Starting phenix.real_space_refine on Sat Sep 12 00:33:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5l_29748/09_2026/8g5l_29748_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5l_29748/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8g5l_29748/09_2026/8g5l_29748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5l_29748/09_2026/8g5l_29748.map" model { file = "/net/cci-nas-00/data/ceres_data/8g5l_29748/09_2026/8g5l_29748_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5l_29748/09_2026/8g5l_29748_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 40 5.49 5 S 62 5.16 5 C 7844 2.51 5 N 2263 2.21 5 O 2414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: 3.24, 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: 1.26 Conformation dependent library (CDL) restraints added in 725.8 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: 2.03 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: 2.58 Time building geometry restraints manager: 1.56 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 1.20e-02 6.94e+03 7.35e+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: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.140 Find NCS groups from input model: 0.190 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:7.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.080 ------------------------------------------------------------------------------- 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= 0.362 Angle : 1.044 30.291 17835 Z= 0.599 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 1.04417 / 0.60 (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 : 0.397 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: 0.4653 time to fit residues: 132.6754 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 : 0.374 ------------------------------------------------------------------------------- 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 = 0.4787 r_free = 0.4787 target = 0.209425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.164793 restraints weight = 54929.301| |-----------------------------------------------------------------------------| r_work (start): 0.4258 rms_B_bonded: 6.51 r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4258 r_free = 0.4258 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4257 r_free = 0.4257 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.4257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12977 Z= 0.165 Angle : 0.742 11.480 17835 Z= 0.373 Chirality : 0.048 0.358 2001 Planarity : 0.005 0.058 2196 Dihedral : 17.758 175.655 2177 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 5.67 % Allowed : 25.52 % Favored : 68.81 % 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 0.039 0.002 TYR A 955 PHE 0.016 0.002 PHE A 539 TRP 0.029 0.002 TRP B 241 HIS 0.012 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (12977) covalent geometry : angle 0.74229 / 0.37 (17835) hydrogen bonds : bond 0.04279 / 2.91 ( 582) hydrogen bonds : angle 4.92287 / 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 : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 TRP cc_start: 0.5603 (p-90) cc_final: 0.4755 (t60) REVERT: A 487 ASP cc_start: 0.6576 (m-30) cc_final: 0.5161 (m-30) REVERT: A 551 LYS cc_start: 0.7774 (pttt) cc_final: 0.7530 (tmmt) REVERT: A 620 TRP cc_start: 0.5629 (m100) cc_final: 0.4133 (m-90) REVERT: A 924 ARG cc_start: 0.6095 (ttm-80) cc_final: 0.5431 (mmt-90) REVERT: A 971 HIS cc_start: 0.7560 (OUTLIER) cc_final: 0.7034 (m-70) REVERT: A 1121 GLU cc_start: 0.6937 (tp30) cc_final: 0.6728 (pt0) REVERT: A 1144 GLU cc_start: 0.7289 (pm20) cc_final: 0.7088 (pm20) REVERT: B 463 LYS cc_start: 0.8142 (mppt) cc_final: 0.7368 (mmmt) REVERT: B 466 MET cc_start: 0.4185 (ttm) cc_final: 0.3878 (ttm) outliers start: 60 outliers final: 22 residues processed: 231 average time/residue: 0.4381 time to fit residues: 113.2555 Evaluate side-chains 191 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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: 0.9980 chunk 123 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 46 optimal weight: 0.0270 chunk 119 optimal weight: 0.0980 chunk 8 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 159 optimal weight: 40.0000 chunk 138 optimal weight: 8.9990 overall best weight: 0.8240 ------------------------------------------------------------------------------- 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 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS B 400 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.208984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.164285 restraints weight = 59280.111| |-----------------------------------------------------------------------------| r_work (start): 0.4248 rms_B_bonded: 7.41 r_work: 0.4048 rms_B_bonded: 7.17 restraints_weight: 2.0000 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4052 r_free = 0.4052 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4052 r_free = 0.4052 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (5 function evaluations) r_final: 0.4052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12977 Z= 0.143 Angle : 0.716 18.436 17835 Z= 0.353 Chirality : 0.046 0.257 2001 Planarity : 0.005 0.057 2196 Dihedral : 17.385 177.248 2165 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 5.67 % Allowed : 27.41 % Favored : 66.92 % 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: -0.29 (0.21), residues: 1606 helix: 1.48 (0.21), residues: 612 sheet: 0.35 (0.36), residues: 207 loop : -1.79 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 101 TYR 0.041 0.002 TYR A 955 PHE 0.013 0.001 PHE B 254 TRP 0.019 0.001 TRP A 897 HIS 0.009 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (12977) covalent geometry : angle 0.71560 / 0.35 (17835) hydrogen bonds : bond 0.03644 / 2.48 ( 582) hydrogen bonds : angle 4.63798 / 3.23 ( 1625) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 185 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6809 (OUTLIER) cc_final: 0.4985 (tpp) REVERT: A 101 ARG cc_start: 0.8308 (ttm110) cc_final: 0.7865 (mtm-85) REVERT: A 157 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6733 (tp) REVERT: A 363 TYR cc_start: 0.6067 (m-80) cc_final: 0.5748 (m-80) REVERT: A 398 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.7023 (mm110) REVERT: A 486 TRP cc_start: 0.5909 (p-90) cc_final: 0.4793 (t60) REVERT: A 487 ASP cc_start: 0.6995 (m-30) cc_final: 0.5523 (m-30) REVERT: A 620 TRP cc_start: 0.5810 (m100) cc_final: 0.3890 (m-90) REVERT: A 924 ARG cc_start: 0.6066 (ttm-80) cc_final: 0.5346 (mmt-90) REVERT: A 1136 GLU cc_start: 0.7455 (tt0) cc_final: 0.7253 (pt0) REVERT: B 203 ARG cc_start: 0.7856 (mmp-170) cc_final: 0.7548 (mmp-170) REVERT: B 466 MET cc_start: 0.5309 (ttm) cc_final: 0.4879 (ttm) outliers start: 60 outliers final: 32 residues processed: 222 average time/residue: 0.3730 time to fit residues: 93.3079 Evaluate side-chains 201 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 596 MET 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 1079 ILE 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 115 TRP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 435 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 93 optimal weight: 0.3980 chunk 20 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** B 261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.208277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.164208 restraints weight = 54322.938| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 7.66 r_work: 0.4037 rms_B_bonded: 7.08 restraints_weight: 2.0000 r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4042 r_free = 0.4042 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4041 r_free = 0.4041 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12977 Z= 0.144 Angle : 0.702 13.668 17835 Z= 0.347 Chirality : 0.046 0.268 2001 Planarity : 0.004 0.057 2196 Dihedral : 17.311 179.272 2165 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 6.71 % Allowed : 27.13 % Favored : 66.16 % 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: -0.23 (0.21), residues: 1606 helix: 1.57 (0.21), residues: 607 sheet: 0.38 (0.36), residues: 207 loop : -1.77 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 823 TYR 0.046 0.002 TYR A 955 PHE 0.022 0.001 PHE A 197 TRP 0.017 0.001 TRP A 897 HIS 0.011 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (12977) covalent geometry : angle 0.70170 / 0.35 (17835) hydrogen bonds : bond 0.03485 / 2.38 ( 582) hydrogen bonds : angle 4.54306 / 3.17 ( 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 243 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 172 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6776 (OUTLIER) cc_final: 0.5064 (tpp) REVERT: A 101 ARG cc_start: 0.8339 (ttm110) cc_final: 0.7939 (mtm-85) REVERT: A 157 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6550 (tp) REVERT: A 363 TYR cc_start: 0.6013 (m-80) cc_final: 0.5666 (m-80) REVERT: A 398 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7087 (mm110) REVERT: A 486 TRP cc_start: 0.5812 (p-90) cc_final: 0.4786 (t60) REVERT: A 487 ASP cc_start: 0.7063 (m-30) cc_final: 0.5704 (m-30) REVERT: A 620 TRP cc_start: 0.5807 (m100) cc_final: 0.3897 (m-90) REVERT: A 924 ARG cc_start: 0.6078 (OUTLIER) cc_final: 0.5372 (mmt-90) REVERT: A 1079 ILE cc_start: 0.4828 (OUTLIER) cc_final: 0.4507 (tt) REVERT: A 1121 GLU cc_start: 0.7393 (tp30) cc_final: 0.6962 (pt0) REVERT: A 1144 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7694 (pm20) REVERT: B 463 LYS cc_start: 0.8422 (mppt) cc_final: 0.8181 (mppt) REVERT: B 465 MET cc_start: 0.7045 (mpt) cc_final: 0.6752 (mpm) REVERT: B 466 MET cc_start: 0.5213 (ttm) cc_final: 0.4789 (ttm) outliers start: 71 outliers final: 34 residues processed: 216 average time/residue: 0.4010 time to fit residues: 97.9498 Evaluate side-chains 205 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 165 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 151 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 211 LEU 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 432 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 924 ARG Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1079 ILE 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 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 235 THR Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 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: 0.6980 chunk 20 optimal weight: 1.9990 chunk 137 optimal weight: 20.0000 chunk 161 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 153 optimal weight: 30.0000 chunk 131 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 163 optimal weight: 20.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 569 HIS ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.202646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.156990 restraints weight = 58982.015| |-----------------------------------------------------------------------------| r_work (start): 0.4158 rms_B_bonded: 6.63 r_work: 0.3966 rms_B_bonded: 6.63 restraints_weight: 2.0000 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3969 r_free = 0.3969 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3969 r_free = 0.3969 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 12977 Z= 0.219 Angle : 0.750 13.697 17835 Z= 0.382 Chirality : 0.047 0.278 2001 Planarity : 0.005 0.057 2196 Dihedral : 17.402 179.299 2165 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 7.75 % Allowed : 26.75 % Favored : 65.50 % 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: 1.10 (0.21), residues: 619 sheet: 0.30 (0.36), residues: 207 loop : -1.96 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 259 TYR 0.048 0.002 TYR A 955 PHE 0.024 0.002 PHE A 197 TRP 0.014 0.002 TRP A 490 HIS 0.010 0.002 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.22 (12977) covalent geometry : angle 0.75032 / 0.38 (17835) hydrogen bonds : bond 0.04080 / 2.79 ( 582) hydrogen bonds : angle 4.83399 / 3.36 ( 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: 82 poor density : 167 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.6587 (ttt) REVERT: A 94 MET cc_start: 0.7425 (ppp) cc_final: 0.6250 (pmm) REVERT: A 101 ARG cc_start: 0.8312 (ttm110) cc_final: 0.7903 (mtm-85) REVERT: A 486 TRP cc_start: 0.5836 (p-90) cc_final: 0.4815 (t60) REVERT: A 924 ARG cc_start: 0.6180 (OUTLIER) cc_final: 0.5471 (mmt-90) REVERT: A 971 HIS cc_start: 0.7905 (OUTLIER) cc_final: 0.7435 (m-70) REVERT: A 1144 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7760 (pm20) REVERT: B 109 ASN cc_start: 0.6995 (m-40) cc_final: 0.6398 (m110) REVERT: B 463 LYS cc_start: 0.8399 (mppt) cc_final: 0.8148 (mppt) REVERT: B 466 MET cc_start: 0.5225 (ttm) cc_final: 0.4930 (ttm) outliers start: 82 outliers final: 42 residues processed: 222 average time/residue: 0.3797 time to fit residues: 95.5239 Evaluate side-chains 205 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 159 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 213 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 432 VAL 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 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 1144 GLU 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 70 LEU 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 377 CYS 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 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: 6.9990 chunk 80 optimal weight: 0.8980 chunk 162 optimal weight: 40.0000 chunk 15 optimal weight: 0.1980 chunk 117 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 201 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.205044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.160634 restraints weight = 58037.752| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 7.13 r_work: 0.3986 rms_B_bonded: 6.99 restraints_weight: 2.0000 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3990 r_free = 0.3990 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3990 r_free = 0.3990 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12977 Z= 0.147 Angle : 0.713 13.128 17835 Z= 0.355 Chirality : 0.046 0.267 2001 Planarity : 0.005 0.057 2196 Dihedral : 17.283 176.840 2165 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 6.62 % Allowed : 27.88 % Favored : 65.50 % 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: 1.30 (0.21), residues: 619 sheet: 0.33 (0.36), residues: 207 loop : -1.95 (0.22), residues: 780 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 0.036 0.002 PHE A 197 TRP 0.020 0.001 TRP A 490 HIS 0.011 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (12977) covalent geometry : angle 0.71257 / 0.36 (17835) hydrogen bonds : bond 0.03582 / 2.45 ( 582) hydrogen bonds : angle 4.61663 / 3.23 ( 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 246 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 176 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6727 (OUTLIER) cc_final: 0.5120 (tpp) REVERT: A 101 ARG cc_start: 0.8362 (ttm110) cc_final: 0.7975 (mtm-85) REVERT: A 460 LYS cc_start: 0.7285 (OUTLIER) cc_final: 0.6929 (tptp) REVERT: A 486 TRP cc_start: 0.5949 (p-90) cc_final: 0.4850 (t60) REVERT: A 487 ASP cc_start: 0.7079 (m-30) cc_final: 0.5719 (m-30) REVERT: A 620 TRP cc_start: 0.5735 (m100) cc_final: 0.3872 (m-90) REVERT: A 924 ARG cc_start: 0.6138 (OUTLIER) cc_final: 0.5350 (mmt-90) REVERT: A 1144 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7799 (pm20) REVERT: B 466 MET cc_start: 0.5251 (ttm) cc_final: 0.4872 (ttm) outliers start: 70 outliers final: 36 residues processed: 225 average time/residue: 0.4133 time to fit residues: 104.8710 Evaluate side-chains 202 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 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 415 LEU Chi-restraints excluded: chain A residue 432 VAL 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 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 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 B residue 86 LEU 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 250 GLN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 411 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 50.0000 chunk 46 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 chunk 65 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS ** A 970 ASN ** 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 = 0.4743 r_free = 0.4743 target = 0.205318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.160361 restraints weight = 67110.939| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 7.82 r_work: 0.3976 rms_B_bonded: 7.46 restraints_weight: 2.0000 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3979 r_free = 0.3979 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3979 r_free = 0.3979 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12977 Z= 0.144 Angle : 0.727 13.615 17835 Z= 0.361 Chirality : 0.045 0.272 2001 Planarity : 0.005 0.058 2196 Dihedral : 17.223 175.412 2165 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 7.09 % Allowed : 27.88 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.21), residues: 1606 helix: 1.32 (0.21), residues: 618 sheet: 0.41 (0.37), residues: 197 loop : -1.94 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 823 TYR 0.041 0.002 TYR A 955 PHE 0.035 0.001 PHE A 197 TRP 0.034 0.002 TRP A 484 HIS 0.010 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (12977) covalent geometry : angle 0.72738 / 0.36 (17835) hydrogen bonds : bond 0.03460 / 2.37 ( 582) hydrogen bonds : angle 4.52007 / 3.16 ( 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 249 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 174 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6722 (OUTLIER) cc_final: 0.5079 (tpp) REVERT: A 94 MET cc_start: 0.7557 (ppp) cc_final: 0.6400 (pmm) REVERT: A 142 LEU cc_start: 0.7691 (mt) cc_final: 0.7368 (mp) REVERT: A 460 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6921 (tptp) REVERT: A 486 TRP cc_start: 0.5935 (p-90) cc_final: 0.4732 (t60) REVERT: A 779 LEU cc_start: 0.5299 (OUTLIER) cc_final: 0.4971 (tt) REVERT: A 924 ARG cc_start: 0.6118 (OUTLIER) cc_final: 0.5320 (mmt-90) REVERT: A 971 HIS cc_start: 0.7857 (OUTLIER) cc_final: 0.7432 (m-70) REVERT: A 1144 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7888 (pm20) REVERT: A 1218 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6980 (pp) REVERT: B 432 TYR cc_start: 0.6562 (m-80) cc_final: 0.6259 (m-80) REVERT: B 463 LYS cc_start: 0.8335 (mppt) cc_final: 0.8073 (mppt) REVERT: B 466 MET cc_start: 0.5105 (ttm) cc_final: 0.4712 (ttm) outliers start: 75 outliers final: 42 residues processed: 224 average time/residue: 0.4093 time to fit residues: 103.3370 Evaluate side-chains 213 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 164 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 432 VAL 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 742 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 779 LEU 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 1140 LEU Chi-restraints excluded: chain A residue 1144 GLU 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 A residue 1218 LEU Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 115 TRP 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 250 GLN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 411 ILE 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: 2.9990 chunk 137 optimal weight: 20.0000 chunk 122 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 23 optimal weight: 0.3980 chunk 81 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 20.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 ** 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 = 0.4723 r_free = 0.4723 target = 0.202882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.158100 restraints weight = 69489.863| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 8.11 r_work: 0.3939 rms_B_bonded: 7.44 restraints_weight: 2.0000 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3941 r_free = 0.3941 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3941 r_free = 0.3941 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.2861 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= 0.182 Angle : 0.752 13.955 17835 Z= 0.378 Chirality : 0.047 0.279 2001 Planarity : 0.005 0.058 2196 Dihedral : 17.260 174.826 2165 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 6.33 % Allowed : 29.21 % 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: -0.57 (0.21), residues: 1606 helix: 1.23 (0.22), residues: 616 sheet: 0.30 (0.36), residues: 207 loop : -1.99 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 101 TYR 0.042 0.002 TYR A 955 PHE 0.035 0.002 PHE A 197 TRP 0.044 0.002 TRP A 484 HIS 0.010 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (12977) covalent geometry : angle 0.75199 / 0.38 (17835) hydrogen bonds : bond 0.03749 / 2.58 ( 582) hydrogen bonds : angle 4.62300 / 3.23 ( 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 239 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 172 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.5129 (tpp) REVERT: A 94 MET cc_start: 0.7713 (ppp) cc_final: 0.6569 (pmm) REVERT: A 101 ARG cc_start: 0.8214 (ttm110) cc_final: 0.7754 (mtm-85) REVERT: A 142 LEU cc_start: 0.7680 (mt) cc_final: 0.7337 (mp) REVERT: A 460 LYS cc_start: 0.7304 (OUTLIER) cc_final: 0.6954 (tptp) REVERT: A 486 TRP cc_start: 0.5924 (p-90) cc_final: 0.4769 (t60) REVERT: A 924 ARG cc_start: 0.6153 (OUTLIER) cc_final: 0.5325 (mmt-90) REVERT: A 971 HIS cc_start: 0.7909 (OUTLIER) cc_final: 0.7467 (m-70) REVERT: A 1144 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7920 (pm20) REVERT: A 1218 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.7075 (pp) REVERT: B 109 ASN cc_start: 0.6970 (m-40) cc_final: 0.6447 (m110) REVERT: B 432 TYR cc_start: 0.6598 (m-80) cc_final: 0.6126 (m-80) REVERT: B 463 LYS cc_start: 0.8354 (mppt) cc_final: 0.8132 (mppt) REVERT: B 466 MET cc_start: 0.5168 (ttm) cc_final: 0.4891 (ttm) outliers start: 67 outliers final: 47 residues processed: 216 average time/residue: 0.4387 time to fit residues: 106.3403 Evaluate side-chains 214 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 161 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 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 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 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 1206 MET Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 235 THR 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 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: 1.9990 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 427 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.204770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.161399 restraints weight = 58845.018| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 7.28 r_work: 0.3990 rms_B_bonded: 6.93 restraints_weight: 2.0000 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3995 r_free = 0.3995 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3995 r_free = 0.3995 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12977 Z= 0.147 Angle : 0.758 14.368 17835 Z= 0.379 Chirality : 0.045 0.275 2001 Planarity : 0.005 0.060 2196 Dihedral : 17.157 173.092 2164 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 6.33 % Allowed : 29.11 % Favored : 64.56 % 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: 1.36 (0.22), residues: 615 sheet: 0.34 (0.38), residues: 197 loop : -1.97 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1071 TYR 0.040 0.002 TYR A 955 PHE 0.035 0.001 PHE A 197 TRP 0.051 0.002 TRP A 484 HIS 0.011 0.001 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (12977) covalent geometry : angle 0.75771 / 0.38 (17835) hydrogen bonds : bond 0.03418 / 2.34 ( 582) hydrogen bonds : angle 4.52160 / 3.15 ( 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 240 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 173 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6716 (OUTLIER) cc_final: 0.5030 (tpp) REVERT: A 94 MET cc_start: 0.7566 (ppp) cc_final: 0.6547 (pmm) REVERT: A 101 ARG cc_start: 0.8223 (ttm110) cc_final: 0.7788 (mtm-85) REVERT: A 460 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.7004 (tptp) REVERT: A 486 TRP cc_start: 0.5898 (p-90) cc_final: 0.4720 (t60) REVERT: A 779 LEU cc_start: 0.5419 (OUTLIER) cc_final: 0.4983 (tt) REVERT: A 924 ARG cc_start: 0.6054 (OUTLIER) cc_final: 0.5310 (mmt-90) REVERT: A 971 HIS cc_start: 0.7851 (OUTLIER) cc_final: 0.7419 (m-70) REVERT: A 1136 GLU cc_start: 0.7532 (pt0) cc_final: 0.7212 (tm-30) REVERT: A 1144 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7916 (pm20) REVERT: A 1218 LEU cc_start: 0.7132 (OUTLIER) cc_final: 0.6904 (pp) REVERT: B 109 ASN cc_start: 0.6998 (m-40) cc_final: 0.6384 (m110) REVERT: B 432 TYR cc_start: 0.6307 (m-80) cc_final: 0.5635 (m-80) REVERT: B 466 MET cc_start: 0.5123 (ttm) cc_final: 0.4720 (ttm) outliers start: 67 outliers final: 43 residues processed: 218 average time/residue: 0.4102 time to fit residues: 101.0040 Evaluate side-chains 213 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 163 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 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 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 B residue 86 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 235 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 151 optimal weight: 50.0000 chunk 72 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 134 optimal weight: 20.0000 chunk 80 optimal weight: 0.7980 chunk 159 optimal weight: 50.0000 chunk 114 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS ** A 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 976 GLN ** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.196199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.148995 restraints weight = 73164.013| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 7.25 r_work: 0.3857 rms_B_bonded: 6.94 restraints_weight: 2.0000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3860 r_free = 0.3860 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3860 r_free = 0.3860 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.126 12977 Z= 0.337 Angle : 0.931 14.282 17835 Z= 0.479 Chirality : 0.055 0.293 2001 Planarity : 0.007 0.065 2196 Dihedral : 17.500 176.513 2164 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 6.33 % Allowed : 29.11 % Favored : 64.56 % 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: -1.31 (0.20), residues: 1606 helix: 0.45 (0.21), residues: 614 sheet: 0.28 (0.37), residues: 194 loop : -2.34 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 574 TYR 0.047 0.003 TYR A 955 PHE 0.034 0.003 PHE A 197 TRP 0.062 0.004 TRP A 620 HIS 0.012 0.002 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00773 / 0.34 (12977) covalent geometry : angle 0.93119 / 0.48 (17835) hydrogen bonds : bond 0.05156 / 3.57 ( 582) hydrogen bonds : angle 5.37142 / 3.75 ( 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 224 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 157 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6800 (OUTLIER) cc_final: 0.6547 (ttp) REVERT: A 94 MET cc_start: 0.7798 (ppp) cc_final: 0.6876 (pmm) REVERT: A 101 ARG cc_start: 0.8246 (ttm110) cc_final: 0.7841 (mtm-85) REVERT: A 423 THR cc_start: 0.8028 (OUTLIER) cc_final: 0.7668 (m) REVERT: A 460 LYS cc_start: 0.7538 (OUTLIER) cc_final: 0.7211 (tptp) REVERT: A 486 TRP cc_start: 0.6049 (p-90) cc_final: 0.4852 (t60) REVERT: A 924 ARG cc_start: 0.6286 (OUTLIER) cc_final: 0.5603 (mmt-90) REVERT: A 1103 SER cc_start: 0.6240 (OUTLIER) cc_final: 0.5789 (t) REVERT: A 1136 GLU cc_start: 0.7735 (pt0) cc_final: 0.7462 (tm-30) REVERT: A 1144 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8117 (pm20) REVERT: B 109 ASN cc_start: 0.7240 (m-40) cc_final: 0.6964 (m-40) REVERT: B 203 ARG cc_start: 0.8077 (mmp-170) cc_final: 0.7788 (mmp-170) REVERT: B 466 MET cc_start: 0.5276 (ttm) cc_final: 0.5042 (ttm) outliers start: 67 outliers final: 39 residues processed: 207 average time/residue: 0.4440 time to fit residues: 103.1709 Evaluate side-chains 197 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 152 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 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 460 LYS Chi-restraints excluded: chain A residue 593 SER 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 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 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 B residue 99 PHE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 235 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 150 optimal weight: 10.0000 chunk 4 optimal weight: 0.0050 chunk 154 optimal weight: 7.9990 chunk 36 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 127 optimal weight: 40.0000 chunk 112 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN A 270 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.198854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.152918 restraints weight = 54682.029| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 6.23 r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4115 r_free = 0.4115 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4115 r_free = 0.4115 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 12977 Z= 0.224 Angle : 0.865 14.778 17835 Z= 0.435 Chirality : 0.050 0.291 2001 Planarity : 0.006 0.058 2196 Dihedral : 17.368 174.210 2163 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 5.48 % Allowed : 30.81 % Favored : 63.71 % 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: -1.11 (0.21), residues: 1606 helix: 0.74 (0.21), residues: 606 sheet: 0.10 (0.37), residues: 204 loop : -2.25 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 574 TYR 0.045 0.003 TYR A 955 PHE 0.035 0.002 PHE A 197 TRP 0.088 0.003 TRP A 620 HIS 0.013 0.002 HIS A 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.22 (12977) covalent geometry : angle 0.86514 / 0.43 (17835) hydrogen bonds : bond 0.04211 / 2.88 ( 582) hydrogen bonds : angle 5.13507 / 3.58 ( 1625) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5396.45 seconds wall clock time: 92 minutes 35.23 seconds (5555.23 seconds total)