Starting phenix.real_space_refine on Sun Dec 29 18:32:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8att_15662/12_2024/8att_15662.cif Found real_map, /net/cci-nas-00/data/ceres_data/8att_15662/12_2024/8att_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8att_15662/12_2024/8att_15662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8att_15662/12_2024/8att_15662.map" model { file = "/net/cci-nas-00/data/ceres_data/8att_15662/12_2024/8att_15662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8att_15662/12_2024/8att_15662.cif" } resolution = 3.44 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= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} 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: {' DC:plan2': 1, ' DG:plan': 1, ' DG:plan2': 1, ' DC:plan': 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: 7.16, per 1000 atoms: 0.64 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: 3.26 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 4.03 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: 5.14 Time building geometry restraints manager: 3.67 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: 0.120 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 32.720 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.270 ------------------------------------------------------------------------------- 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 11493 Z= 0.286 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 (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: 0.87 (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 TRP 0.037 0.001 TRP A 431 HIS 0.005 0.001 HIS A1213 PHE 0.024 0.001 PHE A1338 TYR 0.012 0.001 TYR A 496 ARG 0.003 0.000 ARG A1063 *********************** 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 : 1.207 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: 0.2338 time to fit residues: 56.6487 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 : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11493 Z= 0.320 Angle : 0.639 8.622 15795 Z= 0.342 Chirality : 0.043 0.203 1745 Planarity : 0.005 0.041 1822 Dihedral : 19.526 127.163 2005 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.56 % Allowed : 7.91 % Favored : 90.52 % 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: 0.75 (0.24), residues: 1238 helix: 1.55 (0.20), residues: 683 sheet: -0.70 (0.47), residues: 112 loop : -0.79 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 431 HIS 0.005 0.001 HIS A1213 PHE 0.013 0.002 PHE A 754 TYR 0.034 0.002 TYR B 161 ARG 0.004 0.000 ARG A 797 *********************** 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 : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 ILE cc_start: 0.8592 (mp) cc_final: 0.8337 (mm) REVERT: B 334 MET cc_start: 0.6358 (mmt) cc_final: 0.6066 (mmm) REVERT: A 544 MET cc_start: 0.7763 (mmt) cc_final: 0.7529 (mmt) REVERT: A 553 LYS cc_start: 0.6257 (pptt) cc_final: 0.5889 (pptt) REVERT: A 1070 HIS cc_start: 0.6971 (t-90) cc_final: 0.6650 (t70) REVERT: A 1300 PHE cc_start: 0.6787 (m-80) cc_final: 0.5898 (m-80) outliers start: 17 outliers final: 12 residues processed: 157 average time/residue: 0.2193 time to fit residues: 50.8822 Evaluate side-chains 146 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 1.225 ------------------------------------------------------------------------------- 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 1132 THR Chi-restraints excluded: chain A residue 1327 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 93 optimal weight: 20.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- 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 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11493 Z= 0.289 Angle : 0.606 8.055 15795 Z= 0.323 Chirality : 0.042 0.156 1745 Planarity : 0.004 0.042 1822 Dihedral : 19.519 124.749 2005 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.67 % Allowed : 12.05 % Favored : 85.28 % 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: 0.76 (0.24), residues: 1238 helix: 1.56 (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 TRP 0.019 0.002 TRP A 431 HIS 0.005 0.001 HIS A1213 PHE 0.012 0.001 PHE A 754 TYR 0.022 0.002 TYR B 83 ARG 0.002 0.000 ARG A 827 *********************** 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 170 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.7746 (mmt) cc_final: 0.7527 (mmt) REVERT: A 553 LYS cc_start: 0.6247 (pptt) cc_final: 0.5924 (pptt) REVERT: A 1070 HIS cc_start: 0.7210 (t-90) cc_final: 0.6920 (t70) REVERT: A 1300 PHE cc_start: 0.6636 (m-80) cc_final: 0.5725 (m-80) outliers start: 29 outliers final: 21 residues processed: 155 average time/residue: 0.2358 time to fit residues: 53.7366 Evaluate side-chains 156 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 1.317 ------------------------------------------------------------------------------- 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 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 664 LEU 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 930 MET 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 1118 ILE Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11493 Z= 0.330 Angle : 0.625 8.150 15795 Z= 0.332 Chirality : 0.042 0.161 1745 Planarity : 0.004 0.044 1822 Dihedral : 19.521 123.298 2005 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.59 % Allowed : 12.70 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.59 (0.24), residues: 1238 helix: 1.44 (0.20), residues: 683 sheet: -0.49 (0.49), residues: 106 loop : -0.98 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 431 HIS 0.005 0.001 HIS A 652 PHE 0.019 0.002 PHE A1338 TYR 0.021 0.002 TYR B 83 ARG 0.007 0.000 ARG A 797 *********************** 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 177 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.7817 (mmt) cc_final: 0.7588 (mmt) REVERT: A 553 LYS cc_start: 0.6262 (pptt) cc_final: 0.5952 (pptt) REVERT: A 1070 HIS cc_start: 0.7394 (t-90) cc_final: 0.6990 (t-90) REVERT: A 1300 PHE cc_start: 0.6660 (m-80) cc_final: 0.5662 (m-80) outliers start: 39 outliers final: 29 residues processed: 164 average time/residue: 0.2313 time to fit residues: 55.6632 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 : 1.028 ------------------------------------------------------------------------------- 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 500 LEU Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 664 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 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 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 1131 GLU Chi-restraints excluded: chain A residue 1132 THR Chi-restraints excluded: chain A residue 1200 THR 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 103 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 85 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11493 Z= 0.277 Angle : 0.609 8.230 15795 Z= 0.321 Chirality : 0.041 0.173 1745 Planarity : 0.004 0.043 1822 Dihedral : 19.382 122.064 2005 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.40 % Allowed : 14.54 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.70 (0.24), residues: 1238 helix: 1.53 (0.20), residues: 683 sheet: -0.38 (0.49), residues: 106 loop : -0.97 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 431 HIS 0.004 0.001 HIS A 652 PHE 0.022 0.001 PHE A1338 TYR 0.023 0.002 TYR B 83 ARG 0.003 0.000 ARG A1250 *********************** 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 176 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.7797 (mmt) cc_final: 0.7582 (mmt) REVERT: A 553 LYS cc_start: 0.6261 (pptt) cc_final: 0.6018 (pptt) REVERT: A 1070 HIS cc_start: 0.7429 (t-90) cc_final: 0.7014 (t-90) REVERT: A 1250 ARG cc_start: 0.8503 (mmm160) cc_final: 0.8196 (mmm160) REVERT: A 1300 PHE cc_start: 0.6805 (m-80) cc_final: 0.5784 (m-80) outliers start: 37 outliers final: 28 residues processed: 164 average time/residue: 0.2439 time to fit residues: 58.6387 Evaluate side-chains 162 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 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 656 ILE Chi-restraints excluded: chain A residue 660 ASN 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 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 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 1210 ILE 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 41 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 123 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 660 ASN A 694 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11493 Z= 0.247 Angle : 0.594 8.216 15795 Z= 0.313 Chirality : 0.041 0.154 1745 Planarity : 0.004 0.042 1822 Dihedral : 19.294 120.961 2005 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.59 % Allowed : 14.90 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.84 (0.24), residues: 1238 helix: 1.65 (0.20), residues: 684 sheet: -0.31 (0.49), residues: 106 loop : -0.92 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 431 HIS 0.003 0.001 HIS A 652 PHE 0.023 0.001 PHE A1338 TYR 0.022 0.002 TYR B 83 ARG 0.002 0.000 ARG A1240 *********************** 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 178 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 GLN cc_start: 0.8020 (tt0) cc_final: 0.7327 (tt0) REVERT: B 180 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8796 (mp) REVERT: A 544 MET cc_start: 0.7792 (mmt) cc_final: 0.7571 (mmt) REVERT: A 553 LYS cc_start: 0.6264 (pptt) cc_final: 0.6039 (pptt) REVERT: A 1070 HIS cc_start: 0.7476 (t-90) cc_final: 0.7064 (t-90) REVERT: A 1250 ARG cc_start: 0.8487 (mmm160) cc_final: 0.8173 (mmm160) REVERT: A 1300 PHE cc_start: 0.6813 (m-80) cc_final: 0.5735 (m-80) outliers start: 39 outliers final: 31 residues processed: 169 average time/residue: 0.2262 time to fit residues: 55.8710 Evaluate side-chains 163 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 237 THR 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 512 THR Chi-restraints excluded: chain A residue 609 ILE 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 726 LEU Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 809 ILE 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 1074 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11493 Z= 0.198 Angle : 0.571 7.988 15795 Z= 0.299 Chirality : 0.040 0.150 1745 Planarity : 0.004 0.042 1822 Dihedral : 19.108 118.964 2005 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.40 % Allowed : 15.92 % 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 (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: 1.07 (0.25), residues: 1238 helix: 1.82 (0.20), residues: 684 sheet: -0.18 (0.49), residues: 106 loop : -0.79 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 431 HIS 0.003 0.001 HIS A 939 PHE 0.021 0.001 PHE A1338 TYR 0.047 0.002 TYR B 161 ARG 0.003 0.000 ARG A1240 *********************** 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 182 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 GLN cc_start: 0.8009 (tt0) cc_final: 0.7457 (tt0) REVERT: A 544 MET cc_start: 0.7776 (mmt) cc_final: 0.7560 (mmt) REVERT: A 553 LYS cc_start: 0.6283 (pptt) cc_final: 0.6083 (pptt) REVERT: A 673 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7810 (pp) REVERT: A 1070 HIS cc_start: 0.7471 (t-90) cc_final: 0.7055 (t-90) REVERT: A 1250 ARG cc_start: 0.8454 (mmm160) cc_final: 0.8159 (mmm160) REVERT: A 1300 PHE cc_start: 0.6809 (m-80) cc_final: 0.5700 (m-80) outliers start: 37 outliers final: 31 residues processed: 173 average time/residue: 0.2254 time to fit residues: 57.3786 Evaluate side-chains 169 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 1.382 ------------------------------------------------------------------------------- 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 323 PHE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain A residue 500 LEU 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 726 LEU 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 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 1074 ASP 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 1340 VAL 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 49 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 78 optimal weight: 0.0060 chunk 84 optimal weight: 8.9990 chunk 60 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 96 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 overall best weight: 2.6004 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11493 Z= 0.199 Angle : 0.579 8.679 15795 Z= 0.302 Chirality : 0.040 0.173 1745 Planarity : 0.004 0.042 1822 Dihedral : 19.043 117.336 2005 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.31 % Allowed : 16.65 % Favored : 80.04 % 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: 1.10 (0.25), residues: 1238 helix: 1.80 (0.20), residues: 686 sheet: -0.09 (0.49), residues: 106 loop : -0.73 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 431 HIS 0.003 0.001 HIS A 939 PHE 0.024 0.001 PHE A 936 TYR 0.046 0.002 TYR B 161 ARG 0.004 0.000 ARG A1220 *********************** 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 180 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.7774 (mmt) cc_final: 0.7561 (mmt) REVERT: A 553 LYS cc_start: 0.6282 (pptt) cc_final: 0.6082 (pptt) REVERT: A 673 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7718 (pp) REVERT: A 824 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8003 (mp) REVERT: A 1070 HIS cc_start: 0.7460 (t-90) cc_final: 0.7046 (t-90) REVERT: A 1249 ILE cc_start: 0.8035 (mt) cc_final: 0.7384 (mp) REVERT: A 1250 ARG cc_start: 0.8436 (mmm160) cc_final: 0.8185 (mmm160) REVERT: A 1300 PHE cc_start: 0.6805 (m-80) cc_final: 0.5683 (m-80) outliers start: 36 outliers final: 30 residues processed: 169 average time/residue: 0.2419 time to fit residues: 59.1226 Evaluate side-chains 174 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 1.319 ------------------------------------------------------------------------------- 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 323 PHE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain A residue 500 LEU 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 726 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 801 CYS 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 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 1340 VAL 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 118 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 114 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 121 optimal weight: 50.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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** A 953 HIS ** A1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1347 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11493 Z= 0.201 Angle : 0.574 9.446 15795 Z= 0.298 Chirality : 0.040 0.164 1745 Planarity : 0.004 0.045 1822 Dihedral : 18.986 114.666 2005 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.50 % Allowed : 16.47 % Favored : 80.04 % 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: 1.09 (0.24), residues: 1238 helix: 1.77 (0.20), residues: 687 sheet: -0.06 (0.50), residues: 106 loop : -0.72 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 431 HIS 0.003 0.001 HIS A 939 PHE 0.026 0.001 PHE A 936 TYR 0.023 0.002 TYR B 83 ARG 0.002 0.000 ARG A1240 *********************** 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 185 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 544 MET cc_start: 0.7774 (mmt) cc_final: 0.7557 (mmt) REVERT: A 553 LYS cc_start: 0.6282 (pptt) cc_final: 0.6081 (pptt) REVERT: A 673 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7705 (pp) REVERT: A 824 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8000 (mp) REVERT: A 1070 HIS cc_start: 0.7460 (t-90) cc_final: 0.7060 (t-90) REVERT: A 1223 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7503 (mp0) REVERT: A 1300 PHE cc_start: 0.6903 (m-80) cc_final: 0.5922 (m-80) outliers start: 38 outliers final: 31 residues processed: 173 average time/residue: 0.2380 time to fit residues: 60.3722 Evaluate side-chains 172 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 1.276 ------------------------------------------------------------------------------- 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 323 PHE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 500 LEU 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 726 LEU Chi-restraints excluded: chain A residue 795 SER 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 930 MET 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 1223 GLU Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1340 VAL 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 74 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 chunk 62 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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** ** A1129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11493 Z= 0.308 Angle : 0.639 9.941 15795 Z= 0.330 Chirality : 0.042 0.184 1745 Planarity : 0.004 0.043 1822 Dihedral : 19.124 113.529 2005 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.31 % Allowed : 17.11 % Favored : 79.58 % 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: 0.84 (0.24), residues: 1238 helix: 1.62 (0.20), residues: 684 sheet: -0.24 (0.49), residues: 106 loop : -0.89 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 431 HIS 0.004 0.001 HIS A 652 PHE 0.027 0.002 PHE A 936 TYR 0.024 0.002 TYR A1348 ARG 0.004 0.000 ARG A1250 ********************** 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 174 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 GLN cc_start: 0.8028 (tt0) cc_final: 0.7340 (tt0) REVERT: A 544 MET cc_start: 0.7806 (mmt) cc_final: 0.7568 (mmt) REVERT: A 553 LYS cc_start: 0.6353 (pptt) cc_final: 0.6127 (pptt) REVERT: A 673 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7749 (pp) REVERT: A 824 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8050 (mp) REVERT: A 1189 ASP cc_start: 0.7341 (p0) cc_final: 0.6994 (p0) REVERT: A 1223 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: A 1250 ARG cc_start: 0.8304 (mmm160) cc_final: 0.7768 (tpp80) outliers start: 36 outliers final: 29 residues processed: 165 average time/residue: 0.2669 time to fit residues: 63.9485 Evaluate side-chains 166 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 1.379 ------------------------------------------------------------------------------- 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 323 PHE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 500 LEU 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 726 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 801 CYS Chi-restraints excluded: chain A residue 824 LEU 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 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 1223 GLU Chi-restraints excluded: chain A residue 1327 LEU Chi-restraints excluded: chain A residue 1340 VAL 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 31 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 89 optimal weight: 30.0000 chunk 5 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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 939 HIS ** 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 = 0.168859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.126511 restraints weight = 16592.584| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 3.06 r_work: 0.3429 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11493 Z= 0.289 Angle : 0.626 9.044 15795 Z= 0.325 Chirality : 0.042 0.195 1745 Planarity : 0.004 0.044 1822 Dihedral : 19.091 112.032 2005 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.22 % Allowed : 17.48 % Favored : 79.30 % 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 (0.24), residues: 1238 helix: 1.59 (0.20), residues: 684 sheet: -0.33 (0.48), residues: 110 loop : -0.89 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 431 HIS 0.004 0.001 HIS A 652 PHE 0.033 0.002 PHE A 936 TYR 0.024 0.002 TYR A1348 ARG 0.002 0.000 ARG A1252 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2155.33 seconds wall clock time: 40 minutes 48.69 seconds (2448.69 seconds total)