Starting phenix.real_space_refine on Thu May 15 02:10:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5l_29748/05_2025/8g5l_29748_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5l_29748/05_2025/8g5l_29748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g5l_29748/05_2025/8g5l_29748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5l_29748/05_2025/8g5l_29748.map" model { file = "/net/cci-nas-00/data/ceres_data/8g5l_29748/05_2025/8g5l_29748_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5l_29748/05_2025/8g5l_29748_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.014 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 9} 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: {'GLN:plan1': 13, 'HIS:plan': 15, 'TYR:plan': 11, 'ASN:plan1': 16, 'TRP:plan': 10, 'ASP:plan': 15, 'PHE:plan': 15, 'GLU:plan': 23, 'ARG:plan': 20} 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: 8.95, per 1000 atoms: 0.71 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: 3.53 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 4.68 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: 5.60 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.25: 2046 1.25 - 1.44: 3612 1.44 - 1.63: 7217 1.63 - 1.82: 101 1.82 - 2.01: 1 Bond restraints: 12977 Sorted by residual: bond pdb=" CG PRO B 270 " pdb=" CD PRO B 270 " ideal model delta sigma weight residual 1.503 1.063 0.440 3.40e-02 8.65e+02 1.67e+02 bond pdb=" CG PRO A 611 " pdb=" CD PRO A 611 " ideal model delta sigma weight residual 1.503 1.113 0.390 3.40e-02 8.65e+02 1.31e+02 bond pdb=" CB PRO B 270 " pdb=" CG PRO B 270 " ideal model delta sigma weight residual 1.492 2.012 -0.520 5.00e-02 4.00e+02 1.08e+02 bond pdb=" O3' DG P 28 " pdb=" P B DA P 29 " ideal model delta sigma weight residual 1.607 1.710 -0.103 1.50e-02 4.44e+03 4.71e+01 bond pdb=" CA PRO B 270 " pdb=" CB PRO B 270 " ideal model delta sigma weight residual 1.533 1.447 0.086 1.42e-02 4.96e+03 3.67e+01 ... (remaining 12972 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.06: 17781 6.06 - 12.12: 45 12.12 - 18.17: 4 18.17 - 24.23: 2 24.23 - 30.29: 3 Bond angle restraints: 17835 Sorted by residual: angle pdb=" N PRO B 270 " pdb=" CD PRO B 270 " pdb=" CG PRO B 270 " ideal model delta sigma weight residual 103.20 76.86 26.34 1.50e+00 4.44e-01 3.08e+02 angle pdb=" CA PRO B 270 " pdb=" CB PRO B 270 " pdb=" CG PRO B 270 " ideal model delta sigma weight residual 104.50 74.21 30.29 1.90e+00 2.77e-01 2.54e+02 angle pdb=" N PRO A 611 " pdb=" CD PRO A 611 " pdb=" CG PRO A 611 " ideal model delta sigma weight residual 103.20 81.89 21.31 1.50e+00 4.44e-01 2.02e+02 angle pdb=" CA PRO A 611 " pdb=" CB PRO A 611 " pdb=" CG PRO A 611 " ideal model delta sigma weight residual 104.50 80.80 23.70 1.90e+00 2.77e-01 1.56e+02 angle pdb=" N PRO B 270 " pdb=" CA PRO B 270 " pdb=" CB PRO B 270 " ideal model delta sigma weight residual 103.25 93.04 10.21 1.05e+00 9.07e-01 9.46e+01 ... (remaining 17830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.08: 7186 35.08 - 70.16: 374 70.16 - 105.24: 9 105.24 - 140.32: 1 140.32 - 175.39: 3 Dihedral angle restraints: 7573 sinusoidal: 2878 harmonic: 4695 Sorted by residual: dihedral pdb=" CA SER A 218 " pdb=" C SER A 218 " pdb=" N ALA A 219 " pdb=" CA ALA A 219 " ideal model delta harmonic sigma weight residual -180.00 -156.88 -23.12 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA ARG A 275 " pdb=" C ARG A 275 " pdb=" N ALA A 276 " pdb=" CA ALA A 276 " ideal model delta harmonic sigma weight residual 180.00 157.19 22.81 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA PRO B 270 " pdb=" CB PRO B 270 " pdb=" CG PRO B 270 " pdb=" CD PRO B 270 " ideal model delta sinusoidal sigma weight residual -38.00 -108.84 70.84 1 2.00e+01 2.50e-03 1.61e+01 ... (remaining 7570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 1951 0.126 - 0.252: 22 0.252 - 0.378: 0 0.378 - 0.505: 25 0.505 - 0.631: 3 Chirality restraints: 2001 Sorted by residual: chirality pdb=" P DC T 3 " pdb=" OP1 DC T 3 " pdb=" OP2 DC T 3 " pdb=" O5' DC T 3 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.63 2.00e-01 2.50e+01 9.95e+00 chirality pdb=" P DG T 9 " pdb=" OP1 DG T 9 " pdb=" OP2 DG T 9 " pdb=" O5' DG T 9 " both_signs ideal model delta sigma weight residual True 2.35 -2.87 -0.52 2.00e-01 2.50e+01 6.75e+00 chirality pdb=" P DC T 5 " pdb=" OP1 DC T 5 " pdb=" OP2 DC T 5 " pdb=" O5' DC T 5 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.52 2.00e-01 2.50e+01 6.68e+00 ... (remaining 1998 not shown) Planarity restraints: 2196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 126 " -0.224 9.50e-02 1.11e+02 1.01e-01 6.49e+00 pdb=" NE ARG A 126 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 126 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 126 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 126 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 828 " 0.042 5.00e-02 4.00e+02 6.33e-02 6.40e+00 pdb=" N PRO A 829 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 829 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 829 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 560 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.73e+00 pdb=" C PRO A 560 " -0.038 2.00e-02 2.50e+03 pdb=" O PRO A 560 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS A 561 " 0.013 2.00e-02 2.50e+03 ... (remaining 2193 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 203 2.64 - 3.20: 11755 3.20 - 3.77: 20109 3.77 - 4.33: 26065 4.33 - 4.90: 42184 Nonbonded interactions: 100316 Sorted by model distance: nonbonded pdb=" O ASP A 293 " pdb=" OG SER A 296 " model vdw 2.075 3.040 nonbonded pdb=" O HIS A 805 " pdb=" OG SER A 809 " model vdw 2.083 3.040 nonbonded pdb=" NH1 ARG A1142 " pdb=" OE2 GLU A1144 " model vdw 2.183 3.120 nonbonded pdb=" O TYR B 349 " pdb=" OG SER B 353 " model vdw 2.204 3.040 nonbonded pdb=" O LEU A1083 " pdb=" NH1 ARG A1096 " model vdw 2.206 3.120 ... (remaining 100311 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 68 through 80 and (name N or name CA or name C or name O \ or name CB )) or resid 81 or (resid 82 through 93 and (name N or name CA or name \ C or name O or name CB )) or resid 94 or (resid 95 through 97 and (name N or na \ me CA or name C or name O or name CB )) or resid 98 or (resid 99 and (name N or \ name CA or name C or name O or name CB )) or resid 100 or (resid 101 through 102 \ and (name N or name CA or name C or name O or name CB )) or resid 103 or (resid \ 104 through 135 and (name N or name CA or name C or name O or name CB )) or res \ id 136 or (resid 180 through 187 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 188 through 206 and (name N or name CA or name C or name O o \ r name CB )) or resid 207 or (resid 208 through 211 and (name N or name CA or na \ me C or name O or name CB )) or resid 212 or (resid 213 through 219 and (name N \ or name CA or name C or name O or name CB )) or (resid 229 through 231 and (name \ N or name CA or name C or name O or name CB )) or resid 232 or (resid 233 throu \ gh 282 and (name N or name CA or name C or name O or name CB )) or resid 283 or \ (resid 284 through 285 and (name N or name CA or name C or name O or name CB )) \ or resid 286 or (resid 287 through 295 and (name N or name CA or name C or name \ O or name CB )) or resid 296 or (resid 297 through 306 and (name N or name CA or \ name C or name O or name CB )) or resid 307 or (resid 308 through 316 and (name \ N or name CA or name C or name O or name CB )) or resid 317 or (resid 318 throu \ gh 323 and (name N or name CA or name C or name O or name CB )) or resid 324 or \ (resid 325 through 326 and (name N or name CA or name C or name O or name CB )) \ or resid 327 or (resid 328 through 339 and (name N or name CA or name C or name \ O or name CB )) or resid 340 or (resid 341 through 344 and (name N or name CA or \ name C or name O or name CB )) or resid 345 or (resid 346 through 355 and (name \ N or name CA or name C or name O or name CB )) or (resid 368 through 387 and (n \ ame N or name CA or name C or name O or name CB )) or resid 388 or (resid 389 an \ d (name N or name CA or name C or name O or name CB )) or resid 390 or (resid 39 \ 1 through 400 and (name N or name CA or name C or name O or name CB )) or resid \ 401 or (resid 402 through 409 and (name N or name CA or name C or name O or name \ CB )) or resid 410 or (resid 411 through 415 and (name N or name CA or name C o \ r name O or name CB )) or resid 416 or (resid 417 through 450 and (name N or nam \ e CA or name C or name O or name CB )) or resid 451 or (resid 452 through 485 an \ d (name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 68 through 136 or resid 180 through 219 or resid 229 throu \ gh 485)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 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: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 37.650 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5369 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.520 12977 Z= 0.317 Angle : 1.044 30.291 17835 Z= 0.566 Chirality : 0.071 0.631 2001 Planarity : 0.005 0.101 2196 Dihedral : 18.588 175.394 4537 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.07 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (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 TRP 0.032 0.001 TRP A 897 HIS 0.007 0.001 HIS A 420 PHE 0.035 0.001 PHE A 949 TYR 0.012 0.001 TYR A 614 ARG 0.009 0.001 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.13162 ( 582) hydrogen bonds : angle 6.72257 ( 1625) covalent geometry : bond 0.00880 (12977) covalent geometry : angle 1.04406 (17835) *********************** 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 : 1.319 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: 0.8056 (t) REVERT: A 924 ARG cc_start: 0.6129 (ttm-80) cc_final: 0.5595 (mmt-90) outliers start: 23 outliers final: 15 residues processed: 257 average time/residue: 0.9608 time to fit residues: 274.7062 Evaluate side-chains 186 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 1.332 ------------------------------------------------------------------------------- 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 139 optimal weight: 20.0000 chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 129 optimal weight: 40.0000 chunk 50 optimal weight: 0.0270 chunk 78 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 ASN A 493 GLN A 565 HIS A 803 ASN A 811 GLN A 906 HIS A 959 GLN A 975 GLN A1157 ASN B 216 HIS B 400 GLN B 422 GLN B 427 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.209102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.163356 restraints weight = 66526.846| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 7.22 r_work: 0.4044 rms_B_bonded: 7.09 restraints_weight: 2.0000 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4050 r_free = 0.4050 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4049 r_free = 0.4049 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12977 Z= 0.163 Angle : 0.719 11.291 17835 Z= 0.359 Chirality : 0.044 0.325 2001 Planarity : 0.005 0.059 2196 Dihedral : 17.623 175.285 2177 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 5.58 % Allowed : 25.24 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.21), residues: 1606 helix: 1.55 (0.21), residues: 612 sheet: 0.35 (0.36), residues: 201 loop : -1.83 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 897 HIS 0.011 0.001 HIS A 360 PHE 0.016 0.001 PHE B 254 TYR 0.042 0.002 TYR A 955 ARG 0.003 0.000 ARG B 344 Details of bonding type rmsd hydrogen bonds : bond 0.03964 ( 582) hydrogen bonds : angle 4.72436 ( 1625) covalent geometry : bond 0.00362 (12977) covalent geometry : angle 0.71914 (17835) *********************** 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 242 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 183 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8298 (ttm110) cc_final: 0.7808 (mtm-85) REVERT: A 486 TRP cc_start: 0.5923 (p-90) cc_final: 0.4846 (t60) REVERT: A 487 ASP cc_start: 0.7090 (m-30) cc_final: 0.5617 (m-30) REVERT: A 551 LYS cc_start: 0.7913 (pttt) cc_final: 0.7708 (tmmt) REVERT: A 620 TRP cc_start: 0.5820 (m100) cc_final: 0.3963 (m-90) REVERT: A 924 ARG cc_start: 0.6069 (ttm-80) cc_final: 0.5383 (mmt-90) REVERT: A 971 HIS cc_start: 0.7716 (OUTLIER) cc_final: 0.7193 (m-70) REVERT: A 1121 GLU cc_start: 0.7360 (tp30) cc_final: 0.6962 (pt0) REVERT: B 466 MET cc_start: 0.5325 (ttm) cc_final: 0.4910 (ttm) outliers start: 59 outliers final: 22 residues processed: 226 average time/residue: 0.8905 time to fit residues: 225.1424 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 : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 913 CYS Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 395 LEU 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 55 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 152 optimal weight: 30.0000 chunk 37 optimal weight: 0.2980 chunk 88 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS A 569 HIS A 959 GLN ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.208727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.162973 restraints weight = 76605.833| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 9.30 r_work: 0.3990 rms_B_bonded: 8.24 restraints_weight: 2.0000 r_work: 0.4144 rms_B_bonded: 5.15 restraints_weight: 4.0000 r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4148 r_free = 0.4148 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4148 r_free = 0.4148 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.4148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12977 Z= 0.144 Angle : 0.691 13.333 17835 Z= 0.341 Chirality : 0.043 0.157 2001 Planarity : 0.004 0.058 2196 Dihedral : 17.276 178.745 2165 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 6.62 % Allowed : 25.99 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.21), residues: 1606 helix: 1.55 (0.21), residues: 608 sheet: 0.39 (0.36), residues: 207 loop : -1.76 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 897 HIS 0.010 0.001 HIS A 360 PHE 0.017 0.001 PHE A 197 TYR 0.039 0.002 TYR A 955 ARG 0.008 0.000 ARG A1146 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 582) hydrogen bonds : angle 4.50204 ( 1625) covalent geometry : bond 0.00320 (12977) covalent geometry : angle 0.69075 (17835) *********************** 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 251 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 181 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6662 (OUTLIER) cc_final: 0.4981 (tpp) REVERT: A 157 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6742 (tp) REVERT: A 297 MET cc_start: 0.6630 (OUTLIER) cc_final: 0.6036 (mtm) REVERT: A 363 TYR cc_start: 0.5998 (m-80) cc_final: 0.5716 (m-80) REVERT: A 486 TRP cc_start: 0.5755 (p-90) cc_final: 0.4746 (t60) REVERT: A 487 ASP cc_start: 0.6906 (m-30) cc_final: 0.5442 (m-30) REVERT: A 620 TRP cc_start: 0.5703 (m100) cc_final: 0.3934 (m-90) REVERT: A 924 ARG cc_start: 0.6125 (ttm-80) cc_final: 0.5426 (mmt-90) REVERT: A 1121 GLU cc_start: 0.7247 (tp30) cc_final: 0.6905 (pt0) REVERT: B 201 ASN cc_start: 0.7328 (OUTLIER) cc_final: 0.7104 (t0) REVERT: B 203 ARG cc_start: 0.7895 (mmm160) cc_final: 0.7551 (mmm160) REVERT: B 463 LYS cc_start: 0.8261 (mppt) cc_final: 0.7491 (mmmt) REVERT: B 466 MET cc_start: 0.5021 (ttm) cc_final: 0.4648 (ttm) outliers start: 70 outliers final: 30 residues processed: 227 average time/residue: 0.8278 time to fit residues: 211.5781 Evaluate side-chains 203 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 873 GLU Chi-restraints excluded: chain A residue 913 CYS Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 448 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 92 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 144 optimal weight: 30.0000 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 148 optimal weight: 20.0000 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN A 565 HIS ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.203541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.158728 restraints weight = 53940.516| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 7.18 r_work: 0.3965 rms_B_bonded: 6.83 restraints_weight: 2.0000 r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3968 r_free = 0.3968 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3968 r_free = 0.3968 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 12977 Z= 0.203 Angle : 0.734 13.335 17835 Z= 0.368 Chirality : 0.045 0.180 2001 Planarity : 0.005 0.060 2196 Dihedral : 17.296 179.691 2165 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 6.81 % Allowed : 26.94 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.21), residues: 1606 helix: 1.24 (0.21), residues: 615 sheet: 0.30 (0.36), residues: 209 loop : -1.88 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 897 HIS 0.011 0.002 HIS A 360 PHE 0.022 0.002 PHE B 254 TYR 0.042 0.002 TYR A 955 ARG 0.007 0.001 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.03947 ( 582) hydrogen bonds : angle 4.70815 ( 1625) covalent geometry : bond 0.00459 (12977) covalent geometry : angle 0.73426 (17835) *********************** 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 242 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 170 time to evaluate : 1.401 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6531 (ttt) REVERT: A 94 MET cc_start: 0.7517 (ppp) cc_final: 0.6402 (pmm) REVERT: A 101 ARG cc_start: 0.8384 (ttm110) cc_final: 0.8035 (mtm110) REVERT: A 297 MET cc_start: 0.6892 (OUTLIER) cc_final: 0.6296 (mtm) REVERT: A 486 TRP cc_start: 0.5933 (p-90) cc_final: 0.4908 (t60) REVERT: A 487 ASP cc_start: 0.7136 (m-30) cc_final: 0.5697 (m-30) REVERT: A 779 LEU cc_start: 0.5326 (OUTLIER) cc_final: 0.4859 (tt) REVERT: A 924 ARG cc_start: 0.6187 (ttm-80) cc_final: 0.5437 (mmt-90) REVERT: A 971 HIS cc_start: 0.7943 (OUTLIER) cc_final: 0.7495 (m-70) REVERT: A 1121 GLU cc_start: 0.7473 (tp30) cc_final: 0.7108 (pt0) REVERT: B 109 ASN cc_start: 0.6931 (m-40) cc_final: 0.6292 (m110) REVERT: B 203 ARG cc_start: 0.7954 (mmm160) cc_final: 0.7732 (mmp-170) REVERT: B 466 MET cc_start: 0.5261 (ttm) cc_final: 0.4886 (ttm) outliers start: 72 outliers final: 35 residues processed: 218 average time/residue: 0.9125 time to fit residues: 223.1577 Evaluate side-chains 195 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 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 608 ASP Chi-restraints excluded: chain A residue 742 VAL 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 954 ILE Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 429 TYR 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 88 optimal weight: 0.0070 chunk 37 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 152 optimal weight: 9.9990 chunk 116 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 39 optimal weight: 9.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 GLN A 565 HIS ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.206975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.162297 restraints weight = 53070.513| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 6.36 r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4232 r_free = 0.4232 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4232 r_free = 0.4232 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.4232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12977 Z= 0.132 Angle : 0.686 12.743 17835 Z= 0.339 Chirality : 0.043 0.180 2001 Planarity : 0.004 0.060 2196 Dihedral : 17.079 176.545 2164 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 6.33 % Allowed : 27.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.22), residues: 1606 helix: 1.44 (0.22), residues: 616 sheet: 0.53 (0.36), residues: 204 loop : -1.87 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 897 HIS 0.010 0.001 HIS A 360 PHE 0.030 0.001 PHE A 197 TYR 0.036 0.002 TYR A 955 ARG 0.007 0.000 ARG A1071 Details of bonding type rmsd hydrogen bonds : bond 0.03238 ( 582) hydrogen bonds : angle 4.38574 ( 1625) covalent geometry : bond 0.00286 (12977) covalent geometry : angle 0.68554 (17835) *********************** 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 241 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 174 time to evaluate : 1.332 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.6333 (OUTLIER) cc_final: 0.4970 (tpp) REVERT: A 101 ARG cc_start: 0.8299 (ttm110) cc_final: 0.7870 (mtm-85) REVERT: A 297 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.6078 (mtm) REVERT: A 460 LYS cc_start: 0.7219 (OUTLIER) cc_final: 0.6903 (tptp) REVERT: A 486 TRP cc_start: 0.5599 (p-90) cc_final: 0.4721 (t60) REVERT: A 487 ASP cc_start: 0.6655 (m-30) cc_final: 0.5271 (m-30) REVERT: A 620 TRP cc_start: 0.5759 (m100) cc_final: 0.4179 (m-90) REVERT: A 774 MET cc_start: 0.6660 (OUTLIER) cc_final: 0.6370 (tpp) REVERT: A 924 ARG cc_start: 0.6163 (ttm-80) cc_final: 0.5451 (mmt-90) REVERT: A 1121 GLU cc_start: 0.7042 (tp30) cc_final: 0.6761 (pt0) REVERT: A 1144 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7574 (pm20) REVERT: B 434 GLU cc_start: 0.6221 (mt-10) cc_final: 0.6008 (mt-10) REVERT: B 463 LYS cc_start: 0.8163 (mptt) cc_final: 0.7513 (mmmt) outliers start: 67 outliers final: 27 residues processed: 222 average time/residue: 0.8517 time to fit residues: 215.2121 Evaluate side-chains 199 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 485 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 141 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 112 optimal weight: 0.0970 chunk 64 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS B 366 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.204390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.158312 restraints weight = 77320.557| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 8.84 r_work: 0.3924 rms_B_bonded: 8.03 restraints_weight: 2.0000 r_work: 0.4075 rms_B_bonded: 5.11 restraints_weight: 4.0000 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4077 r_free = 0.4077 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4077 r_free = 0.4077 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.4077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 12977 Z= 0.165 Angle : 0.695 13.474 17835 Z= 0.347 Chirality : 0.044 0.174 2001 Planarity : 0.004 0.060 2196 Dihedral : 17.071 176.638 2164 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 6.52 % Allowed : 27.50 % Favored : 65.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.21), residues: 1606 helix: 1.45 (0.22), residues: 615 sheet: 0.41 (0.36), residues: 207 loop : -1.93 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 484 HIS 0.011 0.001 HIS A 360 PHE 0.032 0.002 PHE A 197 TYR 0.037 0.002 TYR A 955 ARG 0.007 0.000 ARG A1071 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 582) hydrogen bonds : angle 4.47166 ( 1625) covalent geometry : bond 0.00375 (12977) covalent geometry : angle 0.69544 (17835) *********************** 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 240 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 171 time to evaluate : 1.496 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.6690 (OUTLIER) cc_final: 0.5121 (tpp) REVERT: A 94 MET cc_start: 0.7485 (ppp) cc_final: 0.6317 (pmm) REVERT: A 101 ARG cc_start: 0.8312 (ttm110) cc_final: 0.7873 (mtm-85) REVERT: A 297 MET cc_start: 0.6718 (OUTLIER) cc_final: 0.6143 (mtm) REVERT: A 460 LYS cc_start: 0.7292 (OUTLIER) cc_final: 0.6973 (tptp) REVERT: A 486 TRP cc_start: 0.5858 (p-90) cc_final: 0.4736 (t60) REVERT: A 620 TRP cc_start: 0.5845 (m100) cc_final: 0.3985 (m-90) REVERT: A 774 MET cc_start: 0.6856 (OUTLIER) cc_final: 0.6522 (tpp) REVERT: A 924 ARG cc_start: 0.6092 (OUTLIER) cc_final: 0.5364 (mmt-90) REVERT: A 1220 ILE cc_start: 0.7753 (mm) cc_final: 0.7511 (pp) REVERT: B 109 ASN cc_start: 0.6938 (m-40) cc_final: 0.6343 (m110) REVERT: B 463 LYS cc_start: 0.8373 (mptt) cc_final: 0.7598 (mmmt) outliers start: 69 outliers final: 42 residues processed: 215 average time/residue: 0.8351 time to fit residues: 202.7221 Evaluate side-chains 208 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 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 855 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 924 ARG Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 485 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 30.0000 chunk 6 optimal weight: 0.8980 chunk 164 optimal weight: 9.9990 chunk 127 optimal weight: 50.0000 chunk 111 optimal weight: 30.0000 chunk 89 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS A 894 GLN ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.203620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.157167 restraints weight = 63429.154| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 6.90 r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4164 r_free = 0.4164 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4164 r_free = 0.4164 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 12977 Z= 0.168 Angle : 0.716 13.851 17835 Z= 0.359 Chirality : 0.044 0.186 2001 Planarity : 0.005 0.061 2196 Dihedral : 17.050 175.591 2164 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 6.81 % Allowed : 27.79 % Favored : 65.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.21), residues: 1606 helix: 1.43 (0.22), residues: 613 sheet: 0.38 (0.36), residues: 207 loop : -2.02 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 484 HIS 0.011 0.001 HIS A 298 PHE 0.037 0.002 PHE A 197 TYR 0.036 0.002 TYR A 955 ARG 0.008 0.001 ARG A1142 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 582) hydrogen bonds : angle 4.50442 ( 1625) covalent geometry : bond 0.00379 (12977) covalent geometry : angle 0.71580 (17835) *********************** 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 245 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 173 time to evaluate : 1.271 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.6373 (OUTLIER) cc_final: 0.5011 (tpp) REVERT: A 94 MET cc_start: 0.7201 (ppp) cc_final: 0.6349 (pmm) REVERT: A 101 ARG cc_start: 0.8298 (ttm110) cc_final: 0.7871 (mtm-85) REVERT: A 297 MET cc_start: 0.6694 (OUTLIER) cc_final: 0.6162 (mtm) REVERT: A 486 TRP cc_start: 0.5669 (p-90) cc_final: 0.4659 (t60) REVERT: A 774 MET cc_start: 0.6895 (OUTLIER) cc_final: 0.6623 (tpp) REVERT: A 924 ARG cc_start: 0.6125 (OUTLIER) cc_final: 0.5485 (mmt-90) REVERT: A 1103 SER cc_start: 0.5735 (OUTLIER) cc_final: 0.5271 (t) REVERT: B 109 ASN cc_start: 0.6455 (m-40) cc_final: 0.6110 (m110) REVERT: B 434 GLU cc_start: 0.6365 (mt-10) cc_final: 0.6126 (mt-10) REVERT: B 463 LYS cc_start: 0.8164 (mptt) cc_final: 0.7504 (mmmt) outliers start: 72 outliers final: 44 residues processed: 221 average time/residue: 0.9180 time to fit residues: 227.3096 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 : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 924 ARG Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 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 248 SER Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 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 130 optimal weight: 30.0000 chunk 159 optimal weight: 50.0000 chunk 5 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 51 optimal weight: 0.0970 chunk 141 optimal weight: 20.0000 chunk 138 optimal weight: 20.0000 chunk 85 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 133 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.2380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN B 427 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.203828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.156647 restraints weight = 74216.421| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 7.55 r_work: 0.3959 rms_B_bonded: 7.30 restraints_weight: 2.0000 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3962 r_free = 0.3962 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3962 r_free = 0.3962 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12977 Z= 0.160 Angle : 0.724 14.408 17835 Z= 0.361 Chirality : 0.044 0.176 2001 Planarity : 0.005 0.060 2196 Dihedral : 17.016 174.911 2164 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 6.43 % Allowed : 28.45 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.21), residues: 1606 helix: 1.45 (0.22), residues: 613 sheet: 0.38 (0.36), residues: 209 loop : -2.03 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 484 HIS 0.011 0.001 HIS A 360 PHE 0.036 0.001 PHE A 197 TYR 0.034 0.002 TYR A 955 ARG 0.006 0.000 ARG A1146 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 582) hydrogen bonds : angle 4.47577 ( 1625) covalent geometry : bond 0.00360 (12977) covalent geometry : angle 0.72371 (17835) *********************** 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 238 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 170 time to evaluate : 1.288 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.6781 (OUTLIER) cc_final: 0.4986 (tpp) REVERT: A 94 MET cc_start: 0.7630 (ppp) cc_final: 0.6644 (pmm) REVERT: A 101 ARG cc_start: 0.8279 (ttm110) cc_final: 0.7839 (mtm-85) REVERT: A 297 MET cc_start: 0.6623 (OUTLIER) cc_final: 0.6116 (mtm) REVERT: A 363 TYR cc_start: 0.5973 (m-80) cc_final: 0.5694 (m-80) REVERT: A 486 TRP cc_start: 0.5977 (p-90) cc_final: 0.4715 (t60) REVERT: A 774 MET cc_start: 0.6991 (OUTLIER) cc_final: 0.6623 (tpp) REVERT: A 924 ARG cc_start: 0.6043 (OUTLIER) cc_final: 0.5327 (mmt-90) REVERT: A 1062 GLU cc_start: 0.5581 (OUTLIER) cc_final: 0.5112 (pp20) REVERT: A 1136 GLU cc_start: 0.7734 (pt0) cc_final: 0.7367 (tm-30) REVERT: A 1220 ILE cc_start: 0.7790 (mm) cc_final: 0.7566 (pp) REVERT: B 109 ASN cc_start: 0.6870 (m-40) cc_final: 0.6256 (m110) REVERT: B 463 LYS cc_start: 0.8440 (mptt) cc_final: 0.7659 (mmmt) outliers start: 68 outliers final: 48 residues processed: 216 average time/residue: 0.8160 time to fit residues: 200.1460 Evaluate side-chains 215 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 162 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 924 ARG Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 485 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 122 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 146 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 chunk 157 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 152 optimal weight: 40.0000 chunk 2 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS ** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN B 427 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.204549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.159068 restraints weight = 56986.376| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 6.57 r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4191 r_free = 0.4191 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4191 r_free = 0.4191 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.4191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.3153 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= 0.150 Angle : 0.738 18.367 17835 Z= 0.363 Chirality : 0.044 0.172 2001 Planarity : 0.005 0.061 2196 Dihedral : 16.975 174.059 2164 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 5.77 % Allowed : 28.64 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.22), residues: 1606 helix: 1.46 (0.22), residues: 612 sheet: 0.37 (0.36), residues: 209 loop : -2.02 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 484 HIS 0.012 0.001 HIS A 360 PHE 0.034 0.001 PHE A 197 TYR 0.023 0.002 TYR A1108 ARG 0.011 0.001 ARG A1071 Details of bonding type rmsd hydrogen bonds : bond 0.03366 ( 582) hydrogen bonds : angle 4.45136 ( 1625) covalent geometry : bond 0.00335 (12977) covalent geometry : angle 0.73836 (17835) *********************** 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 228 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 167 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6369 (OUTLIER) cc_final: 0.4952 (tpp) REVERT: A 94 MET cc_start: 0.7331 (ppp) cc_final: 0.6549 (pmm) REVERT: A 101 ARG cc_start: 0.8250 (ttm110) cc_final: 0.7826 (mtm-85) REVERT: A 297 MET cc_start: 0.6734 (OUTLIER) cc_final: 0.6198 (mtm) REVERT: A 484 TRP cc_start: 0.6637 (p90) cc_final: 0.6401 (p90) REVERT: A 486 TRP cc_start: 0.5585 (p-90) cc_final: 0.4617 (t60) REVERT: A 774 MET cc_start: 0.6963 (OUTLIER) cc_final: 0.6609 (tpp) REVERT: A 924 ARG cc_start: 0.6102 (OUTLIER) cc_final: 0.5456 (mmt-90) REVERT: A 1062 GLU cc_start: 0.5239 (OUTLIER) cc_final: 0.4572 (pp20) REVERT: A 1136 GLU cc_start: 0.6991 (pt0) cc_final: 0.6674 (tm-30) REVERT: B 109 ASN cc_start: 0.6440 (m-40) cc_final: 0.6096 (m110) REVERT: B 192 HIS cc_start: 0.6953 (m90) cc_final: 0.6679 (p90) REVERT: B 463 LYS cc_start: 0.8302 (mptt) cc_final: 0.7580 (mmmt) outliers start: 61 outliers final: 44 residues processed: 207 average time/residue: 0.8524 time to fit residues: 201.2063 Evaluate side-chains 211 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 162 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 924 ARG Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 352 ASP 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 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 98 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 58 optimal weight: 0.0040 chunk 3 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 134 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS A 959 GLN ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS A 976 GLN B 422 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.205068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.160158 restraints weight = 71313.381| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 7.89 r_work: 0.3964 rms_B_bonded: 7.57 restraints_weight: 2.0000 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3967 r_free = 0.3967 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3967 r_free = 0.3967 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12977 Z= 0.148 Angle : 0.750 16.656 17835 Z= 0.369 Chirality : 0.044 0.179 2001 Planarity : 0.005 0.061 2196 Dihedral : 16.945 173.314 2164 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 5.20 % Allowed : 29.49 % Favored : 65.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.22), residues: 1606 helix: 1.42 (0.22), residues: 614 sheet: 0.46 (0.37), residues: 199 loop : -2.03 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 484 HIS 0.015 0.001 HIS A 360 PHE 0.037 0.001 PHE A 197 TYR 0.023 0.002 TYR A1108 ARG 0.007 0.000 ARG A1146 Details of bonding type rmsd hydrogen bonds : bond 0.03365 ( 582) hydrogen bonds : angle 4.45439 ( 1625) covalent geometry : bond 0.00329 (12977) covalent geometry : angle 0.74964 (17835) ********************** 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 218 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 163 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6764 (OUTLIER) cc_final: 0.4986 (tpp) REVERT: A 94 MET cc_start: 0.7768 (ppp) cc_final: 0.6817 (pmm) REVERT: A 101 ARG cc_start: 0.8202 (ttm110) cc_final: 0.7756 (mtm-85) REVERT: A 297 MET cc_start: 0.6722 (OUTLIER) cc_final: 0.6201 (mtm) REVERT: A 363 TYR cc_start: 0.6136 (m-80) cc_final: 0.5863 (m-80) REVERT: A 486 TRP cc_start: 0.5895 (p-90) cc_final: 0.4713 (t60) REVERT: A 774 MET cc_start: 0.6964 (OUTLIER) cc_final: 0.6487 (tpp) REVERT: A 924 ARG cc_start: 0.6024 (OUTLIER) cc_final: 0.5279 (mmt-90) REVERT: A 1062 GLU cc_start: 0.5394 (OUTLIER) cc_final: 0.4628 (pp20) REVERT: A 1109 LEU cc_start: 0.8281 (tp) cc_final: 0.8031 (tp) REVERT: A 1136 GLU cc_start: 0.7696 (pt0) cc_final: 0.7222 (tm-30) REVERT: B 109 ASN cc_start: 0.6953 (m-40) cc_final: 0.6413 (m110) REVERT: B 192 HIS cc_start: 0.6985 (m90) cc_final: 0.6716 (p90) REVERT: B 463 LYS cc_start: 0.8549 (mptt) cc_final: 0.7663 (mmmt) outliers start: 55 outliers final: 43 residues processed: 198 average time/residue: 0.8480 time to fit residues: 189.5793 Evaluate side-chains 207 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 159 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 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 1062 GLU Chi-restraints excluded: chain A residue 1079 ILE Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1221 TYR Chi-restraints excluded: chain B residue 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 239 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 485 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 62 optimal weight: 0.0020 chunk 118 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 72 optimal weight: 0.0970 chunk 78 optimal weight: 0.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS B 422 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.203957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.157402 restraints weight = 68035.179| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 7.25 r_work: 0.3968 rms_B_bonded: 7.09 restraints_weight: 2.0000 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3971 r_free = 0.3971 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3971 r_free = 0.3971 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12977 Z= 0.159 Angle : 0.751 14.644 17835 Z= 0.372 Chirality : 0.044 0.172 2001 Planarity : 0.005 0.061 2196 Dihedral : 16.956 173.082 2164 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 5.58 % Allowed : 29.58 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.22), residues: 1606 helix: 1.36 (0.22), residues: 614 sheet: 0.47 (0.37), residues: 199 loop : -2.03 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 484 HIS 0.015 0.001 HIS A 360 PHE 0.040 0.001 PHE A 197 TYR 0.023 0.002 TYR A1108 ARG 0.015 0.001 ARG A 823 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 582) hydrogen bonds : angle 4.52551 ( 1625) covalent geometry : bond 0.00359 (12977) covalent geometry : angle 0.75143 (17835) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11449.90 seconds wall clock time: 197 minutes 18.91 seconds (11838.91 seconds total)