Starting phenix.real_space_refine on Wed May 14 03:25:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z5r_39779/05_2025/8z5r_39779.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z5r_39779/05_2025/8z5r_39779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z5r_39779/05_2025/8z5r_39779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z5r_39779/05_2025/8z5r_39779.map" model { file = "/net/cci-nas-00/data/ceres_data/8z5r_39779/05_2025/8z5r_39779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z5r_39779/05_2025/8z5r_39779.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.050 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 11 5.49 5 S 55 5.16 5 C 7151 2.51 5 N 1909 2.21 5 O 2147 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11273 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7812 Classifications: {'peptide': 993} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 43, 'TRANS': 949} Chain breaks: 2 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TPO:plan-1': 2, 'TYR:plan': 1, 'ASP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "C" Number of atoms: 2788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2788 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 264 Unresolved non-hydrogen angles: 322 Unresolved non-hydrogen dihedrals: 221 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 189 Chain: "D" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 642 Classifications: {'peptide': 97} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 28} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 5, 'GLU:plan': 9, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.97, per 1000 atoms: 0.71 Number of scatterers: 11273 At special positions: 0 Unit cell: (119.355, 147.825, 109.5, 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 55 16.00 P 11 15.00 O 2147 8.00 N 1909 7.00 C 7151 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.4 seconds 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2746 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 13 sheets defined 57.9% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 5 through 22 Processing helix chain 'A' and resid 23 through 26 Processing helix chain 'A' and resid 44 through 64 removed outlier: 3.617A pdb=" N LEU A 52 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA A 53 " --> pdb=" O TYR A 49 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASN A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 94 Processing helix chain 'A' and resid 95 through 104 removed outlier: 3.692A pdb=" N LYS A 103 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYR A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 152 removed outlier: 3.908A pdb=" N THR A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.767A pdb=" N LYS A 177 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR A 178 " --> pdb=" O ALA A 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 174 through 178' Processing helix chain 'A' and resid 198 through 212 removed outlier: 3.549A pdb=" N VAL A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.938A pdb=" N LYS A 221 " --> pdb=" O PHE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 227 removed outlier: 4.083A pdb=" N VAL A 227 " --> pdb=" O PRO A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 246 removed outlier: 4.328A pdb=" N VAL A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 262 removed outlier: 3.570A pdb=" N LEU A 260 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 287 Processing helix chain 'A' and resid 329 through 342 removed outlier: 3.599A pdb=" N SER A 342 " --> pdb=" O ASP A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 359 removed outlier: 3.810A pdb=" N ALA A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 380 through 386 Processing helix chain 'A' and resid 400 through 415 Processing helix chain 'A' and resid 419 through 424 removed outlier: 4.042A pdb=" N ILE A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP A 424 " --> pdb=" O PRO A 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 419 through 424' Processing helix chain 'A' and resid 428 through 433 removed outlier: 4.552A pdb=" N THR A 432 " --> pdb=" O ARG A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.845A pdb=" N LEU A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 522 through 526 removed outlier: 3.591A pdb=" N ILE A 525 " --> pdb=" O PRO A 522 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP A 526 " --> pdb=" O GLN A 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 522 through 526' Processing helix chain 'A' and resid 530 through 534 removed outlier: 4.045A pdb=" N ALA A 533 " --> pdb=" O PHE A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 553 removed outlier: 3.548A pdb=" N ARG A 553 " --> pdb=" O TYR A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.940A pdb=" N MET A 570 " --> pdb=" O SER A 567 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 571 " --> pdb=" O HIS A 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 567 through 571' Processing helix chain 'A' and resid 579 through 591 Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.748A pdb=" N THR A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 620 Processing helix chain 'A' and resid 763 through 773 Processing helix chain 'A' and resid 775 through 790 Processing helix chain 'A' and resid 805 through 821 removed outlier: 3.534A pdb=" N GLU A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 820 " --> pdb=" O LYS A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 834 Processing helix chain 'A' and resid 839 through 849 Processing helix chain 'A' and resid 872 through 885 Processing helix chain 'A' and resid 888 through 908 removed outlier: 3.784A pdb=" N ILE A 892 " --> pdb=" O MET A 888 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG A 906 " --> pdb=" O ALA A 902 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 907 " --> pdb=" O MET A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 936 Processing helix chain 'A' and resid 938 through 949 Processing helix chain 'A' and resid 950 through 964 Processing helix chain 'A' and resid 1054 through 1064 Processing helix chain 'A' and resid 1070 through 1082 Processing helix chain 'A' and resid 1095 through 1100 removed outlier: 4.120A pdb=" N GLU A1099 " --> pdb=" O SER A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1116 removed outlier: 3.717A pdb=" N SER A1108 " --> pdb=" O GLU A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1141 Processing helix chain 'A' and resid 1151 through 1170 Processing helix chain 'A' and resid 1185 through 1191 Processing helix chain 'A' and resid 1198 through 1214 removed outlier: 3.714A pdb=" N TYR A1202 " --> pdb=" O GLY A1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 20 Processing helix chain 'C' and resid 60 through 81 removed outlier: 3.581A pdb=" N VAL C 64 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 120 Processing helix chain 'C' and resid 123 through 144 removed outlier: 3.504A pdb=" N LEU C 144 " --> pdb=" O THR C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 154 No H-bonds generated for 'chain 'C' and resid 152 through 154' Processing helix chain 'C' and resid 192 through 199 removed outlier: 3.747A pdb=" N ILE C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 226 Processing helix chain 'C' and resid 234 through 245 Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 258 through 269 removed outlier: 3.665A pdb=" N LYS C 262 " --> pdb=" O SER C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 284 Processing helix chain 'C' and resid 300 through 320 Processing helix chain 'C' and resid 321 through 325 removed outlier: 3.511A pdb=" N VAL C 325 " --> pdb=" O TYR C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 336 Processing helix chain 'C' and resid 340 through 355 Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 377 through 381 Processing helix chain 'D' and resid 6 through 21 removed outlier: 3.921A pdb=" N ASP D 21 " --> pdb=" O PHE D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 41 Processing helix chain 'D' and resid 45 through 57 Processing helix chain 'D' and resid 65 through 74 Processing helix chain 'D' and resid 79 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 43 Processing sheet with id=AA2, first strand: chain 'A' and resid 288 through 289 removed outlier: 3.996A pdb=" N GLY A 292 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 360 through 361 removed outlier: 3.541A pdb=" N ILE A 360 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 374 Processing sheet with id=AA5, first strand: chain 'A' and resid 463 through 464 removed outlier: 4.018A pdb=" N GLU A 463 " --> pdb=" O ILE A 444 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 463 through 464 removed outlier: 4.018A pdb=" N GLU A 463 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 442 " --> pdb=" O GLN A 600 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 471 through 474 removed outlier: 5.812A pdb=" N ARG A 472 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 488 through 489 Processing sheet with id=AA9, first strand: chain 'A' and resid 853 through 855 removed outlier: 6.314A pdb=" N HIS A 853 " --> pdb=" O LEU A 918 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 1092 through 1093 removed outlier: 3.637A pdb=" N LEU A1092 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A1085 " --> pdb=" O LEU A1092 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A1149 " --> pdb=" O GLY A1084 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 25 through 28 removed outlier: 6.726A pdb=" N VAL C 34 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ARG C 28 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER C 32 " --> pdb=" O ARG C 28 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE C 51 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE C 100 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP C 92 " --> pdb=" O VAL C 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 146 through 147 removed outlier: 4.147A pdb=" N VAL C 147 " --> pdb=" O CYS C 173 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N CYS C 173 " --> pdb=" O VAL C 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 156 through 158 removed outlier: 3.786A pdb=" N LEU C 157 " --> pdb=" O LYS C 165 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS C 165 " --> pdb=" O LEU C 157 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 573 hydrogen bonds defined for protein. 1656 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.66 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3683 1.34 - 1.46: 1617 1.46 - 1.58: 6079 1.58 - 1.70: 33 1.70 - 1.81: 89 Bond restraints: 11501 Sorted by residual: bond pdb=" OG1 TPO A1174 " pdb=" P TPO A1174 " ideal model delta sigma weight residual 1.717 1.610 0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" O1P SEP A 101 " pdb=" P SEP A 101 " ideal model delta sigma weight residual 1.610 1.504 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" O2P SEP A 101 " pdb=" P SEP A 101 " ideal model delta sigma weight residual 1.610 1.504 0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" O3P SEP A 101 " pdb=" P SEP A 101 " ideal model delta sigma weight residual 1.610 1.505 0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" CA SEP A 101 " pdb=" C SEP A 101 " ideal model delta sigma weight residual 1.525 1.435 0.090 2.10e-02 2.27e+03 1.83e+01 ... (remaining 11496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 15482 2.38 - 4.75: 132 4.75 - 7.13: 25 7.13 - 9.50: 9 9.50 - 11.88: 1 Bond angle restraints: 15649 Sorted by residual: angle pdb=" O GLU A 100 " pdb=" C GLU A 100 " pdb=" N SEP A 101 " ideal model delta sigma weight residual 123.00 115.95 7.05 1.60e+00 3.91e-01 1.94e+01 angle pdb=" N VAL A 262 " pdb=" CA VAL A 262 " pdb=" C VAL A 262 " ideal model delta sigma weight residual 112.96 108.98 3.98 1.00e+00 1.00e+00 1.58e+01 angle pdb=" CB TPO A1174 " pdb=" OG1 TPO A1174 " pdb=" P TPO A1174 " ideal model delta sigma weight residual 119.31 107.43 11.88 3.00e+00 1.11e-01 1.57e+01 angle pdb=" CA GLU A 306 " pdb=" CB GLU A 306 " pdb=" CG GLU A 306 " ideal model delta sigma weight residual 114.10 121.96 -7.86 2.00e+00 2.50e-01 1.54e+01 angle pdb=" C PRO A 266 " pdb=" N ALA A 267 " pdb=" CA ALA A 267 " ideal model delta sigma weight residual 121.54 128.91 -7.37 1.91e+00 2.74e-01 1.49e+01 ... (remaining 15644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5926 17.97 - 35.93: 707 35.93 - 53.90: 224 53.90 - 71.86: 63 71.86 - 89.83: 18 Dihedral angle restraints: 6938 sinusoidal: 2680 harmonic: 4258 Sorted by residual: dihedral pdb=" CA PRO A 859 " pdb=" C PRO A 859 " pdb=" N PRO A 860 " pdb=" CA PRO A 860 " ideal model delta harmonic sigma weight residual 180.00 149.79 30.21 0 5.00e+00 4.00e-02 3.65e+01 dihedral pdb=" CA LEU A 246 " pdb=" C LEU A 246 " pdb=" N PRO A 247 " pdb=" CA PRO A 247 " ideal model delta harmonic sigma weight residual 180.00 154.29 25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA MET C 200 " pdb=" C MET C 200 " pdb=" N ASN C 201 " pdb=" CA ASN C 201 " ideal model delta harmonic sigma weight residual 180.00 158.49 21.51 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 6935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1355 0.039 - 0.079: 334 0.079 - 0.118: 99 0.118 - 0.157: 7 0.157 - 0.197: 3 Chirality restraints: 1798 Sorted by residual: chirality pdb=" CB ILE C 138 " pdb=" CA ILE C 138 " pdb=" CG1 ILE C 138 " pdb=" CG2 ILE C 138 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CA GLU A 306 " pdb=" N GLU A 306 " pdb=" C GLU A 306 " pdb=" CB GLU A 306 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" CB ILE A1142 " pdb=" CA ILE A1142 " pdb=" CG1 ILE A1142 " pdb=" CG2 ILE A1142 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.63e-01 ... (remaining 1795 not shown) Planarity restraints: 1999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 313 " 0.014 2.00e-02 2.50e+03 2.05e-02 8.39e+00 pdb=" CG TYR A 313 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR A 313 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A 313 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR A 313 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 313 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 313 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 313 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 227 " 0.046 5.00e-02 4.00e+02 6.98e-02 7.79e+00 pdb=" N PRO C 228 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO C 228 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 228 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A1067 " -0.040 5.00e-02 4.00e+02 6.12e-02 5.99e+00 pdb=" N PRO A1068 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A1068 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A1068 " -0.034 5.00e-02 4.00e+02 ... (remaining 1996 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1984 2.77 - 3.30: 10988 3.30 - 3.83: 18364 3.83 - 4.37: 19460 4.37 - 4.90: 34843 Nonbonded interactions: 85639 Sorted by model distance: nonbonded pdb=" O VAL A 504 " pdb=" OG SER A 508 " model vdw 2.234 3.040 nonbonded pdb=" O VAL C 378 " pdb=" OG SER C 381 " model vdw 2.252 3.040 nonbonded pdb=" O GLY A 506 " pdb=" OH TYR A 511 " model vdw 2.277 3.040 nonbonded pdb=" OH TYR A 14 " pdb=" OG SER A 411 " model vdw 2.285 3.040 nonbonded pdb=" O SER A 226 " pdb=" OG SER A 226 " model vdw 2.294 3.040 ... (remaining 85634 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 28.160 Find NCS groups from input model: 0.140 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 11501 Z= 0.168 Angle : 0.590 11.880 15649 Z= 0.294 Chirality : 0.038 0.197 1798 Planarity : 0.004 0.070 1999 Dihedral : 18.190 89.829 4192 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.60 % Allowed : 26.27 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: 1.59 (0.23), residues: 1411 helix: 2.63 (0.20), residues: 723 sheet: 1.65 (0.78), residues: 57 loop : -0.96 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 254 HIS 0.002 0.000 HIS C 285 PHE 0.016 0.001 PHE C 287 TYR 0.050 0.001 TYR A 313 ARG 0.003 0.000 ARG A 10 Details of bonding type rmsd hydrogen bonds : bond 0.13209 ( 572) hydrogen bonds : angle 5.14554 ( 1656) covalent geometry : bond 0.00329 (11501) covalent geometry : angle 0.59041 (15649) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 160 time to evaluate : 1.384 Fit side-chains REVERT: A 483 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.7145 (t80) outliers start: 7 outliers final: 3 residues processed: 162 average time/residue: 0.1923 time to fit residues: 48.6516 Evaluate side-chains 155 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 151 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 TYR Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 203 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 7.9990 chunk 109 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 43 optimal weight: 0.2980 chunk 69 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN A 895 GLN ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN C 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.178991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.131900 restraints weight = 19681.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.132551 restraints weight = 12536.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.132819 restraints weight = 9265.492| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11501 Z= 0.144 Angle : 0.582 10.002 15649 Z= 0.291 Chirality : 0.040 0.204 1798 Planarity : 0.005 0.062 1999 Dihedral : 6.831 88.101 1642 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.38 % Favored : 93.55 % Rotamer: Outliers : 3.00 % Allowed : 24.38 % Favored : 72.62 % 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: 1.45 (0.23), residues: 1411 helix: 2.42 (0.19), residues: 748 sheet: 1.07 (0.70), residues: 62 loop : -1.00 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 328 HIS 0.003 0.001 HIS A 822 PHE 0.018 0.001 PHE C 100 TYR 0.019 0.001 TYR A 171 ARG 0.004 0.000 ARG A 45 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 572) hydrogen bonds : angle 3.84002 ( 1656) covalent geometry : bond 0.00331 (11501) covalent geometry : angle 0.58220 (15649) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 1.160 Fit side-chains revert: symmetry clash REVERT: A 491 ARG cc_start: 0.3411 (ttt180) cc_final: 0.2850 (ttt180) REVERT: A 828 TYR cc_start: 0.6406 (OUTLIER) cc_final: 0.5292 (t80) REVERT: A 916 PHE cc_start: 0.7254 (t80) cc_final: 0.6885 (t80) REVERT: A 1060 LEU cc_start: 0.8336 (mt) cc_final: 0.7803 (tp) REVERT: C 150 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7024 (t0) REVERT: C 207 TYR cc_start: 0.4307 (m-80) cc_final: 0.4069 (m-80) outliers start: 35 outliers final: 18 residues processed: 184 average time/residue: 0.1962 time to fit residues: 54.0867 Evaluate side-chains 162 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 828 TYR Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1159 ASN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 354 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 7 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 128 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 34 optimal weight: 0.4980 chunk 13 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN A 795 ASN ** C 142 HIS ** 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 = 0.4245 r_free = 0.4245 target = 0.178575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.133470 restraints weight = 19494.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.135014 restraints weight = 10962.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.134226 restraints weight = 7534.226| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11501 Z= 0.121 Angle : 0.553 11.507 15649 Z= 0.274 Chirality : 0.039 0.250 1798 Planarity : 0.005 0.066 1999 Dihedral : 6.650 86.493 1636 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.02 % Favored : 93.91 % Rotamer: Outliers : 3.86 % Allowed : 24.21 % Favored : 71.93 % 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: 1.36 (0.23), residues: 1411 helix: 2.41 (0.19), residues: 746 sheet: 0.77 (0.70), residues: 62 loop : -1.10 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 328 HIS 0.002 0.001 HIS A1156 PHE 0.013 0.001 PHE C 100 TYR 0.013 0.001 TYR A 171 ARG 0.006 0.000 ARG A 10 Details of bonding type rmsd hydrogen bonds : bond 0.03224 ( 572) hydrogen bonds : angle 3.65003 ( 1656) covalent geometry : bond 0.00275 (11501) covalent geometry : angle 0.55325 (15649) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 152 time to evaluate : 1.153 Fit side-chains revert: symmetry clash REVERT: A 491 ARG cc_start: 0.3481 (ttt180) cc_final: 0.2888 (ttt180) REVERT: A 828 TYR cc_start: 0.6754 (OUTLIER) cc_final: 0.5754 (t80) REVERT: A 916 PHE cc_start: 0.7380 (t80) cc_final: 0.7005 (t80) REVERT: A 954 MET cc_start: 0.7920 (tpp) cc_final: 0.7243 (ttp) REVERT: C 46 TYR cc_start: 0.6041 (OUTLIER) cc_final: 0.5446 (m-10) REVERT: C 207 TYR cc_start: 0.4395 (m-80) cc_final: 0.4068 (m-80) REVERT: C 289 GLN cc_start: 0.4824 (pp30) cc_final: 0.3841 (pt0) outliers start: 45 outliers final: 24 residues processed: 185 average time/residue: 0.1988 time to fit residues: 55.3610 Evaluate side-chains 171 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 828 TYR Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1144 SER Chi-restraints excluded: chain A residue 1159 ASN Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 354 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 51 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 129 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 0.0980 chunk 7 optimal weight: 0.3980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 HIS ** C 142 HIS ** 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 = 0.4239 r_free = 0.4239 target = 0.178154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.131514 restraints weight = 19403.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.132987 restraints weight = 11411.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.134134 restraints weight = 7480.420| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11501 Z= 0.117 Angle : 0.565 10.851 15649 Z= 0.278 Chirality : 0.039 0.245 1798 Planarity : 0.005 0.067 1999 Dihedral : 6.553 86.580 1636 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.38 % Favored : 93.55 % Rotamer: Outliers : 4.21 % Allowed : 23.95 % Favored : 71.85 % 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: 1.25 (0.23), residues: 1411 helix: 2.36 (0.19), residues: 747 sheet: 0.49 (0.68), residues: 62 loop : -1.19 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 328 HIS 0.002 0.000 HIS A1156 PHE 0.012 0.001 PHE C 100 TYR 0.013 0.001 TYR A 171 ARG 0.006 0.000 ARG A 10 Details of bonding type rmsd hydrogen bonds : bond 0.03142 ( 572) hydrogen bonds : angle 3.57038 ( 1656) covalent geometry : bond 0.00266 (11501) covalent geometry : angle 0.56476 (15649) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 153 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: A 30 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8247 (t) REVERT: A 491 ARG cc_start: 0.3474 (ttt180) cc_final: 0.2861 (ttt180) REVERT: A 828 TYR cc_start: 0.6962 (OUTLIER) cc_final: 0.6069 (t80) REVERT: A 916 PHE cc_start: 0.7500 (t80) cc_final: 0.7136 (t80) REVERT: A 954 MET cc_start: 0.7870 (tpp) cc_final: 0.7240 (ttp) REVERT: C 46 TYR cc_start: 0.6117 (OUTLIER) cc_final: 0.5443 (m-10) REVERT: C 150 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7056 (t0) REVERT: C 207 TYR cc_start: 0.4512 (m-80) cc_final: 0.4200 (m-80) REVERT: C 238 MET cc_start: 0.6875 (OUTLIER) cc_final: 0.6462 (ptp) outliers start: 49 outliers final: 29 residues processed: 190 average time/residue: 0.2137 time to fit residues: 61.8616 Evaluate side-chains 178 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 828 TYR Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1159 ASN Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 277 TYR Chi-restraints excluded: chain C residue 354 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 41 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 109 optimal weight: 0.4980 chunk 108 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 47 optimal weight: 0.0670 chunk 121 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.178866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.130988 restraints weight = 19253.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.133770 restraints weight = 10857.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.134283 restraints weight = 7803.779| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11501 Z= 0.105 Angle : 0.547 10.477 15649 Z= 0.270 Chirality : 0.039 0.230 1798 Planarity : 0.005 0.074 1999 Dihedral : 6.410 87.358 1636 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.17 % Favored : 93.76 % Rotamer: Outliers : 3.61 % Allowed : 24.98 % Favored : 71.42 % 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: 1.26 (0.23), residues: 1411 helix: 2.37 (0.19), residues: 748 sheet: 0.30 (0.67), residues: 62 loop : -1.17 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 328 HIS 0.002 0.000 HIS A 960 PHE 0.010 0.001 PHE A 524 TYR 0.013 0.001 TYR A 313 ARG 0.006 0.000 ARG A 10 Details of bonding type rmsd hydrogen bonds : bond 0.02879 ( 572) hydrogen bonds : angle 3.50194 ( 1656) covalent geometry : bond 0.00235 (11501) covalent geometry : angle 0.54660 (15649) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 1.163 Fit side-chains revert: symmetry clash REVERT: A 30 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8248 (t) REVERT: A 491 ARG cc_start: 0.3406 (ttt180) cc_final: 0.2763 (ttt180) REVERT: A 828 TYR cc_start: 0.7044 (OUTLIER) cc_final: 0.6160 (t80) REVERT: A 916 PHE cc_start: 0.7508 (t80) cc_final: 0.7157 (t80) REVERT: A 920 ILE cc_start: 0.7204 (OUTLIER) cc_final: 0.6937 (mp) REVERT: A 954 MET cc_start: 0.7848 (tpp) cc_final: 0.7206 (ttp) REVERT: C 46 TYR cc_start: 0.6122 (OUTLIER) cc_final: 0.5441 (m-10) REVERT: C 107 MET cc_start: 0.7449 (mtp) cc_final: 0.7155 (mtp) REVERT: C 207 TYR cc_start: 0.4566 (m-80) cc_final: 0.4231 (m-80) REVERT: C 238 MET cc_start: 0.6932 (OUTLIER) cc_final: 0.6459 (ptp) outliers start: 42 outliers final: 29 residues processed: 179 average time/residue: 0.1922 time to fit residues: 52.3799 Evaluate side-chains 176 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 CYS Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 828 TYR Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1159 ASN Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 263 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 134 optimal weight: 0.0470 chunk 37 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 136 optimal weight: 0.1980 chunk 56 optimal weight: 0.0980 chunk 124 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.179769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.133842 restraints weight = 19449.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.134783 restraints weight = 12605.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.135185 restraints weight = 7748.392| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11501 Z= 0.097 Angle : 0.547 9.858 15649 Z= 0.267 Chirality : 0.039 0.203 1798 Planarity : 0.005 0.072 1999 Dihedral : 6.197 88.546 1636 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.17 % Favored : 93.76 % Rotamer: Outliers : 3.52 % Allowed : 25.49 % Favored : 70.99 % 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: 1.29 (0.23), residues: 1411 helix: 2.41 (0.19), residues: 748 sheet: 0.33 (0.68), residues: 62 loop : -1.18 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 254 HIS 0.002 0.000 HIS A 822 PHE 0.010 0.001 PHE A 524 TYR 0.015 0.001 TYR A 313 ARG 0.008 0.000 ARG A 598 Details of bonding type rmsd hydrogen bonds : bond 0.02670 ( 572) hydrogen bonds : angle 3.42259 ( 1656) covalent geometry : bond 0.00213 (11501) covalent geometry : angle 0.54682 (15649) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 1.172 Fit side-chains revert: symmetry clash REVERT: A 30 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8243 (t) REVERT: A 395 MET cc_start: 0.6302 (mtt) cc_final: 0.5984 (mtt) REVERT: A 491 ARG cc_start: 0.3367 (ttt180) cc_final: 0.2596 (ttt180) REVERT: A 828 TYR cc_start: 0.7024 (OUTLIER) cc_final: 0.6076 (t80) REVERT: A 916 PHE cc_start: 0.7515 (t80) cc_final: 0.7137 (t80) REVERT: A 954 MET cc_start: 0.7787 (tpp) cc_final: 0.7192 (ttp) REVERT: C 46 TYR cc_start: 0.6142 (OUTLIER) cc_final: 0.5467 (m-10) REVERT: C 107 MET cc_start: 0.7500 (mtp) cc_final: 0.7225 (mtp) REVERT: C 207 TYR cc_start: 0.4497 (m-80) cc_final: 0.4172 (m-80) REVERT: C 238 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6408 (ptp) REVERT: C 289 GLN cc_start: 0.4749 (pp30) cc_final: 0.3819 (pt0) outliers start: 41 outliers final: 25 residues processed: 182 average time/residue: 0.1976 time to fit residues: 55.0630 Evaluate side-chains 171 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 CYS Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 828 TYR Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 277 TYR Chi-restraints excluded: chain C residue 318 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 112 optimal weight: 0.5980 chunk 118 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 144 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.179468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.131575 restraints weight = 19936.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.133528 restraints weight = 11523.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.134728 restraints weight = 7107.957| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11501 Z= 0.139 Angle : 0.591 10.280 15649 Z= 0.292 Chirality : 0.040 0.190 1798 Planarity : 0.005 0.078 1999 Dihedral : 6.350 89.538 1636 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.80 % Favored : 93.13 % Rotamer: Outliers : 3.86 % Allowed : 25.32 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: 1.06 (0.23), residues: 1411 helix: 2.23 (0.19), residues: 749 sheet: 0.11 (0.66), residues: 62 loop : -1.30 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 328 HIS 0.002 0.001 HIS A1156 PHE 0.011 0.001 PHE A 524 TYR 0.016 0.001 TYR A 313 ARG 0.006 0.000 ARG A 10 Details of bonding type rmsd hydrogen bonds : bond 0.03451 ( 572) hydrogen bonds : angle 3.60907 ( 1656) covalent geometry : bond 0.00324 (11501) covalent geometry : angle 0.59089 (15649) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 141 time to evaluate : 1.360 Fit side-chains revert: symmetry clash REVERT: A 30 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8232 (t) REVERT: A 491 ARG cc_start: 0.3517 (ttt180) cc_final: 0.2753 (ttt180) REVERT: A 828 TYR cc_start: 0.6688 (OUTLIER) cc_final: 0.6029 (t80) REVERT: A 916 PHE cc_start: 0.7553 (t80) cc_final: 0.7182 (t80) REVERT: A 954 MET cc_start: 0.7854 (tpp) cc_final: 0.7207 (ttp) REVERT: A 1077 LYS cc_start: 0.8417 (mmmt) cc_final: 0.8195 (mptt) REVERT: A 1152 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7310 (tm-30) REVERT: C 46 TYR cc_start: 0.6228 (OUTLIER) cc_final: 0.5424 (m-10) REVERT: C 107 MET cc_start: 0.7724 (mtp) cc_final: 0.7507 (mtp) REVERT: C 150 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.7182 (t0) REVERT: C 207 TYR cc_start: 0.4678 (m-80) cc_final: 0.4324 (m-80) REVERT: C 238 MET cc_start: 0.6796 (OUTLIER) cc_final: 0.6442 (ptp) outliers start: 45 outliers final: 31 residues processed: 176 average time/residue: 0.2033 time to fit residues: 53.8276 Evaluate side-chains 174 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 CYS Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 828 TYR Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1152 GLU Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1159 ASN Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 238 MET Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 354 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 84 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN C 145 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.176475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.127189 restraints weight = 19764.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.128714 restraints weight = 13898.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.129472 restraints weight = 9111.590| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11501 Z= 0.184 Angle : 0.641 11.468 15649 Z= 0.320 Chirality : 0.042 0.190 1798 Planarity : 0.005 0.088 1999 Dihedral : 6.771 85.030 1636 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.87 % Favored : 93.05 % Rotamer: Outliers : 3.95 % Allowed : 26.18 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: 0.71 (0.23), residues: 1411 helix: 2.00 (0.19), residues: 748 sheet: -0.44 (0.63), residues: 62 loop : -1.50 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 358 HIS 0.004 0.001 HIS A 960 PHE 0.014 0.002 PHE A 218 TYR 0.020 0.002 TYR A 313 ARG 0.007 0.001 ARG A 10 Details of bonding type rmsd hydrogen bonds : bond 0.04194 ( 572) hydrogen bonds : angle 3.85844 ( 1656) covalent geometry : bond 0.00438 (11501) covalent geometry : angle 0.64106 (15649) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 142 time to evaluate : 1.329 Fit side-chains revert: symmetry clash REVERT: A 30 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8389 (t) REVERT: A 491 ARG cc_start: 0.3568 (ttt180) cc_final: 0.2614 (ttt180) REVERT: A 828 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.6741 (t80) REVERT: A 916 PHE cc_start: 0.7653 (t80) cc_final: 0.7345 (t80) REVERT: A 917 ARG cc_start: 0.8501 (ptp-110) cc_final: 0.8181 (ptm160) REVERT: A 954 MET cc_start: 0.7927 (tpp) cc_final: 0.7286 (ttp) REVERT: A 965 LYS cc_start: 0.7505 (mmtt) cc_final: 0.6769 (mtpp) REVERT: A 1152 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7319 (tm-30) REVERT: C 46 TYR cc_start: 0.6341 (OUTLIER) cc_final: 0.5589 (m-10) REVERT: C 150 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7453 (t0) REVERT: C 289 GLN cc_start: 0.5322 (pp30) cc_final: 0.4326 (pt0) outliers start: 46 outliers final: 35 residues processed: 180 average time/residue: 0.2039 time to fit residues: 55.2016 Evaluate side-chains 178 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 CYS Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 828 TYR Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1152 GLU Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1159 ASN Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 354 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 88 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.177833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.128048 restraints weight = 19792.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.131379 restraints weight = 11771.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.131991 restraints weight = 7771.328| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11501 Z= 0.145 Angle : 0.606 11.523 15649 Z= 0.300 Chirality : 0.040 0.186 1798 Planarity : 0.005 0.088 1999 Dihedral : 6.670 84.234 1636 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.59 % Favored : 93.34 % Rotamer: Outliers : 4.03 % Allowed : 26.52 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: 0.69 (0.23), residues: 1411 helix: 1.99 (0.19), residues: 748 sheet: -0.52 (0.63), residues: 62 loop : -1.49 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 358 HIS 0.004 0.001 HIS A 237 PHE 0.010 0.001 PHE A 341 TYR 0.017 0.001 TYR A 313 ARG 0.007 0.000 ARG A 10 Details of bonding type rmsd hydrogen bonds : bond 0.03601 ( 572) hydrogen bonds : angle 3.73948 ( 1656) covalent geometry : bond 0.00342 (11501) covalent geometry : angle 0.60594 (15649) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 142 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 491 ARG cc_start: 0.3454 (ttt180) cc_final: 0.2727 (ttt180) REVERT: A 828 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.6938 (t80) REVERT: A 916 PHE cc_start: 0.7653 (t80) cc_final: 0.7367 (t80) REVERT: A 917 ARG cc_start: 0.8452 (ptp-110) cc_final: 0.8060 (ptm160) REVERT: A 954 MET cc_start: 0.7913 (tpp) cc_final: 0.7242 (ttp) REVERT: A 1152 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7252 (tm-30) REVERT: C 46 TYR cc_start: 0.6345 (OUTLIER) cc_final: 0.5618 (m-10) REVERT: C 107 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7643 (mtp) REVERT: C 174 GLN cc_start: 0.7096 (pp30) cc_final: 0.6009 (pm20) REVERT: C 289 GLN cc_start: 0.4857 (pp30) cc_final: 0.3865 (pt0) outliers start: 47 outliers final: 40 residues processed: 178 average time/residue: 0.2005 time to fit residues: 53.6798 Evaluate side-chains 182 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 138 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 CYS Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 828 TYR Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1152 GLU Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1159 ASN Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 277 TYR Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 354 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 100 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 127 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 122 optimal weight: 0.0980 chunk 142 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.179803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.130229 restraints weight = 19667.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.134056 restraints weight = 10821.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.134373 restraints weight = 7663.097| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11501 Z= 0.113 Angle : 0.574 10.990 15649 Z= 0.284 Chirality : 0.040 0.186 1798 Planarity : 0.005 0.086 1999 Dihedral : 6.429 83.383 1636 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.59 % Favored : 93.34 % Rotamer: Outliers : 3.09 % Allowed : 27.98 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: 0.86 (0.23), residues: 1411 helix: 2.15 (0.19), residues: 748 sheet: -0.42 (0.64), residues: 62 loop : -1.45 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 358 HIS 0.003 0.001 HIS C 148 PHE 0.010 0.001 PHE A 524 TYR 0.015 0.001 TYR A 313 ARG 0.007 0.000 ARG A 10 Details of bonding type rmsd hydrogen bonds : bond 0.03053 ( 572) hydrogen bonds : angle 3.57947 ( 1656) covalent geometry : bond 0.00259 (11501) covalent geometry : angle 0.57439 (15649) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 491 ARG cc_start: 0.3219 (ttt180) cc_final: 0.2307 (ttt180) REVERT: A 828 TYR cc_start: 0.7192 (OUTLIER) cc_final: 0.6857 (t80) REVERT: A 916 PHE cc_start: 0.7615 (t80) cc_final: 0.7342 (t80) REVERT: A 917 ARG cc_start: 0.8402 (ptp-110) cc_final: 0.7970 (ptm160) REVERT: A 954 MET cc_start: 0.7869 (tpp) cc_final: 0.7209 (ttp) REVERT: A 1077 LYS cc_start: 0.8535 (mptt) cc_final: 0.8200 (mmmt) REVERT: C 21 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7383 (mt-10) REVERT: C 46 TYR cc_start: 0.6409 (OUTLIER) cc_final: 0.5541 (m-10) REVERT: C 107 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7539 (mtp) REVERT: C 131 MET cc_start: 0.8524 (tpp) cc_final: 0.8253 (tpp) REVERT: C 174 GLN cc_start: 0.7100 (pp30) cc_final: 0.6166 (pm20) REVERT: C 289 GLN cc_start: 0.4965 (pp30) cc_final: 0.4008 (pt0) outliers start: 36 outliers final: 30 residues processed: 177 average time/residue: 0.2105 time to fit residues: 56.5638 Evaluate side-chains 177 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 CYS Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 828 TYR Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 956 ASN Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1156 HIS Chi-restraints excluded: chain A residue 1159 ASN Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 277 TYR Chi-restraints excluded: chain C residue 318 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 105 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 94 optimal weight: 0.4980 chunk 108 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.179508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.129876 restraints weight = 19554.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.134192 restraints weight = 10654.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.134215 restraints weight = 7245.274| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11501 Z= 0.121 Angle : 0.583 11.065 15649 Z= 0.289 Chirality : 0.040 0.183 1798 Planarity : 0.005 0.085 1999 Dihedral : 6.368 81.921 1636 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.87 % Favored : 93.05 % Rotamer: Outliers : 3.43 % Allowed : 27.04 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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 (0.23), residues: 1411 helix: 2.13 (0.19), residues: 748 sheet: -0.44 (0.65), residues: 62 loop : -1.46 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 358 HIS 0.006 0.001 HIS C 148 PHE 0.010 0.001 PHE A 524 TYR 0.014 0.001 TYR A 171 ARG 0.007 0.000 ARG A 10 Details of bonding type rmsd hydrogen bonds : bond 0.03221 ( 572) hydrogen bonds : angle 3.61509 ( 1656) covalent geometry : bond 0.00278 (11501) covalent geometry : angle 0.58260 (15649) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3848.98 seconds wall clock time: 68 minutes 9.47 seconds (4089.47 seconds total)