.60294 (15795) hydrogen bonds : bond 0.04303 ( 580) hydrogen bonds : angle 4.48711 ( 1649) Misc. bond : bond 0.00065 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.7925 (mmt) cc_final: 0.7708 (mmt) REVERT: A 553 LYS cc_start: 0.6215 (pptt) cc_final: 0.5979 (pptt) REVERT: A 675 MET cc_start: 0.7856 (mtp) cc_final: 0.7572 (mtm) REVERT: A 764 MET cc_start: 0.7317 (mtp) cc_final: 0.7100 (mtm) REVERT: A 1070 HIS cc_start: 0.7682 (t-90) cc_final: 0.7222 (t-90) REVERT: A 1250 ARG cc_start: 0.8698 (mmm160) cc_final: 0.8397 (mmm160) REVERT: A 1300 PHE cc_start: 0.7108 (m-80) cc_final: 0.6027 (m-80) outliers start: 31 outliers final: 29 residues processed: 161 average time/residue: 0.0864 time to fit residues: 20.7332 Evaluate side-chains 161 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1200 THR Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 117 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 79 optimal weight: 30.0000 chunk 40 optimal weight: 8.9990 chunk 92 optimal weight: 0.5980 chunk 7 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 overall best weight: 6.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 694 GLN ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.167921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.126165 restraints weight = 16745.745| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.74 r_work: 0.3416 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11494 Z= 0.218 Angle : 0.635 8.898 15795 Z= 0.333 Chirality : 0.043 0.166 1745 Planarity : 0.004 0.043 1822 Dihedral : 19.363 119.757 2005 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.50 % Allowed : 15.27 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.24), residues: 1238 helix: 1.56 (0.20), residues: 684 sheet: -0.32 (0.49), residues: 106 loop : -0.91 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 827 TYR 0.026 0.002 TYR A1348 PHE 0.023 0.002 PHE A1338 TRP 0.019 0.002 TRP A 431 HIS 0.005 0.001 HIS A 652 Details of bonding type rmsd covalent geometry : bond 0.00509 (11493) covalent geometry : angle 0.63507 (15795) hydrogen bonds : bond 0.04594 ( 580) hydrogen bonds : angle 4.57124 ( 1649) Misc. bond : bond 0.00071 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.7965 (mmt) cc_final: 0.7721 (mmt) REVERT: A 553 LYS cc_start: 0.6209 (pptt) cc_final: 0.5976 (pptt) REVERT: A 673 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7792 (pp) REVERT: A 764 MET cc_start: 0.7405 (mtp) cc_final: 0.7176 (mtm) REVERT: A 1070 HIS cc_start: 0.7890 (t-90) cc_final: 0.7607 (t70) REVERT: A 1250 ARG cc_start: 0.8719 (mmm160) cc_final: 0.8418 (mmm160) REVERT: A 1300 PHE cc_start: 0.7131 (m-80) cc_final: 0.5990 (m-80) outliers start: 38 outliers final: 34 residues processed: 163 average time/residue: 0.0867 time to fit residues: 21.0167 Evaluate side-chains 163 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1200 THR Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 52 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 59 optimal weight: 40.0000 chunk 110 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 105 optimal weight: 30.0000 chunk 61 optimal weight: 5.9990 chunk 29 optimal weight: 0.0020 chunk 15 optimal weight: 6.9990 overall best weight: 4.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A1129 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 = 0.4161 r_free = 0.4161 target = 0.168824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.126407 restraints weight = 16774.995| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.72 r_work: 0.3428 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11494 Z= 0.185 Angle : 0.621 8.676 15795 Z= 0.322 Chirality : 0.042 0.177 1745 Planarity : 0.004 0.044 1822 Dihedral : 19.259 118.451 2005 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.68 % Allowed : 15.18 % Favored : 81.14 % 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: 0.83 (0.24), residues: 1238 helix: 1.64 (0.20), residues: 684 sheet: -0.37 (0.48), residues: 110 loop : -0.91 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 827 TYR 0.024 0.002 TYR A1348 PHE 0.024 0.001 PHE A 936 TRP 0.017 0.002 TRP A 431 HIS 0.003 0.001 HIS A 652 Details of bonding type rmsd covalent geometry : bond 0.00429 (11493) covalent geometry : angle 0.62132 (15795) hydrogen bonds : bond 0.04337 ( 580) hydrogen bonds : angle 4.50435 ( 1649) Misc. bond : bond 0.00070 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 GLN cc_start: 0.8117 (tt0) cc_final: 0.7446 (tt0) REVERT: A 544 MET cc_start: 0.7933 (mmt) cc_final: 0.7684 (mmt) REVERT: A 553 LYS cc_start: 0.6225 (pptt) cc_final: 0.6014 (pptt) REVERT: A 673 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7779 (pp) REVERT: A 675 MET cc_start: 0.7882 (mtp) cc_final: 0.7578 (mtm) REVERT: A 764 MET cc_start: 0.7438 (mtp) cc_final: 0.7186 (mtm) REVERT: A 824 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8278 (mp) REVERT: A 1070 HIS cc_start: 0.7920 (t-90) cc_final: 0.7621 (t70) REVERT: A 1250 ARG cc_start: 0.8667 (mmm160) cc_final: 0.8371 (mmm160) REVERT: A 1300 PHE cc_start: 0.7193 (m-80) cc_final: 0.6012 (m-80) outliers start: 40 outliers final: 34 residues processed: 165 average time/residue: 0.0853 time to fit residues: 20.9618 Evaluate side-chains 168 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1200 THR Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 69 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 4 optimal weight: 0.1980 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 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 = 0.4180 r_free = 0.4180 target = 0.170539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.127797 restraints weight = 16459.017| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.78 r_work: 0.3458 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11494 Z= 0.143 Angle : 0.594 9.225 15795 Z= 0.307 Chirality : 0.040 0.167 1745 Planarity : 0.004 0.044 1822 Dihedral : 19.103 116.699 2005 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.22 % Allowed : 15.92 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.25), residues: 1238 helix: 1.77 (0.20), residues: 686 sheet: -0.23 (0.48), residues: 110 loop : -0.81 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1240 TYR 0.045 0.002 TYR B 161 PHE 0.026 0.001 PHE A 936 TRP 0.014 0.001 TRP A 431 HIS 0.003 0.001 HIS A1213 Details of bonding type rmsd covalent geometry : bond 0.00328 (11493) covalent geometry : angle 0.59431 (15795) hydrogen bonds : bond 0.03970 ( 580) hydrogen bonds : angle 4.37291 ( 1649) Misc. bond : bond 0.00064 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.7913 (mmt) cc_final: 0.7680 (mmt) REVERT: A 673 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7657 (pp) REVERT: A 675 MET cc_start: 0.7710 (mtp) cc_final: 0.7445 (mtm) REVERT: A 764 MET cc_start: 0.7482 (mtp) cc_final: 0.7228 (mtm) REVERT: A 824 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8221 (mp) REVERT: A 1070 HIS cc_start: 0.7871 (t-90) cc_final: 0.7581 (t70) REVERT: A 1250 ARG cc_start: 0.8617 (mmm160) cc_final: 0.8369 (mmm160) outliers start: 35 outliers final: 31 residues processed: 169 average time/residue: 0.0809 time to fit residues: 20.2968 Evaluate side-chains 166 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 660 ASN Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 844 MET Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain A residue 954 TYR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1025 THR Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1200 THR Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 0.0070 chunk 8 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 27 optimal weight: 0.4980 chunk 33 optimal weight: 0.0040 chunk 15 optimal weight: 0.9980 chunk 118 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 overall best weight: 0.9012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.173050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.129882 restraints weight = 16616.523| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 3.00 r_work: 0.3489 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11494 Z= 0.121 Angle : 0.592 9.695 15795 Z= 0.307 Chirality : 0.040 0.159 1745 Planarity : 0.004 0.045 1822 Dihedral : 18.923 114.082 2005 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.30 % Allowed : 17.02 % Favored : 80.68 % 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: 1.23 (0.25), residues: 1238 helix: 1.90 (0.20), residues: 678 sheet: -0.10 (0.48), residues: 110 loop : -0.59 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1240 TYR 0.022 0.002 TYR B 83 PHE 0.023 0.001 PHE A1338 TRP 0.011 0.001 TRP A 455 HIS 0.004 0.001 HIS A 939 Details of bonding type rmsd covalent geometry : bond 0.00270 (11493) covalent geometry : angle 0.59234 (15795) hydrogen bonds : bond 0.03617 ( 580) hydrogen bonds : angle 4.24257 ( 1649) Misc. bond : bond 0.00055 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 MET cc_start: 0.8345 (mmm) cc_final: 0.7948 (mmm) REVERT: A 544 MET cc_start: 0.7871 (mmt) cc_final: 0.7610 (mmt) REVERT: A 673 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7604 (pp) REVERT: A 675 MET cc_start: 0.7593 (mtp) cc_final: 0.7380 (mtm) REVERT: A 764 MET cc_start: 0.7490 (mtp) cc_final: 0.7262 (mtm) REVERT: A 824 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8242 (mp) REVERT: A 1070 HIS cc_start: 0.7822 (t-90) cc_final: 0.7500 (t70) REVERT: A 1250 ARG cc_start: 0.8540 (mmm160) cc_final: 0.8316 (mmm160) outliers start: 25 outliers final: 20 residues processed: 165 average time/residue: 0.0816 time to fit residues: 20.1309 Evaluate side-chains 163 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 520 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 660 ASN Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 718 ASP Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 845 SER Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 86 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 916 GLN ** 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 = 0.4200 r_free = 0.4200 target = 0.172312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.131664 restraints weight = 16775.567| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.62 r_work: 0.3504 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 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 0.040 11494 Z= 0.132 Angle : 0.592 9.277 15795 Z= 0.304 Chirality : 0.040 0.159 1745 Planarity : 0.004 0.044 1822 Dihedral : 18.893 112.119 2005 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.67 % Allowed : 17.39 % Favored : 79.94 % 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: 1.25 (0.25), residues: 1238 helix: 1.90 (0.20), residues: 679 sheet: -0.20 (0.47), residues: 120 loop : -0.54 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 883 TYR 0.021 0.002 TYR B 83 PHE 0.025 0.001 PHE A 936 TRP 0.014 0.001 TRP A 431 HIS 0.003 0.001 HIS A 939 Details of bonding type rmsd covalent geometry : bond 0.00299 (11493) covalent geometry : angle 0.59230 (15795) hydrogen bonds : bond 0.03696 ( 580) hydrogen bonds : angle 4.24110 ( 1649) Misc. bond : bond 0.00052 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2115.13 seconds wall clock time: 37 minutes 2.07 seconds (2222.07 seconds total)