Starting phenix.real_space_refine on Fri Jul 3 06:22:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5l_29748/07_2026/8g5l_29748_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5l_29748/07_2026/8g5l_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 { model { file = "/net/cci-nas-00/data/ceres_data/8g5l_29748/07_2026/8g5l_29748_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5l_29748/07_2026/8g5l_29748_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g5l_29748/07_2026/8g5l_29748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5l_29748/07_2026/8g5l_29748.map" } 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-dev-6108/lib/python3.11/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: 3.26, per 1000 atoms: 0.26 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: 1.16 Conformation dependent library (CDL) restraints added in 568.6 milliseconds 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: 1.53 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: 2.27 Time building geometry restraints manager: 1.54 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 - 0.128: 1954 0.128 - 0.256: 19 0.256 - 0.385: 0 0.385 - 0.513: 25 0.513 - 0.641: 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 2.34 -2.98 -0.64 2.00e-01 2.50e+01 1.03e+01 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 2.34 -2.87 -0.53 2.00e-01 2.50e+01 7.02e+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 2.34 -2.86 -0.53 2.00e-01 2.50e+01 6.95e+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: 2.670 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.420 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5456 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= 0.359 Angle : 1.048 30.291 17835 Z= 0.589 Chirality : 0.072 0.641 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 are 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/Z covalent geometry : bond 0.00890 / 0.36 (12977) covalent geometry : angle 1.04783 / 0.59 (17835) hydrogen bonds : bond 0.13162 / 8.91 ( 582) hydrogen bonds : angle 6.72257 / 4.69 ( 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 : 0.476 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: 0.4674 time to fit residues: 133.4442 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 : 0.461 ------------------------------------------------------------------------------- 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... ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN A 409 GLN 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 422 GLN B 427 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.209359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.164775 restraints weight = 55278.638| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 6.52 r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4261 r_free = 0.4261 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4260 r_free = 0.4260 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.4260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.1562 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= 0.167 Angle : 0.743 11.715 17835 Z= 0.375 Chirality : 0.047 0.364 2001 Planarity : 0.005 0.057 2196 Dihedral : 17.788 175.781 2177 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 5.67 % Allowed : 25.33 % Favored : 69.00 % 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 are not related in a simple way. whole: -0.34 (0.21), residues: 1606 helix: 1.49 (0.21), residues: 612 sheet: 0.31 (0.36), residues: 201 loop : -1.85 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1148 TYR 0.040 0.002 TYR A 955 PHE 0.016 0.002 PHE A 539 TRP 0.028 0.002 TRP B 241 HIS 0.012 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 (12977) covalent geometry : angle 0.74297 / 0.37 (17835) hydrogen bonds : bond 0.04223 / 2.88 ( 582) hydrogen bonds : angle 4.92428 / 3.42 ( 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 249 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 189 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 486 TRP cc_start: 0.5600 (p-90) cc_final: 0.4754 (t60) REVERT: A 487 ASP cc_start: 0.6529 (m-30) cc_final: 0.5094 (m-30) REVERT: A 551 LYS cc_start: 0.7806 (pttt) cc_final: 0.7567 (tmmt) REVERT: A 620 TRP cc_start: 0.5632 (m100) cc_final: 0.4128 (m-90) REVERT: A 924 ARG cc_start: 0.6087 (ttm-80) cc_final: 0.5419 (mmt-90) REVERT: A 971 HIS cc_start: 0.7580 (OUTLIER) cc_final: 0.7052 (m-70) REVERT: A 1121 GLU cc_start: 0.6948 (tp30) cc_final: 0.6730 (pt0) REVERT: A 1144 GLU cc_start: 0.7324 (pm20) cc_final: 0.7100 (pm20) REVERT: B 466 MET cc_start: 0.4208 (ttm) cc_final: 0.3904 (ttm) outliers start: 60 outliers final: 22 residues processed: 231 average time/residue: 0.4272 time to fit residues: 110.4914 Evaluate side-chains 189 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 353 VAL 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 248 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 485 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 160 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 56 optimal weight: 0.0570 chunk 57 optimal weight: 0.8980 chunk 159 optimal weight: 40.0000 chunk 138 optimal weight: 20.0000 overall best weight: 2.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 GLN A 565 HIS A 569 HIS ** A 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 400 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.203018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.156967 restraints weight = 60535.215| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 6.75 r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4165 r_free = 0.4165 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4164 r_free = 0.4164 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 12977 Z= 0.223 Angle : 0.781 19.719 17835 Z= 0.393 Chirality : 0.048 0.258 2001 Planarity : 0.005 0.057 2196 Dihedral : 17.561 176.532 2165 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 7.75 % Allowed : 25.71 % Favored : 66.54 % 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 are not related in a simple way. whole: -0.62 (0.21), residues: 1606 helix: 1.14 (0.21), residues: 611 sheet: 0.13 (0.36), residues: 209 loop : -1.91 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 823 TYR 0.039 0.003 TYR A 955 PHE 0.019 0.002 PHE A 770 TRP 0.019 0.002 TRP A1099 HIS 0.011 0.002 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.22 (12977) covalent geometry : angle 0.78062 / 0.39 (17835) hydrogen bonds : bond 0.04345 / 2.98 ( 582) hydrogen bonds : angle 5.00140 / 3.48 ( 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 254 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 172 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6563 (tp) REVERT: A 398 GLN cc_start: 0.7076 (OUTLIER) cc_final: 0.6738 (mm110) REVERT: A 486 TRP cc_start: 0.5623 (p-90) cc_final: 0.4832 (t60) REVERT: A 487 ASP cc_start: 0.6681 (m-30) cc_final: 0.5339 (m-30) REVERT: A 924 ARG cc_start: 0.6246 (ttm-80) cc_final: 0.5545 (mmt-90) REVERT: A 971 HIS cc_start: 0.7798 (OUTLIER) cc_final: 0.7264 (m-70) REVERT: B 203 ARG cc_start: 0.7681 (mmp-170) cc_final: 0.7441 (mmm160) REVERT: B 231 ILE cc_start: 0.6044 (mm) cc_final: 0.5815 (mm) REVERT: B 463 LYS cc_start: 0.8246 (mppt) cc_final: 0.7972 (mppt) REVERT: B 466 MET cc_start: 0.4299 (ttm) cc_final: 0.3990 (ttm) outliers start: 82 outliers final: 38 residues processed: 226 average time/residue: 0.4402 time to fit residues: 111.4548 Evaluate side-chains 200 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 159 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 348 LEU Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 593 SER 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 742 VAL Chi-restraints excluded: chain A residue 796 LYS 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 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 971 HIS 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 1206 MET Chi-restraints excluded: chain A residue 1212 ILE 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 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 392 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 435 MET 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: 6.9990 chunk 71 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 97 optimal weight: 0.4980 chunk 104 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 93 optimal weight: 0.0470 chunk 20 optimal weight: 1.9990 overall best weight: 1.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.205993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.161116 restraints weight = 53979.714| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 6.32 r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4213 r_free = 0.4213 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4213 r_free = 0.4213 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 12977 Z= 0.151 Angle : 0.723 13.436 17835 Z= 0.358 Chirality : 0.046 0.242 2001 Planarity : 0.005 0.057 2196 Dihedral : 17.407 178.924 2164 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 6.71 % Allowed : 26.75 % Favored : 66.54 % 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 are not related in a simple way. whole: -0.49 (0.21), residues: 1606 helix: 1.32 (0.21), residues: 608 sheet: 0.20 (0.36), residues: 209 loop : -1.89 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 101 TYR 0.046 0.002 TYR A 955 PHE 0.021 0.001 PHE A 197 TRP 0.021 0.001 TRP A 897 HIS 0.010 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (12977) covalent geometry : angle 0.72282 / 0.36 (17835) hydrogen bonds : bond 0.03675 / 2.49 ( 582) hydrogen bonds : angle 4.71345 / 3.27 ( 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 240 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 169 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8260 (ttm110) cc_final: 0.7843 (mtm-85) REVERT: A 486 TRP cc_start: 0.5584 (p-90) cc_final: 0.4809 (t60) REVERT: A 487 ASP cc_start: 0.6536 (m-30) cc_final: 0.5229 (m-30) REVERT: A 620 TRP cc_start: 0.5625 (m100) cc_final: 0.4118 (m-90) REVERT: A 924 ARG cc_start: 0.6208 (OUTLIER) cc_final: 0.5514 (mmt-90) REVERT: A 971 HIS cc_start: 0.7740 (OUTLIER) cc_final: 0.7144 (m-70) REVERT: A 1144 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7401 (pm20) REVERT: B 231 ILE cc_start: 0.6017 (mm) cc_final: 0.5811 (mm) REVERT: B 463 LYS cc_start: 0.8136 (mppt) cc_final: 0.7913 (mppt) REVERT: B 466 MET cc_start: 0.4338 (ttm) cc_final: 0.4106 (ttm) outliers start: 71 outliers final: 30 residues processed: 216 average time/residue: 0.3879 time to fit residues: 94.4655 Evaluate side-chains 195 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 151 LEU 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 348 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 599 THR 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 924 ARG Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 72 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 395 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 61 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 137 optimal weight: 20.0000 chunk 161 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 153 optimal weight: 40.0000 chunk 131 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 163 optimal weight: 20.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.204026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.158213 restraints weight = 59889.945| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 6.64 r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4175 r_free = 0.4175 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4175 r_free = 0.4175 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 12977 Z= 0.180 Angle : 0.716 13.106 17835 Z= 0.362 Chirality : 0.046 0.247 2001 Planarity : 0.005 0.057 2196 Dihedral : 17.379 179.807 2164 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 7.66 % Allowed : 26.28 % Favored : 66.07 % 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 are not related in a simple way. whole: -0.60 (0.21), residues: 1606 helix: 1.18 (0.21), residues: 615 sheet: 0.27 (0.36), residues: 207 loop : -1.97 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 823 TYR 0.043 0.002 TYR A 955 PHE 0.027 0.002 PHE A 197 TRP 0.018 0.002 TRP A 490 HIS 0.011 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (12977) covalent geometry : angle 0.71645 / 0.36 (17835) hydrogen bonds : bond 0.03777 / 2.58 ( 582) hydrogen bonds : angle 4.72791 / 3.29 ( 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 249 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 168 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.7074 (ppp) cc_final: 0.6133 (pmm) REVERT: A 101 ARG cc_start: 0.8250 (ttm110) cc_final: 0.7824 (mtm-85) REVERT: A 486 TRP cc_start: 0.5602 (p-90) cc_final: 0.4706 (t60) REVERT: A 924 ARG cc_start: 0.6251 (OUTLIER) cc_final: 0.5548 (mmt-90) REVERT: A 971 HIS cc_start: 0.7792 (OUTLIER) cc_final: 0.7181 (m-70) REVERT: A 1144 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7486 (pm20) REVERT: B 239 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7625 (tp) REVERT: B 466 MET cc_start: 0.4356 (ttm) cc_final: 0.4126 (ttm) outliers start: 81 outliers final: 43 residues processed: 228 average time/residue: 0.4171 time to fit residues: 107.0447 Evaluate side-chains 206 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 159 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 348 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 596 MET 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 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 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 1079 ILE Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain A residue 1153 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 72 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 128 VAL 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 413 VAL 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: 20.0000 chunk 0 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 162 optimal weight: 30.0000 chunk 15 optimal weight: 0.0670 chunk 117 optimal weight: 0.9990 chunk 107 optimal weight: 0.0670 chunk 16 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 GLN ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 366 ASN B 422 GLN B 427 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.205534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.160316 restraints weight = 57710.745| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 6.62 r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4205 r_free = 0.4205 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4205 r_free = 0.4205 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12977 Z= 0.142 Angle : 0.704 13.336 17835 Z= 0.352 Chirality : 0.045 0.245 2001 Planarity : 0.004 0.058 2196 Dihedral : 17.286 177.107 2164 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 6.81 % Allowed : 27.98 % Favored : 65.22 % 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 are not related in a simple way. whole: -0.48 (0.21), residues: 1606 helix: 1.32 (0.22), residues: 614 sheet: 0.34 (0.36), residues: 207 loop : -1.94 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 823 TYR 0.040 0.002 TYR A 955 PHE 0.034 0.001 PHE A 197 TRP 0.020 0.001 TRP A 490 HIS 0.010 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (12977) covalent geometry : angle 0.70405 / 0.35 (17835) hydrogen bonds : bond 0.03454 / 2.35 ( 582) hydrogen bonds : angle 4.53176 / 3.15 ( 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 244 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 172 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6441 (OUTLIER) cc_final: 0.4992 (tpp) REVERT: A 101 ARG cc_start: 0.8267 (ttm110) cc_final: 0.7858 (mtm-85) REVERT: A 189 ILE cc_start: 0.7079 (OUTLIER) cc_final: 0.6848 (tp) REVERT: A 486 TRP cc_start: 0.5621 (p-90) cc_final: 0.4625 (t60) REVERT: A 620 TRP cc_start: 0.5761 (m100) cc_final: 0.4096 (m-90) REVERT: A 924 ARG cc_start: 0.6201 (OUTLIER) cc_final: 0.5484 (mmt-90) REVERT: A 971 HIS cc_start: 0.7765 (OUTLIER) cc_final: 0.7173 (m-70) REVERT: A 1144 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7580 (pm20) REVERT: B 466 MET cc_start: 0.4167 (ttm) cc_final: 0.3933 (ttm) outliers start: 72 outliers final: 38 residues processed: 218 average time/residue: 0.4245 time to fit residues: 104.0052 Evaluate side-chains 204 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 161 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 189 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL 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 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 831 TYR 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 924 ARG Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1144 GLU 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 128 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 220 ASP 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 435 MET Chi-restraints excluded: chain B residue 448 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 40.0000 chunk 46 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 HIS ** 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 261 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.206195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.160440 restraints weight = 66960.061| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 7.19 r_work: 0.4001 rms_B_bonded: 7.11 restraints_weight: 2.0000 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4004 r_free = 0.4004 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4004 r_free = 0.4004 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12977 Z= 0.137 Angle : 0.714 13.692 17835 Z= 0.356 Chirality : 0.045 0.248 2001 Planarity : 0.004 0.059 2196 Dihedral : 17.216 175.156 2164 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 6.62 % Allowed : 27.69 % Favored : 65.69 % 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 are not related in a simple way. whole: -0.42 (0.21), residues: 1606 helix: 1.42 (0.22), residues: 615 sheet: 0.39 (0.37), residues: 195 loop : -1.94 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 823 TYR 0.043 0.002 TYR B 432 PHE 0.036 0.001 PHE A 197 TRP 0.035 0.002 TRP A 484 HIS 0.011 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (12977) covalent geometry : angle 0.71413 / 0.36 (17835) hydrogen bonds : bond 0.03376 / 2.31 ( 582) hydrogen bonds : angle 4.42679 / 3.09 ( 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 242 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 172 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6795 (OUTLIER) cc_final: 0.5076 (tpp) REVERT: A 94 MET cc_start: 0.7515 (ppp) cc_final: 0.6466 (pmm) REVERT: A 189 ILE cc_start: 0.7184 (OUTLIER) cc_final: 0.6978 (tp) REVERT: A 486 TRP cc_start: 0.5875 (p-90) cc_final: 0.4729 (t60) REVERT: A 620 TRP cc_start: 0.5886 (m100) cc_final: 0.3988 (m-90) REVERT: A 924 ARG cc_start: 0.6095 (OUTLIER) cc_final: 0.5300 (mmt-90) REVERT: A 1109 LEU cc_start: 0.8326 (tp) cc_final: 0.8108 (tp) REVERT: A 1144 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7854 (pm20) REVERT: A 1218 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6922 (pp) REVERT: B 466 MET cc_start: 0.5083 (ttm) cc_final: 0.4721 (ttm) outliers start: 70 outliers final: 43 residues processed: 219 average time/residue: 0.3640 time to fit residues: 90.5803 Evaluate side-chains 210 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 162 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 189 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL 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 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 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 924 ARG Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1069 ILE 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 1144 GLU 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 128 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 239 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 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 431 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 43 optimal weight: 1.9990 chunk 137 optimal weight: 20.0000 chunk 122 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 0.2980 chunk 81 optimal weight: 4.9990 chunk 72 optimal weight: 0.3980 chunk 108 optimal weight: 0.9990 chunk 99 optimal weight: 20.0000 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 565 HIS ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.206664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.163321 restraints weight = 69346.878| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 7.70 r_work: 0.3994 rms_B_bonded: 7.50 restraints_weight: 2.0000 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3998 r_free = 0.3998 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3998 r_free = 0.3998 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.2848 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= 0.136 Angle : 0.717 14.039 17835 Z= 0.358 Chirality : 0.045 0.254 2001 Planarity : 0.004 0.059 2196 Dihedral : 17.165 173.384 2164 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 6.05 % Allowed : 28.54 % Favored : 65.41 % 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 are not related in a simple way. whole: -0.41 (0.21), residues: 1606 helix: 1.41 (0.22), residues: 615 sheet: 0.44 (0.37), residues: 195 loop : -1.92 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 101 TYR 0.051 0.002 TYR B 432 PHE 0.034 0.001 PHE A 197 TRP 0.040 0.002 TRP A 484 HIS 0.010 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (12977) covalent geometry : angle 0.71655 / 0.36 (17835) hydrogen bonds : bond 0.03304 / 2.27 ( 582) hydrogen bonds : angle 4.37124 / 3.06 ( 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 234 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 170 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6793 (OUTLIER) cc_final: 0.5021 (tpp) REVERT: A 94 MET cc_start: 0.7549 (ppp) cc_final: 0.6469 (pmm) REVERT: A 101 ARG cc_start: 0.8345 (ttm110) cc_final: 0.8088 (mtm-85) REVERT: A 189 ILE cc_start: 0.7178 (OUTLIER) cc_final: 0.6818 (mp) REVERT: A 486 TRP cc_start: 0.5854 (p-90) cc_final: 0.4697 (t60) REVERT: A 620 TRP cc_start: 0.5834 (m100) cc_final: 0.3911 (m-90) REVERT: A 924 ARG cc_start: 0.6093 (OUTLIER) cc_final: 0.5295 (mmt-90) REVERT: A 1144 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7880 (pm20) REVERT: A 1218 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6891 (pp) REVERT: B 466 MET cc_start: 0.5043 (ttm) cc_final: 0.4703 (ttm) outliers start: 64 outliers final: 39 residues processed: 214 average time/residue: 0.3836 time to fit residues: 92.9654 Evaluate side-chains 205 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 189 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 598 VAL 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 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 954 ILE Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1144 GLU 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 185 LEU Chi-restraints excluded: chain B residue 239 LEU 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 429 TYR Chi-restraints excluded: chain B residue 431 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 88 optimal weight: 0.0170 chunk 8 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 146 optimal weight: 20.0000 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 GLN ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.206884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.161859 restraints weight = 58358.103| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 6.63 r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4226 r_free = 0.4226 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4226 r_free = 0.4226 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.2922 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= 0.137 Angle : 0.727 14.332 17835 Z= 0.364 Chirality : 0.045 0.258 2001 Planarity : 0.004 0.060 2196 Dihedral : 17.128 171.945 2164 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % 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 are not related in a simple way. whole: -0.40 (0.22), residues: 1606 helix: 1.38 (0.22), residues: 618 sheet: 0.47 (0.37), residues: 195 loop : -1.90 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 101 TYR 0.063 0.002 TYR B 432 PHE 0.033 0.001 PHE A 197 TRP 0.047 0.002 TRP A 484 HIS 0.008 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (12977) covalent geometry : angle 0.72729 / 0.36 (17835) hydrogen bonds : bond 0.03324 / 2.31 ( 582) hydrogen bonds : angle 4.34922 / 3.05 ( 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 234 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 172 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6373 (OUTLIER) cc_final: 0.4933 (tpp) REVERT: A 94 MET cc_start: 0.7192 (ppp) cc_final: 0.6315 (pmm) REVERT: A 101 ARG cc_start: 0.8249 (ttm110) cc_final: 0.7798 (mtm-85) REVERT: A 189 ILE cc_start: 0.7139 (OUTLIER) cc_final: 0.6726 (mp) REVERT: A 460 LYS cc_start: 0.7289 (OUTLIER) cc_final: 0.6876 (tptp) REVERT: A 484 TRP cc_start: 0.6652 (p90) cc_final: 0.6431 (p90) REVERT: A 486 TRP cc_start: 0.5522 (p-90) cc_final: 0.4576 (t60) REVERT: A 620 TRP cc_start: 0.5668 (m100) cc_final: 0.4138 (m-90) REVERT: A 924 ARG cc_start: 0.6142 (OUTLIER) cc_final: 0.5442 (mmt-90) REVERT: A 1144 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7643 (pm20) REVERT: A 1192 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.5842 (mp0) REVERT: B 466 MET cc_start: 0.4093 (ttm) cc_final: 0.3884 (ttm) outliers start: 62 outliers final: 42 residues processed: 214 average time/residue: 0.4050 time to fit residues: 97.6925 Evaluate side-chains 212 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 164 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 139 PHE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 353 VAL 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 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 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 954 ILE 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 1144 GLU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1192 GLU 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 128 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 239 LEU 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 431 LYS Chi-restraints excluded: chain B residue 448 LEU 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: 0.0060 chunk 101 optimal weight: 10.0000 chunk 38 optimal weight: 0.0970 chunk 18 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 134 optimal weight: 20.0000 chunk 80 optimal weight: 0.9990 chunk 159 optimal weight: 50.0000 chunk 114 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.207298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.163066 restraints weight = 72654.836| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 8.35 r_work: 0.4001 rms_B_bonded: 7.66 restraints_weight: 2.0000 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4005 r_free = 0.4005 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4005 r_free = 0.4005 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.3012 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= 0.142 Angle : 0.781 15.264 17835 Z= 0.388 Chirality : 0.046 0.260 2001 Planarity : 0.004 0.060 2196 Dihedral : 17.101 170.635 2164 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 4.73 % Allowed : 30.81 % Favored : 64.46 % 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 are not related in a simple way. whole: -0.44 (0.22), residues: 1606 helix: 1.34 (0.22), residues: 616 sheet: 0.46 (0.37), residues: 195 loop : -1.91 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 101 TYR 0.035 0.002 TYR A 955 PHE 0.035 0.001 PHE A 197 TRP 0.048 0.002 TRP A 484 HIS 0.011 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (12977) covalent geometry : angle 0.78086 / 0.39 (17835) hydrogen bonds : bond 0.03300 / 2.29 ( 582) hydrogen bonds : angle 4.37938 / 3.07 ( 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 219 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 169 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6758 (OUTLIER) cc_final: 0.5098 (tpp) REVERT: A 94 MET cc_start: 0.7639 (ppp) cc_final: 0.6554 (pmm) REVERT: A 101 ARG cc_start: 0.8295 (ttm110) cc_final: 0.7837 (mtm-85) REVERT: A 486 TRP cc_start: 0.5798 (p-90) cc_final: 0.4728 (t60) REVERT: A 620 TRP cc_start: 0.5804 (m100) cc_final: 0.3870 (m-90) REVERT: A 924 ARG cc_start: 0.5995 (OUTLIER) cc_final: 0.5271 (mmt-90) REVERT: A 1109 LEU cc_start: 0.8334 (tp) cc_final: 0.8085 (tp) REVERT: A 1144 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7870 (pm20) REVERT: A 1192 GLU cc_start: 0.6207 (OUTLIER) cc_final: 0.5719 (mp0) REVERT: B 109 ASN cc_start: 0.6984 (m-40) cc_final: 0.6393 (m110) REVERT: B 466 MET cc_start: 0.4973 (ttm) cc_final: 0.4633 (ttm) outliers start: 50 outliers final: 37 residues processed: 202 average time/residue: 0.3881 time to fit residues: 88.8171 Evaluate side-chains 208 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 167 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 189 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 603 MET 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 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 954 ILE Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1192 GLU 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 128 VAL Chi-restraints excluded: chain B residue 185 LEU 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 429 TYR Chi-restraints excluded: chain B residue 448 LEU 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: 5.9990 chunk 4 optimal weight: 0.9990 chunk 154 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 127 optimal weight: 50.0000 chunk 112 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.205398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.160707 restraints weight = 52451.464| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 6.22 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4211 r_free = 0.4211 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4211 r_free = 0.4211 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12977 Z= 0.164 Angle : 0.790 14.328 17835 Z= 0.394 Chirality : 0.047 0.379 2001 Planarity : 0.005 0.059 2196 Dihedral : 17.128 170.350 2164 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 5.10 % Allowed : 30.43 % Favored : 64.46 % 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 are not related in a simple way. whole: -0.52 (0.21), residues: 1606 helix: 1.27 (0.22), residues: 615 sheet: 0.45 (0.37), residues: 195 loop : -1.97 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 823 TYR 0.036 0.002 TYR A 955 PHE 0.034 0.002 PHE A 197 TRP 0.037 0.002 TRP A 484 HIS 0.012 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (12977) covalent geometry : angle 0.78962 / 0.39 (17835) hydrogen bonds : bond 0.03516 / 2.44 ( 582) hydrogen bonds : angle 4.50718 / 3.17 ( 1625) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4838.16 seconds wall clock time: 83 minutes 10.76 seconds (4990.76 seconds total)