Starting phenix.real_space_refine on Wed Jul 30 16:50:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g5l_29748/07_2025/8g5l_29748_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g5l_29748/07_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_29748/07_2025/8g5l_29748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g5l_29748/07_2025/8g5l_29748.map" model { file = "/net/cci-nas-00/data/ceres_data/8g5l_29748/07_2025/8g5l_29748_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g5l_29748/07_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-5711/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: 8.34, per 1000 atoms: 0.66 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: 3.30 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: 3.65 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: 4.50 Time building geometry restraints manager: 3.90 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 34.250 Find NCS groups from input model: 0.380 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:10.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.570 ------------------------------------------------------------------------------- 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 : 1.227 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: 0.9935 time to fit residues: 284.6668 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 : 1.239 ------------------------------------------------------------------------------- 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 = 56)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.163362 restraints weight = 66526.879| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 7.21 r_work: 0.4043 rms_B_bonded: 7.11 restraints_weight: 2.0000 r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4049 r_free = 0.4049 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 = 0.4048 r_free = 0.4048 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 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 : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8304 (ttm110) cc_final: 0.7816 (mtm-85) REVERT: A 486 TRP cc_start: 0.5933 (p-90) cc_final: 0.4851 (t60) REVERT: A 487 ASP cc_start: 0.7085 (m-30) cc_final: 0.5620 (m-30) REVERT: A 551 LYS cc_start: 0.7913 (pttt) cc_final: 0.7709 (tmmt) REVERT: A 620 TRP cc_start: 0.5823 (m100) cc_final: 0.3963 (m-90) REVERT: A 924 ARG cc_start: 0.6068 (ttm-80) cc_final: 0.5383 (mmt-90) REVERT: A 971 HIS cc_start: 0.7712 (OUTLIER) cc_final: 0.7187 (m-70) REVERT: A 1121 GLU cc_start: 0.7361 (tp30) cc_final: 0.6963 (pt0) REVERT: B 466 MET cc_start: 0.5327 (ttm) cc_final: 0.4917 (ttm) outliers start: 59 outliers final: 22 residues processed: 226 average time/residue: 1.1243 time to fit residues: 285.9588 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 : 1.833 ------------------------------------------------------------------------------- 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: 2.9990 chunk 65 optimal weight: 3.9990 chunk 161 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 0.0970 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.4767 r_free = 0.4767 target = 0.207557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.161785 restraints weight = 77336.300| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 9.34 r_work: 0.3975 rms_B_bonded: 8.14 restraints_weight: 2.0000 r_work: 0.4126 rms_B_bonded: 5.16 restraints_weight: 4.0000 r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4129 r_free = 0.4129 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4129 r_free = 0.4129 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.4129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 12977 Z= 0.158 Angle : 0.696 13.839 17835 Z= 0.345 Chirality : 0.043 0.157 2001 Planarity : 0.005 0.058 2196 Dihedral : 17.292 178.800 2165 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 6.62 % Allowed : 26.09 % Favored : 67.30 % 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: -0.27 (0.21), residues: 1606 helix: 1.52 (0.21), residues: 608 sheet: 0.34 (0.36), residues: 209 loop : -1.79 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 897 HIS 0.011 0.001 HIS B 258 PHE 0.016 0.001 PHE A 197 TYR 0.040 0.002 TYR A 955 ARG 0.008 0.001 ARG A1146 Details of bonding type rmsd hydrogen bonds : bond 0.03577 ( 582) hydrogen bonds : angle 4.54107 ( 1625) covalent geometry : bond 0.00350 (12977) covalent geometry : angle 0.69608 (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 247 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 177 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6678 (OUTLIER) cc_final: 0.5116 (tpp) REVERT: A 157 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6604 (tp) REVERT: A 297 MET cc_start: 0.6699 (OUTLIER) cc_final: 0.6087 (mtm) REVERT: A 363 TYR cc_start: 0.5965 (m-80) cc_final: 0.5664 (m-80) REVERT: A 486 TRP cc_start: 0.5783 (p-90) cc_final: 0.4780 (t60) REVERT: A 487 ASP cc_start: 0.6940 (m-30) cc_final: 0.5527 (m-30) REVERT: A 620 TRP cc_start: 0.5691 (m100) cc_final: 0.3969 (m-90) REVERT: A 924 ARG cc_start: 0.6130 (ttm-80) cc_final: 0.5405 (mmt-90) REVERT: A 1121 GLU cc_start: 0.7243 (tp30) cc_final: 0.6920 (pt0) REVERT: B 203 ARG cc_start: 0.7917 (mmm160) cc_final: 0.7669 (mmm160) REVERT: B 463 LYS cc_start: 0.8232 (mppt) cc_final: 0.7481 (mmmt) REVERT: B 466 MET cc_start: 0.5041 (ttm) cc_final: 0.4626 (ttm) outliers start: 70 outliers final: 31 residues processed: 222 average time/residue: 0.8689 time to fit residues: 216.9200 Evaluate side-chains 199 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 596 MET Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 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 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: 6.9990 chunk 86 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 144 optimal weight: 30.0000 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 148 optimal weight: 20.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.202772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.157520 restraints weight = 53684.319| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 6.26 r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4170 r_free = 0.4170 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4170 r_free = 0.4170 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.4170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 12977 Z= 0.207 Angle : 0.739 13.061 17835 Z= 0.372 Chirality : 0.045 0.181 2001 Planarity : 0.005 0.059 2196 Dihedral : 17.320 179.833 2165 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 7.28 % Allowed : 26.18 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.55 (0.21), residues: 1606 helix: 1.18 (0.21), residues: 615 sheet: 0.33 (0.36), residues: 207 loop : -1.92 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 897 HIS 0.012 0.002 HIS A 360 PHE 0.024 0.002 PHE B 254 TYR 0.043 0.002 TYR A 955 ARG 0.009 0.001 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 582) hydrogen bonds : angle 4.77072 ( 1625) covalent geometry : bond 0.00470 (12977) covalent geometry : angle 0.73892 (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 248 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 171 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.7283 (ppp) cc_final: 0.6256 (pmm) REVERT: A 101 ARG cc_start: 0.8322 (ttm110) cc_final: 0.7885 (mtm-85) REVERT: A 142 LEU cc_start: 0.7366 (mt) cc_final: 0.7079 (mp) REVERT: A 423 THR cc_start: 0.7579 (OUTLIER) cc_final: 0.7286 (m) REVERT: A 486 TRP cc_start: 0.5665 (p-90) cc_final: 0.4828 (t60) REVERT: A 487 ASP cc_start: 0.6753 (m-30) cc_final: 0.5406 (m-30) REVERT: A 779 LEU cc_start: 0.5205 (OUTLIER) cc_final: 0.4937 (tt) REVERT: A 924 ARG cc_start: 0.6270 (ttm-80) cc_final: 0.5535 (mmt-90) REVERT: A 971 HIS cc_start: 0.7836 (OUTLIER) cc_final: 0.7387 (m-70) REVERT: B 109 ASN cc_start: 0.6535 (m-40) cc_final: 0.6161 (m110) REVERT: B 203 ARG cc_start: 0.7730 (mmm160) cc_final: 0.7473 (mmm160) REVERT: B 463 LYS cc_start: 0.8120 (mppt) cc_final: 0.7401 (mmmt) REVERT: B 466 MET cc_start: 0.4249 (ttm) cc_final: 0.3970 (ttm) outliers start: 77 outliers final: 37 residues processed: 222 average time/residue: 0.9234 time to fit residues: 229.8125 Evaluate side-chains 198 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 596 MET Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 88 optimal weight: 0.0570 chunk 37 optimal weight: 0.2980 chunk 71 optimal weight: 0.9990 chunk 158 optimal weight: 20.0000 chunk 117 optimal weight: 1.9990 chunk 152 optimal weight: 20.0000 chunk 116 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 overall best weight: 0.6100 ------------------------------------------------------------------------------- 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** B 366 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.206235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.161498 restraints weight = 53456.068| |-----------------------------------------------------------------------------| r_work (start): 0.4225 rms_B_bonded: 6.28 r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4225 r_free = 0.4225 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4225 r_free = 0.4225 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.4225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.2598 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= 0.133 Angle : 0.685 12.740 17835 Z= 0.339 Chirality : 0.043 0.163 2001 Planarity : 0.005 0.098 2196 Dihedral : 17.088 176.550 2164 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 6.52 % Allowed : 27.60 % Favored : 65.88 % 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: -0.36 (0.21), residues: 1606 helix: 1.43 (0.21), residues: 611 sheet: 0.39 (0.36), residues: 207 loop : -1.86 (0.22), residues: 788 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 0.026 0.001 PHE A 197 TYR 0.036 0.002 TYR A 955 ARG 0.008 0.000 ARG A1146 Details of bonding type rmsd hydrogen bonds : bond 0.03285 ( 582) hydrogen bonds : angle 4.41916 ( 1625) covalent geometry : bond 0.00292 (12977) covalent geometry : angle 0.68548 (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 245 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 176 time to evaluate : 1.247 Fit side-chains revert: symmetry clash REVERT: A 101 ARG cc_start: 0.8273 (ttm110) cc_final: 0.7856 (mtm-85) REVERT: A 460 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6966 (tptp) REVERT: A 486 TRP cc_start: 0.5594 (p-90) cc_final: 0.4742 (t60) REVERT: A 487 ASP cc_start: 0.6661 (m-30) cc_final: 0.5264 (m-30) REVERT: A 620 TRP cc_start: 0.5636 (m100) cc_final: 0.4179 (m-90) REVERT: A 924 ARG cc_start: 0.6159 (ttm-80) cc_final: 0.5435 (mmt-90) REVERT: A 1144 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7508 (pm20) REVERT: B 201 ASN cc_start: 0.7300 (OUTLIER) cc_final: 0.7008 (t0) REVERT: B 434 GLU cc_start: 0.6231 (mt-10) cc_final: 0.6010 (mt-10) REVERT: B 463 LYS cc_start: 0.8101 (mppt) cc_final: 0.7378 (mmmt) outliers start: 69 outliers final: 31 residues processed: 226 average time/residue: 0.8738 time to fit residues: 223.4079 Evaluate side-chains 199 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 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 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 119 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 201 ASN 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 411 ILE 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: 4.9990 chunk 87 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.205019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.159293 restraints weight = 77100.179| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 8.84 r_work: 0.3938 rms_B_bonded: 8.04 restraints_weight: 2.0000 r_work: 0.4089 rms_B_bonded: 5.07 restraints_weight: 4.0000 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4091 r_free = 0.4091 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4091 r_free = 0.4091 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.4091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12977 Z= 0.152 Angle : 0.705 13.499 17835 Z= 0.348 Chirality : 0.044 0.169 2001 Planarity : 0.005 0.094 2196 Dihedral : 17.056 176.335 2164 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 6.24 % Allowed : 28.26 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.39 (0.21), residues: 1606 helix: 1.42 (0.22), residues: 617 sheet: 0.62 (0.37), residues: 194 loop : -1.96 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 484 HIS 0.011 0.001 HIS A 360 PHE 0.036 0.001 PHE A 197 TYR 0.037 0.002 TYR A 955 ARG 0.009 0.000 ARG A1146 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 582) hydrogen bonds : angle 4.44860 ( 1625) covalent geometry : bond 0.00340 (12977) covalent geometry : angle 0.70529 (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 243 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 177 time to evaluate : 1.310 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.7381 (ppp) cc_final: 0.6296 (pmm) REVERT: A 101 ARG cc_start: 0.8332 (ttm110) cc_final: 0.7902 (mtm-85) REVERT: A 460 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.7029 (tptp) REVERT: A 486 TRP cc_start: 0.5825 (p-90) cc_final: 0.4737 (t60) REVERT: A 620 TRP cc_start: 0.5773 (m100) cc_final: 0.3994 (m-90) REVERT: A 924 ARG cc_start: 0.6111 (OUTLIER) cc_final: 0.5400 (mmt-90) REVERT: A 1103 SER cc_start: 0.5624 (OUTLIER) cc_final: 0.5150 (t) REVERT: A 1144 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7757 (pm20) REVERT: A 1220 ILE cc_start: 0.7699 (mm) cc_final: 0.7487 (pp) REVERT: B 463 LYS cc_start: 0.8275 (mppt) cc_final: 0.7531 (mmmt) outliers start: 66 outliers final: 36 residues processed: 224 average time/residue: 0.8743 time to fit residues: 220.5171 Evaluate side-chains 201 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 161 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 924 ARG Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 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 335 VAL Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 485 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 40.0000 chunk 6 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 127 optimal weight: 50.0000 chunk 111 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS A 894 GLN ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 971 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 976 GLN ** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.198458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.151822 restraints weight = 64595.927| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 6.86 r_work: 0.3907 rms_B_bonded: 6.75 restraints_weight: 2.0000 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3910 r_free = 0.3910 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3910 r_free = 0.3910 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 12977 Z= 0.243 Angle : 0.790 13.939 17835 Z= 0.401 Chirality : 0.047 0.208 2001 Planarity : 0.006 0.112 2196 Dihedral : 17.240 177.202 2164 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 6.81 % Allowed : 27.60 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.21), residues: 1606 helix: 0.96 (0.21), residues: 615 sheet: 0.38 (0.36), residues: 206 loop : -2.17 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 484 HIS 0.012 0.002 HIS A 360 PHE 0.041 0.002 PHE A 197 TYR 0.041 0.003 TYR A 955 ARG 0.008 0.001 ARG A1146 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 582) hydrogen bonds : angle 4.94485 ( 1625) covalent geometry : bond 0.00555 (12977) covalent geometry : angle 0.78976 (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 233 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 161 time to evaluate : 1.238 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.6748 (OUTLIER) cc_final: 0.5159 (tpp) REVERT: A 94 MET cc_start: 0.7744 (ppp) cc_final: 0.6737 (pmm) REVERT: A 423 THR cc_start: 0.7897 (OUTLIER) cc_final: 0.7545 (m) REVERT: A 460 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.7077 (tptp) REVERT: A 486 TRP cc_start: 0.5963 (p-90) cc_final: 0.4714 (t60) REVERT: A 774 MET cc_start: 0.6766 (OUTLIER) cc_final: 0.6361 (tpp) REVERT: A 924 ARG cc_start: 0.6168 (OUTLIER) cc_final: 0.5482 (mmt-90) REVERT: A 1103 SER cc_start: 0.5918 (OUTLIER) cc_final: 0.5524 (t) REVERT: A 1144 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8028 (pm20) REVERT: B 109 ASN cc_start: 0.7061 (m-40) cc_final: 0.6660 (m110) REVERT: B 463 LYS cc_start: 0.8281 (mppt) cc_final: 0.7557 (mmmt) REVERT: B 466 MET cc_start: 0.5138 (ttm) cc_final: 0.4859 (ttm) outliers start: 72 outliers final: 40 residues processed: 214 average time/residue: 0.8856 time to fit residues: 212.5162 Evaluate side-chains 203 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 156 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 423 THR 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 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 1103 SER Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1177 VAL 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 235 THR Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 429 TYR 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: 0.5980 chunk 87 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 141 optimal weight: 20.0000 chunk 138 optimal weight: 30.0000 chunk 85 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 133 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 = 0.4723 r_free = 0.4723 target = 0.202805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.157529 restraints weight = 74341.290| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 8.31 r_work: 0.3926 rms_B_bonded: 7.68 restraints_weight: 2.0000 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3927 r_free = 0.3927 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3926 r_free = 0.3926 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.3214 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= 0.151 Angle : 0.744 13.717 17835 Z= 0.370 Chirality : 0.044 0.176 2001 Planarity : 0.005 0.075 2196 Dihedral : 17.049 174.647 2163 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 6.05 % Allowed : 29.21 % Favored : 64.74 % 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: -0.66 (0.21), residues: 1606 helix: 1.24 (0.21), residues: 616 sheet: 0.27 (0.37), residues: 201 loop : -2.11 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 484 HIS 0.012 0.001 HIS A 360 PHE 0.035 0.001 PHE A 197 TYR 0.016 0.002 TYR A 831 ARG 0.006 0.000 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 582) hydrogen bonds : angle 4.58654 ( 1625) covalent geometry : bond 0.00335 (12977) covalent geometry : angle 0.74442 (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 235 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 171 time to evaluate : 1.233 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.7676 (ppp) cc_final: 0.6812 (pmm) REVERT: A 101 ARG cc_start: 0.8168 (ttm110) cc_final: 0.7751 (mtm-85) REVERT: A 189 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.7249 (tp) REVERT: A 363 TYR cc_start: 0.6142 (m-80) cc_final: 0.5840 (m-80) REVERT: A 460 LYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6939 (tptp) REVERT: A 486 TRP cc_start: 0.5893 (p-90) cc_final: 0.4660 (t60) REVERT: A 774 MET cc_start: 0.6778 (OUTLIER) cc_final: 0.6310 (tpp) REVERT: A 924 ARG cc_start: 0.6071 (OUTLIER) cc_final: 0.5318 (mmt-90) REVERT: A 1062 GLU cc_start: 0.5518 (OUTLIER) cc_final: 0.5059 (pp20) REVERT: A 1144 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7996 (pm20) REVERT: B 109 ASN cc_start: 0.6956 (m-40) cc_final: 0.6315 (m110) REVERT: B 463 LYS cc_start: 0.8387 (mppt) cc_final: 0.7641 (mmmt) outliers start: 64 outliers final: 42 residues processed: 213 average time/residue: 0.8656 time to fit residues: 208.5496 Evaluate side-chains 210 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 162 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 427 MET 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 620 TRP 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 1062 GLU Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 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 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 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: 0.8980 chunk 85 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 146 optimal weight: 20.0000 chunk 69 optimal weight: 0.3980 chunk 157 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 68 optimal weight: 0.0020 chunk 28 optimal weight: 1.9990 chunk 152 optimal weight: 40.0000 chunk 2 optimal weight: 8.9990 overall best weight: 0.8390 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.204007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.159219 restraints weight = 57270.639| |-----------------------------------------------------------------------------| r_work (start): 0.4170 rms_B_bonded: 7.80 r_work: 0.3967 rms_B_bonded: 7.07 restraints_weight: 2.0000 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3963 r_free = 0.3963 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3963 r_free = 0.3963 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.3258 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= 0.147 Angle : 0.741 13.925 17835 Z= 0.368 Chirality : 0.044 0.197 2001 Planarity : 0.005 0.081 2196 Dihedral : 16.975 174.104 2163 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 5.48 % Allowed : 29.40 % 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: -0.56 (0.21), residues: 1606 helix: 1.33 (0.22), residues: 615 sheet: 0.31 (0.37), residues: 201 loop : -2.05 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 484 HIS 0.009 0.001 HIS A 360 PHE 0.029 0.001 PHE A 197 TYR 0.056 0.002 TYR B 432 ARG 0.008 0.001 ARG A 574 Details of bonding type rmsd hydrogen bonds : bond 0.03365 ( 582) hydrogen bonds : angle 4.49189 ( 1625) covalent geometry : bond 0.00328 (12977) covalent geometry : angle 0.74138 (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 224 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 166 time to evaluate : 2.321 Fit side-chains revert: symmetry clash REVERT: A 78 MET cc_start: 0.6675 (OUTLIER) cc_final: 0.5035 (tpp) REVERT: A 94 MET cc_start: 0.7698 (ppp) cc_final: 0.6801 (pmm) REVERT: A 101 ARG cc_start: 0.8141 (ttm110) cc_final: 0.7735 (mtm-85) REVERT: A 189 ILE cc_start: 0.7485 (OUTLIER) cc_final: 0.7195 (tp) REVERT: A 363 TYR cc_start: 0.6180 (m-80) cc_final: 0.5910 (m-80) REVERT: A 460 LYS cc_start: 0.7288 (OUTLIER) cc_final: 0.7061 (tptp) REVERT: A 486 TRP cc_start: 0.5856 (p-90) cc_final: 0.4671 (t60) REVERT: A 593 SER cc_start: 0.6853 (m) cc_final: 0.6559 (p) REVERT: A 774 MET cc_start: 0.6858 (OUTLIER) cc_final: 0.6348 (tpp) REVERT: A 833 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6933 (pt0) REVERT: A 924 ARG cc_start: 0.6057 (OUTLIER) cc_final: 0.5298 (mmt-90) REVERT: A 1062 GLU cc_start: 0.5404 (OUTLIER) cc_final: 0.4956 (pp20) REVERT: A 1136 GLU cc_start: 0.7640 (pt0) cc_final: 0.7264 (tm-30) REVERT: A 1144 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7987 (pm20) REVERT: B 109 ASN cc_start: 0.6945 (m-40) cc_final: 0.6345 (m110) REVERT: B 192 HIS cc_start: 0.6981 (m90) cc_final: 0.6675 (p90) REVERT: B 463 LYS cc_start: 0.8347 (mppt) cc_final: 0.7586 (mmmt) outliers start: 58 outliers final: 39 residues processed: 204 average time/residue: 0.9422 time to fit residues: 219.4181 Evaluate side-chains 207 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 160 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 189 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 427 MET 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 620 TRP Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 833 GLU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 858 THR Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 924 ARG Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1103 SER Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 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 239 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 485 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 55 optimal weight: 0.0020 chunk 79 optimal weight: 0.7980 chunk 134 optimal weight: 20.0000 chunk 83 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.205390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.160977 restraints weight = 71282.370| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 8.01 r_work: 0.3965 rms_B_bonded: 7.59 restraints_weight: 2.0000 r_work (final): 0.3965 ------------------------------------------------------------------------------- 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 = 0.01 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-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: 0.6712 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12977 Z= 0.144 Angle : 0.754 14.151 17835 Z= 0.375 Chirality : 0.044 0.205 2001 Planarity : 0.005 0.070 2196 Dihedral : 16.923 172.695 2163 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 5.20 % Allowed : 29.96 % 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: -0.51 (0.21), residues: 1606 helix: 1.37 (0.22), residues: 614 sheet: 0.50 (0.38), residues: 193 loop : -2.04 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 484 HIS 0.013 0.001 HIS A 360 PHE 0.032 0.001 PHE A 197 TYR 0.022 0.002 TYR A1108 ARG 0.011 0.001 ARG B 203 Details of bonding type rmsd hydrogen bonds : bond 0.03315 ( 582) hydrogen bonds : angle 4.45628 ( 1625) covalent geometry : bond 0.00320 (12977) covalent geometry : angle 0.75412 (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 223 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 168 time to evaluate : 1.337 Fit side-chains revert: symmetry clash REVERT: A 94 MET cc_start: 0.7720 (ppp) cc_final: 0.6867 (pmm) REVERT: A 101 ARG cc_start: 0.8126 (ttm110) cc_final: 0.7720 (mtm-85) REVERT: A 363 TYR cc_start: 0.6167 (m-80) cc_final: 0.5954 (m-80) REVERT: A 460 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.7016 (tptp) REVERT: A 486 TRP cc_start: 0.5960 (p-90) cc_final: 0.4708 (t60) REVERT: A 566 LEU cc_start: 0.6840 (mt) cc_final: 0.6172 (pp) REVERT: A 774 MET cc_start: 0.6822 (OUTLIER) cc_final: 0.6423 (tpp) REVERT: A 833 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6976 (pt0) REVERT: A 924 ARG cc_start: 0.6026 (OUTLIER) cc_final: 0.5271 (mmt-90) REVERT: A 1062 GLU cc_start: 0.5459 (OUTLIER) cc_final: 0.4992 (pp20) REVERT: A 1136 GLU cc_start: 0.7626 (pt0) cc_final: 0.7311 (pp20) REVERT: A 1144 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7984 (pm20) REVERT: B 109 ASN cc_start: 0.6911 (m-40) cc_final: 0.6313 (m110) REVERT: B 192 HIS cc_start: 0.7009 (m90) cc_final: 0.6753 (p90) REVERT: B 463 LYS cc_start: 0.8315 (mppt) cc_final: 0.7541 (mmmt) outliers start: 55 outliers final: 40 residues processed: 204 average time/residue: 0.8655 time to fit residues: 198.9844 Evaluate side-chains 202 residues out of total 1418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 156 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 189 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 620 TRP Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 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 1103 SER Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1144 GLU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 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 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 413 VAL Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 485 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 7.9990 chunk 49 optimal weight: 0.5980 chunk 89 optimal weight: 0.0050 chunk 62 optimal weight: 0.0050 chunk 118 optimal weight: 0.2980 chunk 92 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.3808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 HIS ** A 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 HIS B 427 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4763 r_free = 0.4763 target = 0.206980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.163610 restraints weight = 66970.391| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 7.58 r_work: 0.4001 rms_B_bonded: 7.46 restraints_weight: 2.0000 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3996 r_free = 0.3996 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3996 r_free = 0.3996 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 12977 Z= 0.139 Angle : 0.767 14.138 17835 Z= 0.377 Chirality : 0.044 0.213 2001 Planarity : 0.005 0.073 2196 Dihedral : 16.871 171.350 2163 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 4.91 % Allowed : 30.53 % Favored : 64.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.48 (0.21), residues: 1606 helix: 1.38 (0.22), residues: 614 sheet: 0.50 (0.37), residues: 193 loop : -2.01 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 484 HIS 0.013 0.001 HIS A 360 PHE 0.031 0.001 PHE A 197 TYR 0.025 0.002 TYR A1108 ARG 0.014 0.001 ARG A 823 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 582) hydrogen bonds : angle 4.43001 ( 1625) covalent geometry : bond 0.00311 (12977) covalent geometry : angle 0.76728 (17835) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12063.87 seconds wall clock time: 211 minutes 10.64 seconds (12670.64 seconds total)