Starting phenix.real_space_refine on Sat Aug 23 14:06:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5l_29748/08_2025/8g5l_29748_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5l_29748/08_2025/8g5l_29748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g5l_29748/08_2025/8g5l_29748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5l_29748/08_2025/8g5l_29748.map" model { file = "/net/cci-nas-00/data/ceres_data/8g5l_29748/08_2025/8g5l_29748_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5l_29748/08_2025/8g5l_29748_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.014 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 40 5.49 5 S 62 5.16 5 C 7844 2.51 5 N 2263 2.21 5 O 2414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12623 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 913, 7099 Classifications: {'peptide': 913} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 61, 'TRANS': 851} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 8, 'PHE:plan': 2, 'ARG:plan': 9, 'HIS:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 130 Chain: "B" Number of atoms: 2942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2942 Classifications: {'peptide': 363} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 346} Chain breaks: 3 Chain: "C" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 1763 Classifications: {'peptide': 358} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 319} Link IDs: {'PTRANS': 17, 'TRANS': 340} Chain breaks: 3 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1213 Unresolved non-hydrogen angles: 1562 Unresolved non-hydrogen dihedrals: 1044 Unresolved non-hydrogen chiralities: 102 Planarities with less than four sites: {'GLU:plan': 23, 'GLN:plan1': 13, 'ARG:plan': 20, 'HIS:plan': 15, 'PHE:plan': 15, 'ASP:plan': 15, 'ASN:plan1': 16, 'TRP:plan': 10, 'TYR:plan': 11} Unresolved non-hydrogen planarities: 669 Chain: "P" Number of atoms: 435 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 20, 415 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 20, 415 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 444 Chain: "T" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 384 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P A DA P 29 " occ=0.50 ... (38 atoms not shown) pdb=" C4 B DA P 29 " occ=0.50 residue: pdb=" P DC T 3 " occ=0.50 ... (17 atoms not shown) pdb=" C6 DC T 3 " occ=0.50 Time building chain proxies: 2.83, per 1000 atoms: 0.22 Number of scatterers: 12623 At special positions: 0 Unit cell: (90.86, 100.772, 141.246, 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 62 16.00 P 40 15.00 O 2414 8.00 N 2263 7.00 C 7844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 470.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3036 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 10 sheets defined 40.3% alpha, 11.4% beta 18 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 134 through 159 Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 305 through 316 removed outlier: 3.895A pdb=" N LEU A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 388 through 418 Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 420 through 429 removed outlier: 3.756A pdb=" N LEU A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 472 removed outlier: 4.121A pdb=" N GLU A 442 " --> pdb=" O ASN A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 542 through 549 removed outlier: 3.969A pdb=" N ARG A 546 " --> pdb=" O ASP A 542 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 577 Processing helix chain 'A' and resid 598 through 602 Processing helix chain 'A' and resid 788 through 809 WARNING: missing atoms! removed outlier: 4.841A pdb=" N PHE A 800 " --> pdb=" O LYS A 796 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N TRP A 801 " --> pdb=" O MET A 797 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N LYS A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ARG A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 907 Processing helix chain 'A' and resid 914 through 923 removed outlier: 3.541A pdb=" N LEU A 921 " --> pdb=" O GLY A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 940 Processing helix chain 'A' and resid 945 through 954 Processing helix chain 'A' and resid 958 through 970 Processing helix chain 'A' and resid 973 through 986 removed outlier: 3.557A pdb=" N TYR A 986 " --> pdb=" O ALA A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1066 Processing helix chain 'A' and resid 1093 through 1123 removed outlier: 3.665A pdb=" N VAL A1101 " --> pdb=" O VAL A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1169 Processing helix chain 'A' and resid 1174 through 1179 removed outlier: 4.191A pdb=" N PHE A1179 " --> pdb=" O GLN A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1206 Processing helix chain 'B' and resid 70 through 77 removed outlier: 4.012A pdb=" N GLN B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 93 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 192 through 200 removed outlier: 3.780A pdb=" N VAL B 200 " --> pdb=" O CYS B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 265 removed outlier: 4.669A pdb=" N ASN B 249 " --> pdb=" O PRO B 245 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N GLN B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 342 through 354 Processing helix chain 'B' and resid 394 through 408 removed outlier: 3.926A pdb=" N VAL B 398 " --> pdb=" O GLU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 435 removed outlier: 3.787A pdb=" N LEU B 428 " --> pdb=" O SER B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 removed outlier: 4.106A pdb=" N LEU B 448 " --> pdb=" O GLU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 485 Processing helix chain 'C' and resid 68 through 76 Processing helix chain 'C' and resid 87 through 93 removed outlier: 3.953A pdb=" N LEU C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 119 Processing helix chain 'C' and resid 185 through 200 removed outlier: 4.142A pdb=" N VAL C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASN C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP C 198 " --> pdb=" O VAL C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 264 removed outlier: 3.703A pdb=" N LEU C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 318 through 323 Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 391 through 410 Processing helix chain 'C' and resid 424 through 435 Processing helix chain 'C' and resid 444 through 451 removed outlier: 3.703A pdb=" N LEU C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 484 removed outlier: 4.459A pdb=" N LYS C 472 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASP C 473 " --> pdb=" O SER C 469 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 174 through 176 removed outlier: 4.127A pdb=" N GLY A 174 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU A 200 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ALA A 212 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ASP A 198 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 268 removed outlier: 6.422A pdb=" N VAL A 266 " --> pdb=" O LEU A 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 435 through 437 Processing sheet with id=AA4, first strand: chain 'A' and resid 1136 through 1138 removed outlier: 3.923A pdb=" N ASP A1186 " --> pdb=" O LEU A 886 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.579A pdb=" N PHE B 126 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ILE B 211 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE B 300 " --> pdb=" O ASP B 341 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LEU B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TYR B 291 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN B 305 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N LYS B 285 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 325 removed outlier: 3.616A pdb=" N GLY B 324 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 331 " --> pdb=" O GLY B 324 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 413 through 415 removed outlier: 6.001A pdb=" N ALA B 384 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL B 443 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP B 386 " --> pdb=" O VAL B 443 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 125 through 127 removed outlier: 3.768A pdb=" N ALA C 209 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AB1, first strand: chain 'C' and resid 413 through 414 removed outlier: 6.733A pdb=" N TRP C 414 " --> pdb=" O ILE C 381 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LYS C 382 " --> pdb=" O PHE C 439 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL C 441 " --> pdb=" O LYS C 382 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET C 462 " --> pdb=" O SER C 457 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1533 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 2.30 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.25: 2046 1.25 - 1.44: 3612 1.44 - 1.63: 7217 1.63 - 1.82: 101 1.82 - 2.01: 1 Bond restraints: 12977 Sorted by residual: bond pdb=" CG PRO B 270 " pdb=" CD PRO B 270 " ideal model delta sigma weight residual 1.503 1.063 0.440 3.40e-02 8.65e+02 1.67e+02 bond pdb=" CG PRO A 611 " pdb=" CD PRO A 611 " ideal model delta sigma weight residual 1.503 1.113 0.390 3.40e-02 8.65e+02 1.31e+02 bond pdb=" CB PRO B 270 " pdb=" CG PRO B 270 " ideal model delta sigma weight residual 1.492 2.012 -0.520 5.00e-02 4.00e+02 1.08e+02 bond pdb=" O3' DG P 28 " pdb=" P B DA P 29 " ideal model delta sigma weight residual 1.607 1.710 -0.103 1.50e-02 4.44e+03 4.71e+01 bond pdb=" CA PRO B 270 " pdb=" CB PRO B 270 " ideal model delta sigma weight residual 1.533 1.447 0.086 1.42e-02 4.96e+03 3.67e+01 ... (remaining 12972 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.06: 17781 6.06 - 12.12: 45 12.12 - 18.17: 4 18.17 - 24.23: 2 24.23 - 30.29: 3 Bond angle restraints: 17835 Sorted by residual: angle pdb=" N PRO B 270 " pdb=" CD PRO B 270 " pdb=" CG PRO B 270 " ideal model delta sigma weight residual 103.20 76.86 26.34 1.50e+00 4.44e-01 3.08e+02 angle pdb=" CA PRO B 270 " pdb=" CB PRO B 270 " pdb=" CG PRO B 270 " ideal model delta sigma weight residual 104.50 74.21 30.29 1.90e+00 2.77e-01 2.54e+02 angle pdb=" N PRO A 611 " pdb=" CD PRO A 611 " pdb=" CG PRO A 611 " ideal model delta sigma weight residual 103.20 81.89 21.31 1.50e+00 4.44e-01 2.02e+02 angle pdb=" CA PRO A 611 " pdb=" CB PRO A 611 " pdb=" CG PRO A 611 " ideal model delta sigma weight residual 104.50 80.80 23.70 1.90e+00 2.77e-01 1.56e+02 angle pdb=" N PRO B 270 " pdb=" CA PRO B 270 " pdb=" CB PRO B 270 " ideal model delta sigma weight residual 103.25 93.04 10.21 1.05e+00 9.07e-01 9.46e+01 ... (remaining 17830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.08: 7186 35.08 - 70.16: 374 70.16 - 105.24: 9 105.24 - 140.32: 1 140.32 - 175.39: 3 Dihedral angle restraints: 7573 sinusoidal: 2878 harmonic: 4695 Sorted by residual: dihedral pdb=" CA SER A 218 " pdb=" C SER A 218 " pdb=" N ALA A 219 " pdb=" CA ALA A 219 " ideal model delta harmonic sigma weight residual -180.00 -156.88 -23.12 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA ARG A 275 " pdb=" C ARG A 275 " pdb=" N ALA A 276 " pdb=" CA ALA A 276 " ideal model delta harmonic sigma weight residual 180.00 157.19 22.81 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA PRO B 270 " pdb=" CB PRO B 270 " pdb=" CG PRO B 270 " pdb=" CD PRO B 270 " ideal model delta sinusoidal sigma weight residual -38.00 -108.84 70.84 1 2.00e+01 2.50e-03 1.61e+01 ... (remaining 7570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 1951 0.126 - 0.252: 22 0.252 - 0.378: 0 0.378 - 0.505: 25 0.505 - 0.631: 3 Chirality restraints: 2001 Sorted by residual: chirality pdb=" P DC T 3 " pdb=" OP1 DC T 3 " pdb=" OP2 DC T 3 " pdb=" O5' DC T 3 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.63 2.00e-01 2.50e+01 9.95e+00 chirality pdb=" P DG T 9 " pdb=" OP1 DG T 9 " pdb=" OP2 DG T 9 " pdb=" O5' DG T 9 " both_signs ideal model delta sigma weight residual True 2.35 -2.87 -0.52 2.00e-01 2.50e+01 6.75e+00 chirality pdb=" P DC T 5 " pdb=" OP1 DC T 5 " pdb=" OP2 DC T 5 " pdb=" O5' DC T 5 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.52 2.00e-01 2.50e+01 6.68e+00 ... (remaining 1998 not shown) Planarity restraints: 2196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 126 " -0.224 9.50e-02 1.11e+02 1.01e-01 6.49e+00 pdb=" NE ARG A 126 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 126 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 126 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 126 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 828 " 0.042 5.00e-02 4.00e+02 6.33e-02 6.40e+00 pdb=" N PRO A 829 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 829 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 829 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 560 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.73e+00 pdb=" C PRO A 560 " -0.038 2.00e-02 2.50e+03 pdb=" O PRO A 560 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS A 561 " 0.013 2.00e-02 2.50e+03 ... (remaining 2193 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 203 2.64 - 3.20: 11755 3.20 - 3.77: 20109 3.77 - 4.33: 26065 4.33 - 4.90: 42184 Nonbonded interactions: 100316 Sorted by model distance: nonbonded pdb=" O ASP A 293 " pdb=" OG SER A 296 " model vdw 2.075 3.040 nonbonded pdb=" O HIS A 805 " pdb=" OG SER A 809 " model vdw 2.083 3.040 nonbonded pdb=" NH1 ARG A1142 " pdb=" OE2 GLU A1144 " model vdw 2.183 3.120 nonbonded pdb=" O TYR B 349 " pdb=" OG SER B 353 " model vdw 2.204 3.040 nonbonded pdb=" O LEU A1083 " pdb=" NH1 ARG A1096 " model vdw 2.206 3.120 ... (remaining 100311 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 Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 68 through 80 and (name N or name CA or name C or name O \ or name CB )) or resid 81 or (resid 82 through 93 and (name N or name CA or name \ C or name O or name CB )) or resid 94 or (resid 95 through 97 and (name N or na \ me CA or name C or name O or name CB )) or resid 98 or (resid 99 and (name N or \ name CA or name C or name O or name CB )) or resid 100 or (resid 101 through 102 \ and (name N or name CA or name C or name O or name CB )) or resid 103 or (resid \ 104 through 135 and (name N or name CA or name C or name O or name CB )) or res \ id 136 or (resid 180 through 187 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 188 through 206 and (name N or name CA or name C or name O o \ r name CB )) or resid 207 or (resid 208 through 211 and (name N or name CA or na \ me C or name O or name CB )) or resid 212 or (resid 213 through 219 and (name N \ or name CA or name C or name O or name CB )) or (resid 229 through 231 and (name \ N or name CA or name C or name O or name CB )) or resid 232 or (resid 233 throu \ gh 282 and (name N or name CA or name C or name O or name CB )) or resid 283 or \ (resid 284 through 285 and (name N or name CA or name C or name O or name CB )) \ or resid 286 or (resid 287 through 295 and (name N or name CA or name C or name \ O or name CB )) or resid 296 or (resid 297 through 306 and (name N or name CA or \ name C or name O or name CB )) or resid 307 or (resid 308 through 316 and (name \ N or name CA or name C or name O or name CB )) or resid 317 or (resid 318 throu \ gh 323 and (name N or name CA or name C or name O or name CB )) or resid 324 or \ (resid 325 through 326 and (name N or name CA or name C or name O or name CB )) \ or resid 327 or (resid 328 through 339 and (name N or name CA or name C or name \ O or name CB )) or resid 340 or (resid 341 through 344 and (name N or name CA or \ name C or name O or name CB )) or resid 345 or (resid 346 through 355 and (name \ N or name CA or name C or name O or name CB )) or (resid 368 through 387 and (n \ ame N or name CA or name C or name O or name CB )) or resid 388 or (resid 389 an \ d (name N or name CA or name C or name O or name CB )) or resid 390 or (resid 39 \ 1 through 400 and (name N or name CA or name C or name O or name CB )) or resid \ 401 or (resid 402 through 409 and (name N or name CA or name C or name O or name \ CB )) or resid 410 or (resid 411 through 415 and (name N or name CA or name C o \ r name O or name CB )) or resid 416 or (resid 417 through 450 and (name N or nam \ e CA or name C or name O or name CB )) or resid 451 or (resid 452 through 485 an \ d (name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 68 through 136 or resid 180 through 219 or resid 229 throu \ gh 485)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.430 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5369 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 : 0.009 0.520 12977 Z= 0.317 Angle : 1.044 30.291 17835 Z= 0.566 Chirality : 0.071 0.631 2001 Planarity : 0.005 0.101 2196 Dihedral : 18.588 175.394 4537 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.78 % Favored : 92.15 % Rotamer: Outliers : 2.17 % Allowed : 25.80 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.22), residues: 1606 helix: 1.85 (0.23), residues: 590 sheet: 0.32 (0.37), residues: 199 loop : -1.90 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 126 TYR 0.012 0.001 TYR A 614 PHE 0.035 0.001 PHE A 949 TRP 0.032 0.001 TRP A 897 HIS 0.007 0.001 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00880 (12977) covalent geometry : angle 1.04406 (17835) hydrogen bonds : bond 0.13162 ( 582) hydrogen bonds : angle 6.72257 ( 1625) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 241 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 LEU cc_start: 0.7664 (mt) cc_final: 0.7414 (mp) REVERT: A 486 TRP cc_start: 0.5837 (p-90) cc_final: 0.4993 (t60) REVERT: A 611 PRO cc_start: 0.4001 (OUTLIER) cc_final: 0.3674 (Cg_endo) REVERT: A 893 SER cc_start: 0.8282 (m) cc_final: 0.8059 (t) REVERT: A 924 ARG cc_start: 0.6129 (ttm-80) cc_final: 0.5594 (mmt-90) outliers start: 23 outliers final: 15 residues processed: 257 average time/residue: 0.4026 time to fit residues: 114.8044 Evaluate side-chains 185 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 611 PRO Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 1132 SER Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 412 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 ASN A 493 GLN A 565 HIS A 803 ASN A 811 GLN A 906 HIS A 959 GLN A 975 GLN A1157 ASN B 216 HIS B 400 GLN B 422 GLN B 427 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.209024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.165126 restraints weight = 59740.118| |-----------------------------------------------------------------------------| r_work (start): 0.4248 rms_B_bonded: 7.43 r_work: 0.4040 rms_B_bonded: 7.15 restraints_weight: 2.0000 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4046 r_free = 0.4046 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4045 r_free = 0.4045 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12977 Z= 0.170 Angle : 0.723 11.526 17835 Z= 0.361 Chirality : 0.045 0.312 2001 Planarity : 0.005 0.059 2196 Dihedral : 17.603 175.176 2177 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 5.20 % Allowed : 26.09 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.21), residues: 1606 helix: 1.57 (0.22), residues: 612 sheet: 0.35 (0.36), residues: 201 loop : -1.83 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1096 TYR 0.041 0.002 TYR A 955 PHE 0.016 0.001 PHE B 254 TRP 0.024 0.002 TRP A 897 HIS 0.012 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00382 (12977) covalent geometry : angle 0.72324 (17835) hydrogen bonds : bond 0.04099 ( 582) hydrogen bonds : angle 4.76119 ( 1625) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 183 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8287 (ttm110) cc_final: 0.7794 (mtm-85) REVERT: A 486 TRP cc_start: 0.5918 (p-90) cc_final: 0.4802 (t60) REVERT: A 487 ASP cc_start: 0.7078 (m-30) cc_final: 0.5607 (m-30) REVERT: A 551 LYS cc_start: 0.7921 (pttt) cc_final: 0.7713 (tmmt) REVERT: A 620 TRP cc_start: 0.5785 (m100) cc_final: 0.3918 (m-90) REVERT: A 924 ARG cc_start: 0.6041 (ttm-80) cc_final: 0.5314 (mmt-90) REVERT: A 971 HIS cc_start: 0.7704 (OUTLIER) cc_final: 0.7182 (m-70) REVERT: A 1121 GLU cc_start: 0.7392 (tp30) cc_final: 0.6971 (pt0) REVERT: A 1147 TYR cc_start: 0.6828 (m-80) cc_final: 0.6618 (m-80) REVERT: B 466 MET cc_start: 0.5267 (ttm) cc_final: 0.4817 (ttm) outliers start: 55 outliers final: 20 residues processed: 224 average time/residue: 0.3939 time to fit residues: 98.1283 Evaluate side-chains 188 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 913 CYS Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 395 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 160 optimal weight: 8.9990 chunk 123 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 46 optimal weight: 0.0570 chunk 119 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 159 optimal weight: 40.0000 chunk 138 optimal weight: 10.0000 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS A 569 HIS ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.207582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.161408 restraints weight = 62049.917| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 6.97 r_work: 0.4027 rms_B_bonded: 6.92 restraints_weight: 2.0000 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4034 r_free = 0.4034 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4034 r_free = 0.4034 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.4034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 12977 Z= 0.156 Angle : 0.691 13.057 17835 Z= 0.343 Chirality : 0.044 0.154 2001 Planarity : 0.005 0.058 2196 Dihedral : 17.303 178.266 2165 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 6.33 % Allowed : 26.09 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.21), residues: 1606 helix: 1.54 (0.21), residues: 608 sheet: 0.34 (0.36), residues: 209 loop : -1.80 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 257 TYR 0.040 0.002 TYR A 955 PHE 0.015 0.001 PHE A 197 TRP 0.020 0.001 TRP A 897 HIS 0.010 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00347 (12977) covalent geometry : angle 0.69071 (17835) hydrogen bonds : bond 0.03635 ( 582) hydrogen bonds : angle 4.55658 ( 1625) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 178 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6764 (OUTLIER) cc_final: 0.5070 (tpp) REVERT: A 297 MET cc_start: 0.6716 (OUTLIER) cc_final: 0.6117 (mtm) REVERT: A 363 TYR cc_start: 0.6054 (m-80) cc_final: 0.5700 (m-80) REVERT: A 486 TRP cc_start: 0.5889 (p-90) cc_final: 0.4828 (t60) REVERT: A 487 ASP cc_start: 0.7068 (m-30) cc_final: 0.5632 (m-30) REVERT: A 620 TRP cc_start: 0.5781 (m100) cc_final: 0.3956 (m-90) REVERT: A 924 ARG cc_start: 0.6083 (ttm-80) cc_final: 0.5377 (mmt-90) REVERT: A 1079 ILE cc_start: 0.4939 (OUTLIER) cc_final: 0.4542 (tt) REVERT: A 1121 GLU cc_start: 0.7416 (tp30) cc_final: 0.6999 (pt0) REVERT: B 463 LYS cc_start: 0.8263 (mppt) cc_final: 0.7503 (mmmt) REVERT: B 466 MET cc_start: 0.5203 (ttm) cc_final: 0.4778 (ttm) outliers start: 67 outliers final: 30 residues processed: 219 average time/residue: 0.3504 time to fit residues: 86.4754 Evaluate side-chains 198 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 596 MET Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 913 CYS Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 485 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 62 optimal weight: 0.5980 chunk 71 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 93 optimal weight: 0.0000 chunk 20 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.207330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.162269 restraints weight = 56837.973| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 6.56 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4223 r_free = 0.4223 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4223 r_free = 0.4223 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.4223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12977 Z= 0.149 Angle : 0.689 12.699 17835 Z= 0.340 Chirality : 0.043 0.161 2001 Planarity : 0.005 0.085 2196 Dihedral : 17.208 179.326 2165 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 6.14 % Allowed : 27.22 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.21), residues: 1606 helix: 1.50 (0.21), residues: 614 sheet: 0.37 (0.36), residues: 207 loop : -1.81 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 101 TYR 0.038 0.002 TYR A 955 PHE 0.022 0.001 PHE B 254 TRP 0.018 0.001 TRP A 897 HIS 0.010 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00332 (12977) covalent geometry : angle 0.68950 (17835) hydrogen bonds : bond 0.03440 ( 582) hydrogen bonds : angle 4.48346 ( 1625) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 173 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6398 (OUTLIER) cc_final: 0.5086 (tpp) REVERT: A 101 ARG cc_start: 0.8328 (ttm110) cc_final: 0.7905 (mtm-85) REVERT: A 297 MET cc_start: 0.6726 (OUTLIER) cc_final: 0.6129 (mtm) REVERT: A 486 TRP cc_start: 0.5556 (p-90) cc_final: 0.4754 (t60) REVERT: A 487 ASP cc_start: 0.6642 (m-30) cc_final: 0.5285 (m-30) REVERT: A 620 TRP cc_start: 0.5659 (m100) cc_final: 0.4167 (m-90) REVERT: A 924 ARG cc_start: 0.6193 (ttm-80) cc_final: 0.5487 (mmt-90) REVERT: A 1121 GLU cc_start: 0.7058 (tp30) cc_final: 0.6839 (pt0) REVERT: B 463 LYS cc_start: 0.8070 (mppt) cc_final: 0.7366 (mmmt) REVERT: B 466 MET cc_start: 0.4182 (ttm) cc_final: 0.3955 (ttm) outliers start: 65 outliers final: 35 residues processed: 215 average time/residue: 0.3555 time to fit residues: 85.9663 Evaluate side-chains 199 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 596 MET Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 485 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 61 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 137 optimal weight: 20.0000 chunk 161 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 153 optimal weight: 50.0000 chunk 131 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS ** A 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 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 = 0.4662 r_free = 0.4662 target = 0.197191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.150382 restraints weight = 61051.041| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 6.60 r_work: 0.3886 rms_B_bonded: 6.55 restraints_weight: 2.0000 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3888 r_free = 0.3888 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3888 r_free = 0.3888 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.128 12977 Z= 0.306 Angle : 0.831 12.945 17835 Z= 0.429 Chirality : 0.049 0.234 2001 Planarity : 0.006 0.076 2196 Dihedral : 17.490 179.998 2165 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 8.70 % Allowed : 25.05 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.21), residues: 1606 helix: 0.63 (0.21), residues: 614 sheet: 0.31 (0.36), residues: 204 loop : -2.23 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1071 TYR 0.046 0.003 TYR A 955 PHE 0.033 0.003 PHE A 197 TRP 0.023 0.003 TRP A 484 HIS 0.013 0.002 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00697 (12977) covalent geometry : angle 0.83143 (17835) hydrogen bonds : bond 0.04925 ( 582) hydrogen bonds : angle 5.31234 ( 1625) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 163 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6777 (OUTLIER) cc_final: 0.6508 (ttt) REVERT: A 94 MET cc_start: 0.7531 (ppp) cc_final: 0.6378 (pmm) REVERT: A 297 MET cc_start: 0.6990 (OUTLIER) cc_final: 0.6344 (mtm) REVERT: A 423 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7711 (m) REVERT: A 460 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.7148 (tptp) REVERT: A 486 TRP cc_start: 0.5987 (p-90) cc_final: 0.4768 (t60) REVERT: A 924 ARG cc_start: 0.6246 (OUTLIER) cc_final: 0.5577 (mmt-90) REVERT: A 971 HIS cc_start: 0.7969 (OUTLIER) cc_final: 0.7503 (m-70) REVERT: A 1103 SER cc_start: 0.6215 (OUTLIER) cc_final: 0.5826 (t) REVERT: B 109 ASN cc_start: 0.7079 (m-40) cc_final: 0.6749 (m-40) REVERT: B 239 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7640 (tp) REVERT: B 466 MET cc_start: 0.5283 (ttm) cc_final: 0.5024 (ttm) outliers start: 92 outliers final: 44 residues processed: 229 average time/residue: 0.3763 time to fit residues: 96.2805 Evaluate side-chains 205 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 153 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 924 ARG Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 485 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 163 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 chunk 162 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 73 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS B 366 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.201690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.155510 restraints weight = 59438.075| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 6.58 r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4142 r_free = 0.4142 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4142 r_free = 0.4142 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.4142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 12977 Z= 0.165 Angle : 0.734 13.008 17835 Z= 0.368 Chirality : 0.045 0.191 2001 Planarity : 0.005 0.083 2196 Dihedral : 17.210 177.091 2163 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 6.43 % Allowed : 27.60 % Favored : 65.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.21), residues: 1606 helix: 1.04 (0.21), residues: 616 sheet: 0.20 (0.36), residues: 209 loop : -2.12 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 574 TYR 0.040 0.002 TYR A 955 PHE 0.029 0.002 PHE A 197 TRP 0.022 0.002 TRP A 484 HIS 0.011 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00369 (12977) covalent geometry : angle 0.73353 (17835) hydrogen bonds : bond 0.03726 ( 582) hydrogen bonds : angle 4.80959 ( 1625) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 174 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6407 (OUTLIER) cc_final: 0.5023 (tpp) REVERT: A 94 MET cc_start: 0.7221 (ppp) cc_final: 0.6444 (pmm) REVERT: A 101 ARG cc_start: 0.8160 (ttm110) cc_final: 0.7729 (mtm-85) REVERT: A 288 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6173 (mmp80) REVERT: A 297 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.6110 (mtm) REVERT: A 460 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6921 (tptp) REVERT: A 486 TRP cc_start: 0.5624 (p-90) cc_final: 0.4599 (t60) REVERT: A 924 ARG cc_start: 0.6204 (ttm-80) cc_final: 0.5530 (mmt-90) REVERT: B 109 ASN cc_start: 0.6501 (m-40) cc_final: 0.6150 (m110) REVERT: B 239 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7529 (tp) REVERT: B 344 ARG cc_start: 0.6672 (mtm180) cc_final: 0.6452 (mtm180) REVERT: B 463 LYS cc_start: 0.8127 (mptt) cc_final: 0.7528 (mmmt) REVERT: B 466 MET cc_start: 0.4428 (ttm) cc_final: 0.4171 (ttm) outliers start: 68 outliers final: 38 residues processed: 219 average time/residue: 0.3925 time to fit residues: 95.4746 Evaluate side-chains 208 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 165 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 620 TRP Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1177 VAL Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 485 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 20.0000 chunk 46 optimal weight: 8.9990 chunk 38 optimal weight: 0.0870 chunk 109 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 0.0060 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 GLN A 565 HIS ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.204823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.159379 restraints weight = 69874.312| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 8.11 r_work: 0.3959 rms_B_bonded: 7.60 restraints_weight: 2.0000 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3963 r_free = 0.3963 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3963 r_free = 0.3963 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12977 Z= 0.139 Angle : 0.713 14.175 17835 Z= 0.355 Chirality : 0.043 0.173 2001 Planarity : 0.004 0.062 2196 Dihedral : 17.034 175.249 2163 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 5.86 % Allowed : 28.54 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.21), residues: 1606 helix: 1.34 (0.22), residues: 613 sheet: 0.22 (0.37), residues: 206 loop : -2.03 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1146 TYR 0.028 0.002 TYR A 955 PHE 0.036 0.001 PHE A 197 TRP 0.036 0.002 TRP A 484 HIS 0.009 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00300 (12977) covalent geometry : angle 0.71329 (17835) hydrogen bonds : bond 0.03286 ( 582) hydrogen bonds : angle 4.51826 ( 1625) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 184 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6671 (OUTLIER) cc_final: 0.4873 (tpp) REVERT: A 94 MET cc_start: 0.7576 (ppp) cc_final: 0.6628 (pmm) REVERT: A 101 ARG cc_start: 0.8172 (ttm110) cc_final: 0.7759 (mtm-85) REVERT: A 288 ARG cc_start: 0.7023 (OUTLIER) cc_final: 0.6314 (mmp80) REVERT: A 297 MET cc_start: 0.6379 (OUTLIER) cc_final: 0.5870 (mtm) REVERT: A 460 LYS cc_start: 0.7233 (OUTLIER) cc_final: 0.6992 (tptp) REVERT: A 486 TRP cc_start: 0.5934 (p-90) cc_final: 0.4657 (t60) REVERT: A 774 MET cc_start: 0.6496 (tpp) cc_final: 0.6122 (tpp) REVERT: A 833 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7170 (pt0) REVERT: A 924 ARG cc_start: 0.6040 (OUTLIER) cc_final: 0.5295 (mmt-90) REVERT: A 1218 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6921 (pp) REVERT: B 463 LYS cc_start: 0.8406 (mptt) cc_final: 0.7667 (mmmt) REVERT: B 466 MET cc_start: 0.5232 (ttm) cc_final: 0.4891 (ttm) outliers start: 62 outliers final: 38 residues processed: 227 average time/residue: 0.3634 time to fit residues: 92.7094 Evaluate side-chains 218 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 173 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 924 ARG Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 485 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 43 optimal weight: 0.5980 chunk 137 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 72 optimal weight: 0.0050 chunk 108 optimal weight: 0.9990 chunk 99 optimal weight: 20.0000 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 HIS ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.205212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.159622 restraints weight = 69958.703| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 8.33 r_work: 0.3953 rms_B_bonded: 7.74 restraints_weight: 2.0000 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3957 r_free = 0.3957 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3957 r_free = 0.3957 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12977 Z= 0.140 Angle : 0.726 15.024 17835 Z= 0.359 Chirality : 0.044 0.197 2001 Planarity : 0.005 0.062 2196 Dihedral : 16.972 174.393 2163 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 6.33 % Allowed : 28.64 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.21), residues: 1606 helix: 1.30 (0.22), residues: 613 sheet: 0.24 (0.37), residues: 208 loop : -1.98 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 823 TYR 0.031 0.002 TYR A 955 PHE 0.032 0.001 PHE A 197 TRP 0.039 0.002 TRP A 484 HIS 0.011 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00311 (12977) covalent geometry : angle 0.72554 (17835) hydrogen bonds : bond 0.03203 ( 582) hydrogen bonds : angle 4.50692 ( 1625) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 175 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6720 (OUTLIER) cc_final: 0.5005 (tpp) REVERT: A 94 MET cc_start: 0.7623 (ppp) cc_final: 0.6698 (pmm) REVERT: A 101 ARG cc_start: 0.8167 (ttm110) cc_final: 0.7763 (mtm-85) REVERT: A 288 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.6344 (mmp80) REVERT: A 297 MET cc_start: 0.6474 (OUTLIER) cc_final: 0.5985 (mtm) REVERT: A 460 LYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6946 (tptp) REVERT: A 486 TRP cc_start: 0.6001 (p-90) cc_final: 0.4687 (t60) REVERT: A 774 MET cc_start: 0.6588 (OUTLIER) cc_final: 0.6227 (tpp) REVERT: A 833 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7139 (pt0) REVERT: A 924 ARG cc_start: 0.6030 (OUTLIER) cc_final: 0.5300 (mmt-90) REVERT: A 1062 GLU cc_start: 0.5402 (OUTLIER) cc_final: 0.4828 (pp20) REVERT: A 1218 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6926 (pp) REVERT: B 109 ASN cc_start: 0.6940 (m-40) cc_final: 0.6294 (m110) REVERT: B 463 LYS cc_start: 0.8388 (mptt) cc_final: 0.7619 (mmmt) REVERT: B 466 MET cc_start: 0.5297 (ttm) cc_final: 0.4933 (ttm) outliers start: 67 outliers final: 44 residues processed: 216 average time/residue: 0.3540 time to fit residues: 85.6687 Evaluate side-chains 218 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 165 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 924 ARG Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 485 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 88 optimal weight: 0.1980 chunk 8 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 106 optimal weight: 0.2980 chunk 146 optimal weight: 20.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 HIS ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.206584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.161099 restraints weight = 58212.918| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 6.70 r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4217 r_free = 0.4217 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4217 r_free = 0.4217 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.4217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12977 Z= 0.135 Angle : 0.739 14.437 17835 Z= 0.364 Chirality : 0.044 0.205 2001 Planarity : 0.004 0.062 2196 Dihedral : 16.901 172.742 2163 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 5.58 % Allowed : 30.15 % Favored : 64.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.22), residues: 1606 helix: 1.36 (0.22), residues: 612 sheet: 0.18 (0.37), residues: 204 loop : -1.90 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 823 TYR 0.037 0.002 TYR B 432 PHE 0.029 0.001 PHE A 197 TRP 0.043 0.002 TRP A 484 HIS 0.011 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00298 (12977) covalent geometry : angle 0.73854 (17835) hydrogen bonds : bond 0.03171 ( 582) hydrogen bonds : angle 4.43019 ( 1625) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 172 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8112 (ttm110) cc_final: 0.7706 (mtm-85) REVERT: A 288 ARG cc_start: 0.6926 (OUTLIER) cc_final: 0.6174 (mmp80) REVERT: A 297 MET cc_start: 0.6625 (OUTLIER) cc_final: 0.6108 (mtm) REVERT: A 484 TRP cc_start: 0.6559 (p90) cc_final: 0.6336 (p90) REVERT: A 486 TRP cc_start: 0.5602 (p-90) cc_final: 0.4554 (t60) REVERT: A 774 MET cc_start: 0.6780 (OUTLIER) cc_final: 0.6462 (tpp) REVERT: A 833 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7093 (pt0) REVERT: A 924 ARG cc_start: 0.6060 (OUTLIER) cc_final: 0.5418 (mmt-90) REVERT: A 1062 GLU cc_start: 0.5076 (OUTLIER) cc_final: 0.4679 (pp20) REVERT: B 109 ASN cc_start: 0.6493 (m-40) cc_final: 0.6192 (m110) REVERT: B 192 HIS cc_start: 0.6971 (m90) cc_final: 0.6720 (p90) REVERT: B 434 GLU cc_start: 0.5819 (mt-10) cc_final: 0.5580 (mt-10) REVERT: B 463 LYS cc_start: 0.8080 (mptt) cc_final: 0.7372 (mmmt) outliers start: 59 outliers final: 42 residues processed: 209 average time/residue: 0.3661 time to fit residues: 85.9408 Evaluate side-chains 209 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 161 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 924 ARG Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 485 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 151 optimal weight: 50.0000 chunk 72 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 134 optimal weight: 20.0000 chunk 80 optimal weight: 0.4980 chunk 159 optimal weight: 50.0000 chunk 114 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 976 GLN ** B 258 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 = 0.4717 r_free = 0.4717 target = 0.202441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.156825 restraints weight = 73764.770| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 8.18 r_work: 0.3920 rms_B_bonded: 7.53 restraints_weight: 2.0000 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3921 r_free = 0.3921 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3921 r_free = 0.3921 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 12977 Z= 0.185 Angle : 0.783 15.945 17835 Z= 0.387 Chirality : 0.046 0.207 2001 Planarity : 0.005 0.061 2196 Dihedral : 17.008 173.802 2163 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 5.20 % Allowed : 30.91 % Favored : 63.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.21), residues: 1606 helix: 1.24 (0.22), residues: 610 sheet: 0.41 (0.36), residues: 208 loop : -2.01 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 574 TYR 0.045 0.002 TYR A 955 PHE 0.035 0.002 PHE A 197 TRP 0.038 0.002 TRP A 484 HIS 0.011 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00420 (12977) covalent geometry : angle 0.78296 (17835) hydrogen bonds : bond 0.03618 ( 582) hydrogen bonds : angle 4.65535 ( 1625) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 165 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.7662 (ppp) cc_final: 0.6628 (pmm) REVERT: A 101 ARG cc_start: 0.8204 (ttm110) cc_final: 0.7799 (mtm-85) REVERT: A 288 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.6358 (mmp80) REVERT: A 297 MET cc_start: 0.6760 (OUTLIER) cc_final: 0.6244 (mtm) REVERT: A 486 TRP cc_start: 0.5939 (p-90) cc_final: 0.4777 (t60) REVERT: A 774 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.6482 (tpp) REVERT: A 833 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7020 (pt0) REVERT: A 924 ARG cc_start: 0.6050 (OUTLIER) cc_final: 0.5345 (mmt-90) REVERT: A 1062 GLU cc_start: 0.5323 (OUTLIER) cc_final: 0.4733 (pp20) REVERT: B 109 ASN cc_start: 0.7014 (m-40) cc_final: 0.6628 (m110) REVERT: B 192 HIS cc_start: 0.7030 (m90) cc_final: 0.6702 (p90) REVERT: B 463 LYS cc_start: 0.8426 (mptt) cc_final: 0.7636 (mmmt) outliers start: 55 outliers final: 38 residues processed: 201 average time/residue: 0.3584 time to fit residues: 80.6642 Evaluate side-chains 201 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 157 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 924 ARG Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 485 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 150 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 154 optimal weight: 6.9990 chunk 36 optimal weight: 0.0370 chunk 29 optimal weight: 0.9980 chunk 127 optimal weight: 50.0000 chunk 112 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 140 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 overall best weight: 1.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS ** A1059 ASN ** 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 = 0.4711 r_free = 0.4711 target = 0.201754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.156077 restraints weight = 55669.376| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 6.37 r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4150 r_free = 0.4150 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4150 r_free = 0.4150 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.4150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 12977 Z= 0.189 Angle : 0.793 14.720 17835 Z= 0.394 Chirality : 0.046 0.188 2001 Planarity : 0.005 0.060 2196 Dihedral : 17.038 173.598 2163 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 5.10 % Allowed : 31.47 % Favored : 63.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.21), residues: 1606 helix: 1.18 (0.22), residues: 605 sheet: 0.32 (0.36), residues: 211 loop : -2.11 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 823 TYR 0.043 0.002 TYR A 955 PHE 0.036 0.002 PHE A 197 TRP 0.044 0.002 TRP A 484 HIS 0.014 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00430 (12977) covalent geometry : angle 0.79279 (17835) hydrogen bonds : bond 0.03744 ( 582) hydrogen bonds : angle 4.76977 ( 1625) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4572.64 seconds wall clock time: 78 minutes 24.10 seconds (4704.10 seconds total)