Starting phenix.real_space_refine on Sun Apr 5 11:10:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d3w_27166/04_2026/8d3w_27166_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d3w_27166/04_2026/8d3w_27166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d3w_27166/04_2026/8d3w_27166_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d3w_27166/04_2026/8d3w_27166_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d3w_27166/04_2026/8d3w_27166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d3w_27166/04_2026/8d3w_27166.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 3 5.49 5 S 61 5.16 5 C 6418 2.51 5 N 1684 2.21 5 O 1880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10046 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7413 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 960, 7402 Classifications: {'peptide': 960} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 40, 'TRANS': 919} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Conformer: "B" Number of residues, atoms: 960, 7402 Classifications: {'peptide': 960} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 40, 'TRANS': 919} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 bond proxies already assigned to first conformer: 7529 Chain: "B" Number of atoms: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2348 Classifications: {'peptide': 288} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 267} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 254 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ACP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 824 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 824 " occ=0.50 Time building chain proxies: 3.30, per 1000 atoms: 0.33 Number of scatterers: 10046 At special positions: 0 Unit cell: (140.4, 112.32, 127.44, 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 61 16.00 P 3 15.00 O 1880 8.00 N 1684 7.00 C 6418 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 276 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 718.0 milliseconds 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2368 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 10 sheets defined 47.0% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 37 through 45 removed outlier: 3.927A pdb=" N VAL A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 66 removed outlier: 3.909A pdb=" N GLN A 59 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 87 Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 91 through 108 removed outlier: 3.541A pdb=" N GLN A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 150 removed outlier: 3.572A pdb=" N SER A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 removed outlier: 4.433A pdb=" N VAL A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 273 through 304 Processing helix chain 'A' and resid 308 through 322 Processing helix chain 'A' and resid 325 through 344 removed outlier: 3.575A pdb=" N LYS A 344 " --> pdb=" O ARG A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 405 through 416 removed outlier: 3.726A pdb=" N VAL A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 452 removed outlier: 6.115A pdb=" N LEU A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 452 " --> pdb=" O LYS A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 464 removed outlier: 3.548A pdb=" N ASN A 464 " --> pdb=" O MET A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 506 removed outlier: 4.084A pdb=" N ASP A 506 " --> pdb=" O GLU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 537 removed outlier: 3.517A pdb=" N GLU A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 610 through 622 Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 646 through 650 removed outlier: 3.549A pdb=" N ASP A 649 " --> pdb=" O ASN A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 661 removed outlier: 3.521A pdb=" N LYS A 661 " --> pdb=" O GLY A 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 657 through 661' Processing helix chain 'A' and resid 664 through 674 Processing helix chain 'A' and resid 684 through 696 removed outlier: 3.755A pdb=" N GLN A 696 " --> pdb=" O VAL A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 710 No H-bonds generated for 'chain 'A' and resid 708 through 710' Processing helix chain 'A' and resid 711 through 718 Processing helix chain 'A' and resid 729 through 735 Processing helix chain 'A' and resid 745 through 772 removed outlier: 3.717A pdb=" N VAL A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE A 759 " --> pdb=" O GLY A 755 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP A 760 " --> pdb=" O ARG A 756 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER A 772 " --> pdb=" O TYR A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 793 through 802 Processing helix chain 'A' and resid 807 through 815 removed outlier: 3.619A pdb=" N TYR A 814 " --> pdb=" O SER A 811 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU A 815 " --> pdb=" O LEU A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 846 removed outlier: 3.793A pdb=" N GLN A 846 " --> pdb=" O MET A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 866 removed outlier: 3.895A pdb=" N ILE A 850 " --> pdb=" O GLN A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 873 removed outlier: 3.618A pdb=" N LEU A 873 " --> pdb=" O PRO A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 881 Processing helix chain 'A' and resid 897 through 927 removed outlier: 3.617A pdb=" N VAL A 903 " --> pdb=" O GLU A 899 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A 904 " --> pdb=" O GLN A 900 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA A 922 " --> pdb=" O VAL A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 937 Processing helix chain 'A' and resid 941 through 961 removed outlier: 4.227A pdb=" N ILE A 945 " --> pdb=" O ASN A 941 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 959 " --> pdb=" O ALA A 955 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 980 removed outlier: 3.617A pdb=" N PHE A 979 " --> pdb=" O SER A 976 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS A 980 " --> pdb=" O TRP A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1002 Processing helix chain 'A' and resid 1005 through 1011 Processing helix chain 'B' and resid 32 through 60 removed outlier: 3.751A pdb=" N LEU B 36 " --> pdb=" O TRP B 32 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 97 Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 111 through 117 removed outlier: 6.355A pdb=" N ASP B 114 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N SER B 115 " --> pdb=" O TYR B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 217 through 222 removed outlier: 3.666A pdb=" N ASP B 222 " --> pdb=" O ASP B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 removed outlier: 3.854A pdb=" N SER B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 243 removed outlier: 3.746A pdb=" N TYR B 242 " --> pdb=" O PRO B 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 58 Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 171 removed outlier: 3.588A pdb=" N VAL A 161 " --> pdb=" O MET A 168 " (cutoff:3.500A) removed outlier: 11.681A pdb=" N GLN A 158 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N LYS A 184 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU A 160 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 180 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR A 243 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ALA A 198 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG A 245 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASP A 192 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 216 removed outlier: 6.365A pdb=" N ASP A 204 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N CYS A 239 " --> pdb=" O ASP A 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 348 removed outlier: 6.894A pdb=" N VAL A 702 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N VAL A 722 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL A 704 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N MET A 724 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N THR A 362 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N THR A 705 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N CYS A 364 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ILE A 363 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL A 606 " --> pdb=" O ILE A 363 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N SER A 365 " --> pdb=" O VAL A 606 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL A 603 " --> pdb=" O ILE A 678 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N PHE A 680 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N MET A 605 " --> pdb=" O PHE A 680 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 389 removed outlier: 3.635A pdb=" N PHE A 383 " --> pdb=" O GLN A 386 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS A 380 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY A 577 " --> pdb=" O PHE A 545 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 466 through 470 removed outlier: 6.300A pdb=" N ILE A 482 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU A 469 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU A 480 " --> pdb=" O GLU A 469 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TYR A 493 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 510 through 513 Processing sheet with id=AA7, first strand: chain 'A' and resid 888 through 889 Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 79 Processing sheet with id=AA9, first strand: chain 'B' and resid 87 through 90 Processing sheet with id=AB1, first strand: chain 'B' and resid 123 through 124 441 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.72 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.20 - 0.53: 1 0.53 - 0.86: 0 0.86 - 1.20: 0 1.20 - 1.53: 9713 1.53 - 1.87: 541 Warning: very small bond lengths. Bond restraints: 10255 Sorted by residual: bond pdb=" CG PRO A 829 " pdb=" CD PRO A 829 " ideal model delta sigma weight residual 1.503 0.197 1.306 3.40e-02 8.65e+02 1.48e+03 bond pdb=" C1' ACP A2001 " pdb=" O4' ACP A2001 " ideal model delta sigma weight residual 1.390 1.628 -0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C1' ACP A2001 " pdb=" C2' ACP A2001 " ideal model delta sigma weight residual 1.527 1.306 0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" N PRO A 829 " pdb=" CD PRO A 829 " ideal model delta sigma weight residual 1.473 1.588 -0.115 1.40e-02 5.10e+03 6.76e+01 bond pdb=" N PRO A 829 " pdb=" CA PRO A 829 " ideal model delta sigma weight residual 1.471 1.371 0.100 1.32e-02 5.74e+03 5.70e+01 ... (remaining 10250 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.76: 13897 8.76 - 17.52: 8 17.52 - 26.28: 3 26.28 - 35.04: 0 35.04 - 43.79: 1 Bond angle restraints: 13909 Sorted by residual: angle pdb=" N PRO A 829 " pdb=" CD PRO A 829 " pdb=" CG PRO A 829 " ideal model delta sigma weight residual 103.20 59.41 43.79 1.50e+00 4.44e-01 8.52e+02 angle pdb=" CA PRO A 829 " pdb=" N PRO A 829 " pdb=" CD PRO A 829 " ideal model delta sigma weight residual 112.00 92.69 19.31 1.40e+00 5.10e-01 1.90e+02 angle pdb=" CA PRO A 829 " pdb=" CB PRO A 829 " pdb=" CG PRO A 829 " ideal model delta sigma weight residual 104.50 79.23 25.27 1.90e+00 2.77e-01 1.77e+02 angle pdb=" N PRO A 829 " pdb=" CA PRO A 829 " pdb=" CB PRO A 829 " ideal model delta sigma weight residual 103.48 94.95 8.53 1.00e+00 1.00e+00 7.28e+01 angle pdb=" CB PRO A 829 " pdb=" CG PRO A 829 " pdb=" CD PRO A 829 " ideal model delta sigma weight residual 106.10 81.78 24.32 3.20e+00 9.77e-02 5.78e+01 ... (remaining 13904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.44: 5410 19.44 - 38.87: 618 38.87 - 58.31: 116 58.31 - 77.75: 30 77.75 - 97.18: 11 Dihedral angle restraints: 6185 sinusoidal: 2497 harmonic: 3688 Sorted by residual: dihedral pdb=" CA SER A 444 " pdb=" C SER A 444 " pdb=" N ALA A 445 " pdb=" CA ALA A 445 " ideal model delta harmonic sigma weight residual 180.00 160.92 19.08 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA SER A 442 " pdb=" C SER A 442 " pdb=" N GLU A 443 " pdb=" CA GLU A 443 " ideal model delta harmonic sigma weight residual 180.00 161.09 18.91 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA GLN G 35 " pdb=" C GLN G 35 " pdb=" N THR G 36 " pdb=" CA THR G 36 " ideal model delta harmonic sigma weight residual 180.00 162.47 17.53 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 6182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1437 0.072 - 0.144: 135 0.144 - 0.215: 1 0.215 - 0.287: 1 0.287 - 0.359: 1 Chirality restraints: 1575 Sorted by residual: chirality pdb=" C2' ACP A2001 " pdb=" C1' ACP A2001 " pdb=" C3' ACP A2001 " pdb=" O2' ACP A2001 " both_signs ideal model delta sigma weight residual False -2.75 -2.39 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CA PRO A 829 " pdb=" N PRO A 829 " pdb=" C PRO A 829 " pdb=" CB PRO A 829 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA VAL B 129 " pdb=" N VAL B 129 " pdb=" C VAL B 129 " pdb=" CB VAL B 129 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 1572 not shown) Planarity restraints: 1787 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 828 " 0.089 5.00e-02 4.00e+02 1.20e-01 2.30e+01 pdb=" N PRO A 829 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO A 829 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 829 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 174 " 0.015 2.00e-02 2.50e+03 2.90e-02 8.42e+00 pdb=" C GLU A 174 " -0.050 2.00e-02 2.50e+03 pdb=" O GLU A 174 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL A 175 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 444 " -0.014 2.00e-02 2.50e+03 2.73e-02 7.45e+00 pdb=" C SER A 444 " 0.047 2.00e-02 2.50e+03 pdb=" O SER A 444 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA A 445 " -0.016 2.00e-02 2.50e+03 ... (remaining 1784 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 542 2.73 - 3.27: 10031 3.27 - 3.81: 16102 3.81 - 4.36: 18820 4.36 - 4.90: 33571 Nonbonded interactions: 79066 Sorted by model distance: nonbonded pdb=" OG1 THR A 804 " pdb=" OE1 GLN A 920 " model vdw 2.186 3.040 nonbonded pdb=" OE1 GLN A 846 " pdb=" OH TYR A 991 " model vdw 2.211 3.040 nonbonded pdb=" O VAL A 129 " pdb=" OG1 THR A 133 " model vdw 2.216 3.040 nonbonded pdb=" O LEU A 86 " pdb=" OG SER A 91 " model vdw 2.233 3.040 nonbonded pdb=" N GLU B 197 " pdb=" OE1 GLU B 197 " model vdw 2.243 3.120 ... (remaining 79061 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 0.870 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 11.680 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 : 0.014 1.306 10257 Z= 0.472 Angle : 0.840 43.794 13913 Z= 0.453 Chirality : 0.043 0.359 1575 Planarity : 0.005 0.120 1787 Dihedral : 17.167 97.183 3811 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.09 % Allowed : 25.23 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.24), residues: 1273 helix: 1.03 (0.24), residues: 528 sheet: -1.16 (0.41), residues: 144 loop : -0.97 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 107 TYR 0.012 0.001 TYR A 478 PHE 0.013 0.001 PHE A 297 TRP 0.023 0.001 TRP A 307 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.01442 (10255) covalent geometry : angle 0.84037 (13909) SS BOND : bond 0.00048 ( 2) SS BOND : angle 0.45771 ( 4) hydrogen bonds : bond 0.17680 ( 441) hydrogen bonds : angle 5.91296 ( 1236) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.383 Fit side-chains REVERT: A 434 LYS cc_start: 0.9072 (ttpp) cc_final: 0.8782 (ttpp) REVERT: A 923 ASP cc_start: 0.8604 (t0) cc_final: 0.8220 (t0) outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.1025 time to fit residues: 18.2070 Evaluate side-chains 122 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.0970 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 123 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN ** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 ASN A 413 HIS A 427 GLN A 491 ASN ** A 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 ASN A 687 GLN A 872 ASN A 886 ASN B 104 ASN B 158 ASN B 256 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.160648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.129439 restraints weight = 21846.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.121005 restraints weight = 27201.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.119876 restraints weight = 25831.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.121703 restraints weight = 15924.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.121672 restraints weight = 11227.333| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 10257 Z= 0.119 Angle : 0.559 9.406 13913 Z= 0.293 Chirality : 0.042 0.151 1575 Planarity : 0.005 0.064 1787 Dihedral : 7.594 98.263 1412 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.65 % Allowed : 23.49 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.24), residues: 1273 helix: 1.36 (0.24), residues: 530 sheet: -1.11 (0.41), residues: 145 loop : -0.98 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 830 TYR 0.013 0.001 TYR A 478 PHE 0.013 0.001 PHE A 297 TRP 0.019 0.001 TRP A 307 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00286 (10255) covalent geometry : angle 0.55915 (13909) SS BOND : bond 0.00103 ( 2) SS BOND : angle 0.50470 ( 4) hydrogen bonds : bond 0.04181 ( 441) hydrogen bonds : angle 4.55433 ( 1236) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.365 Fit side-chains REVERT: A 132 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8378 (mt) REVERT: A 434 LYS cc_start: 0.9063 (ttpp) cc_final: 0.8784 (ttpp) REVERT: A 466 LYS cc_start: 0.7054 (OUTLIER) cc_final: 0.6577 (pttt) REVERT: A 522 GLU cc_start: 0.7371 (tp30) cc_final: 0.7158 (tp30) REVERT: B 177 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8817 (mp) outliers start: 29 outliers final: 17 residues processed: 159 average time/residue: 0.1064 time to fit residues: 23.7718 Evaluate side-chains 143 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 221 CYS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 466 LYS Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain G residue 46 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 28 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 84 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 116 optimal weight: 0.3980 chunk 37 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 223 HIS ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.162681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.129944 restraints weight = 18549.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.122391 restraints weight = 24490.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.122059 restraints weight = 18384.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.123233 restraints weight = 13268.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.123208 restraints weight = 10234.494| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10257 Z= 0.114 Angle : 0.531 7.148 13913 Z= 0.275 Chirality : 0.041 0.143 1575 Planarity : 0.004 0.044 1787 Dihedral : 7.285 98.204 1412 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.83 % Allowed : 23.03 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.24), residues: 1273 helix: 1.48 (0.24), residues: 530 sheet: -1.20 (0.39), residues: 151 loop : -0.96 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 118 TYR 0.018 0.001 TYR A 138 PHE 0.013 0.001 PHE A 297 TRP 0.019 0.001 TRP A 307 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00268 (10255) covalent geometry : angle 0.53065 (13909) SS BOND : bond 0.00058 ( 2) SS BOND : angle 0.32656 ( 4) hydrogen bonds : bond 0.03781 ( 441) hydrogen bonds : angle 4.29774 ( 1236) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.349 Fit side-chains REVERT: A 61 ILE cc_start: 0.7668 (tt) cc_final: 0.7420 (tt) REVERT: A 132 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8436 (mt) REVERT: A 434 LYS cc_start: 0.9113 (ttpp) cc_final: 0.8837 (ttpp) REVERT: A 466 LYS cc_start: 0.6992 (OUTLIER) cc_final: 0.6785 (ptpt) REVERT: B 110 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6776 (tp30) REVERT: B 177 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8827 (mp) REVERT: B 268 MET cc_start: 0.7068 (mmm) cc_final: 0.6849 (mpp) outliers start: 31 outliers final: 18 residues processed: 153 average time/residue: 0.1021 time to fit residues: 22.1319 Evaluate side-chains 141 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 466 LYS Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain G residue 46 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 35 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 4 optimal weight: 0.0060 chunk 94 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.163902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.127037 restraints weight = 17010.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.127040 restraints weight = 35012.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.130281 restraints weight = 16309.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.130156 restraints weight = 9679.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.131541 restraints weight = 7654.537| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 10257 Z= 0.106 Angle : 0.515 7.130 13913 Z= 0.269 Chirality : 0.041 0.142 1575 Planarity : 0.004 0.044 1787 Dihedral : 7.184 98.653 1412 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.47 % Allowed : 23.13 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.24), residues: 1273 helix: 1.50 (0.24), residues: 532 sheet: -1.13 (0.39), residues: 151 loop : -0.92 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 107 TYR 0.012 0.001 TYR A 859 PHE 0.013 0.001 PHE A 297 TRP 0.018 0.001 TRP A 307 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00250 (10255) covalent geometry : angle 0.51470 (13909) SS BOND : bond 0.00057 ( 2) SS BOND : angle 0.34756 ( 4) hydrogen bonds : bond 0.03508 ( 441) hydrogen bonds : angle 4.20374 ( 1236) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.374 Fit side-chains REVERT: A 132 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8434 (mt) REVERT: A 434 LYS cc_start: 0.9150 (ttpp) cc_final: 0.8880 (ttpp) REVERT: A 637 ARG cc_start: 0.6838 (tmm-80) cc_final: 0.6597 (ttt-90) REVERT: A 677 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7008 (mt-10) REVERT: B 110 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6786 (tp30) REVERT: B 177 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8762 (mp) outliers start: 27 outliers final: 18 residues processed: 139 average time/residue: 0.0991 time to fit residues: 19.9375 Evaluate side-chains 138 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 674 ASN Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 177 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 121 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 396 GLN A 872 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.155641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.125396 restraints weight = 27464.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.125606 restraints weight = 43001.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.126846 restraints weight = 10608.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.127981 restraints weight = 6187.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.127849 restraints weight = 5074.262| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 10257 Z= 0.251 Angle : 0.639 10.178 13913 Z= 0.335 Chirality : 0.046 0.190 1575 Planarity : 0.005 0.049 1787 Dihedral : 7.672 104.675 1412 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.11 % Allowed : 22.30 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.24), residues: 1273 helix: 1.07 (0.23), residues: 527 sheet: -1.12 (0.40), residues: 144 loop : -1.11 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 146 TYR 0.015 0.002 TYR A 859 PHE 0.017 0.002 PHE A 82 TRP 0.014 0.002 TRP B 155 HIS 0.017 0.002 HIS A 675 Details of bonding type rmsd covalent geometry : bond 0.00621 (10255) covalent geometry : angle 0.63875 (13909) SS BOND : bond 0.00207 ( 2) SS BOND : angle 0.53304 ( 4) hydrogen bonds : bond 0.04828 ( 441) hydrogen bonds : angle 4.36153 ( 1236) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 124 time to evaluate : 0.372 Fit side-chains REVERT: A 79 TRP cc_start: 0.6567 (p90) cc_final: 0.6246 (p-90) REVERT: A 132 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8444 (mp) REVERT: A 387 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8160 (tp) REVERT: A 434 LYS cc_start: 0.9130 (ttpp) cc_final: 0.8900 (ttpp) REVERT: A 529 GLN cc_start: 0.8541 (tp40) cc_final: 0.8332 (tp40) REVERT: A 637 ARG cc_start: 0.6814 (tmm-80) cc_final: 0.6376 (ttt-90) REVERT: B 57 MET cc_start: 0.8787 (tmm) cc_final: 0.8172 (ttp) REVERT: B 110 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6749 (tp30) REVERT: B 177 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8781 (mp) outliers start: 45 outliers final: 29 residues processed: 161 average time/residue: 0.0963 time to fit residues: 22.5059 Evaluate side-chains 149 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 385 ASN Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 674 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain G residue 46 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 76 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 69 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 chunk 91 optimal weight: 0.8980 chunk 51 optimal weight: 0.0030 chunk 13 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 ASN A 872 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.160563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.130473 restraints weight = 20543.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.130748 restraints weight = 41766.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.130189 restraints weight = 12367.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.131678 restraints weight = 7148.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.131690 restraints weight = 5322.194| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 10257 Z= 0.107 Angle : 0.526 7.163 13913 Z= 0.275 Chirality : 0.041 0.147 1575 Planarity : 0.004 0.046 1787 Dihedral : 7.420 100.840 1412 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.74 % Allowed : 24.22 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.24), residues: 1273 helix: 1.48 (0.24), residues: 526 sheet: -1.10 (0.39), residues: 151 loop : -0.99 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 931 TYR 0.011 0.001 TYR A 859 PHE 0.020 0.001 PHE A 82 TRP 0.016 0.001 TRP B 155 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00248 (10255) covalent geometry : angle 0.52637 (13909) SS BOND : bond 0.00134 ( 2) SS BOND : angle 0.45486 ( 4) hydrogen bonds : bond 0.03562 ( 441) hydrogen bonds : angle 4.14618 ( 1236) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.365 Fit side-chains REVERT: A 79 TRP cc_start: 0.6553 (p90) cc_final: 0.6182 (p-90) REVERT: A 132 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8447 (mt) REVERT: A 434 LYS cc_start: 0.9135 (ttpp) cc_final: 0.8895 (ttpp) REVERT: A 518 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7301 (tm-30) REVERT: A 637 ARG cc_start: 0.6690 (tmm-80) cc_final: 0.6258 (ttt-90) REVERT: B 77 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8918 (mp) REVERT: B 110 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6837 (tp30) REVERT: B 177 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8705 (mp) outliers start: 30 outliers final: 19 residues processed: 152 average time/residue: 0.1011 time to fit residues: 21.8070 Evaluate side-chains 141 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 674 ASN Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain G residue 46 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 81 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 120 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 ASN A 872 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.160074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.123747 restraints weight = 14896.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.121600 restraints weight = 27396.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.123680 restraints weight = 18144.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.126323 restraints weight = 9521.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.126685 restraints weight = 7655.249| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10257 Z= 0.117 Angle : 0.537 7.204 13913 Z= 0.280 Chirality : 0.042 0.146 1575 Planarity : 0.004 0.046 1787 Dihedral : 7.361 101.247 1412 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.29 % Allowed : 23.86 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.24), residues: 1273 helix: 1.56 (0.24), residues: 526 sheet: -1.13 (0.39), residues: 150 loop : -0.98 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 931 TYR 0.013 0.001 TYR A 859 PHE 0.012 0.001 PHE A 297 TRP 0.017 0.001 TRP A 307 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00280 (10255) covalent geometry : angle 0.53657 (13909) SS BOND : bond 0.00077 ( 2) SS BOND : angle 0.43194 ( 4) hydrogen bonds : bond 0.03554 ( 441) hydrogen bonds : angle 4.10546 ( 1236) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 0.411 Fit side-chains REVERT: A 132 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8415 (mt) REVERT: A 412 SER cc_start: 0.8162 (OUTLIER) cc_final: 0.7961 (t) REVERT: A 434 LYS cc_start: 0.9187 (ttpp) cc_final: 0.8948 (ttpp) REVERT: A 518 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7116 (tm-30) REVERT: A 637 ARG cc_start: 0.6712 (tmm-80) cc_final: 0.6316 (ttt-90) REVERT: A 677 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7044 (mt-10) REVERT: B 110 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6854 (tp30) REVERT: B 177 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8716 (mp) REVERT: B 268 MET cc_start: 0.6799 (mmp) cc_final: 0.6439 (mpp) outliers start: 36 outliers final: 25 residues processed: 148 average time/residue: 0.0915 time to fit residues: 19.9997 Evaluate side-chains 145 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 872 ASN Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain G residue 46 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 72 optimal weight: 0.3980 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.160071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.129145 restraints weight = 31386.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.129467 restraints weight = 41750.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.131146 restraints weight = 10110.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.131640 restraints weight = 5785.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.131640 restraints weight = 4711.466| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10257 Z= 0.123 Angle : 0.545 7.233 13913 Z= 0.284 Chirality : 0.042 0.143 1575 Planarity : 0.004 0.045 1787 Dihedral : 7.348 101.819 1412 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.20 % Allowed : 24.22 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.24), residues: 1273 helix: 1.56 (0.24), residues: 526 sheet: -1.19 (0.38), residues: 150 loop : -0.99 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 931 TYR 0.020 0.001 TYR A 478 PHE 0.012 0.001 PHE A 297 TRP 0.019 0.001 TRP B 155 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00300 (10255) covalent geometry : angle 0.54512 (13909) SS BOND : bond 0.00071 ( 2) SS BOND : angle 0.39230 ( 4) hydrogen bonds : bond 0.03560 ( 441) hydrogen bonds : angle 4.13677 ( 1236) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 0.414 Fit side-chains REVERT: A 132 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8441 (mt) REVERT: A 412 SER cc_start: 0.8099 (OUTLIER) cc_final: 0.7816 (t) REVERT: A 434 LYS cc_start: 0.9132 (ttpp) cc_final: 0.8888 (ttpp) REVERT: A 637 ARG cc_start: 0.6553 (tmm-80) cc_final: 0.6109 (ttt-90) REVERT: A 677 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6947 (mt-10) REVERT: B 110 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6880 (tp30) REVERT: B 177 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8715 (mp) REVERT: B 268 MET cc_start: 0.6662 (mmp) cc_final: 0.6313 (mpp) outliers start: 35 outliers final: 23 residues processed: 145 average time/residue: 0.0949 time to fit residues: 19.9692 Evaluate side-chains 142 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 307 TRP Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain G residue 46 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 86 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 118 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.159046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.128602 restraints weight = 25897.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.128911 restraints weight = 41064.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.130772 restraints weight = 10582.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.131372 restraints weight = 5819.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.131659 restraints weight = 4646.969| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10257 Z= 0.165 Angle : 0.575 7.446 13913 Z= 0.300 Chirality : 0.043 0.245 1575 Planarity : 0.004 0.045 1787 Dihedral : 7.509 104.300 1412 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.02 % Allowed : 24.41 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.24), residues: 1273 helix: 1.43 (0.24), residues: 526 sheet: -1.30 (0.38), residues: 150 loop : -1.02 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 194 TYR 0.016 0.001 TYR A 478 PHE 0.012 0.001 PHE A 297 TRP 0.023 0.002 TRP B 155 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00410 (10255) covalent geometry : angle 0.57541 (13909) SS BOND : bond 0.00124 ( 2) SS BOND : angle 0.48181 ( 4) hydrogen bonds : bond 0.03985 ( 441) hydrogen bonds : angle 4.18862 ( 1236) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 0.365 Fit side-chains REVERT: A 132 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8459 (mt) REVERT: A 412 SER cc_start: 0.8105 (OUTLIER) cc_final: 0.7867 (t) REVERT: A 434 LYS cc_start: 0.9114 (ttpp) cc_final: 0.8887 (ttpp) REVERT: A 518 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7326 (tm-30) REVERT: A 519 PRO cc_start: 0.6907 (Cg_exo) cc_final: 0.6660 (Cg_endo) REVERT: A 677 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6846 (mt-10) REVERT: B 110 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6858 (tp30) REVERT: B 177 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8726 (mp) REVERT: B 268 MET cc_start: 0.6427 (mmp) cc_final: 0.6126 (mpp) outliers start: 33 outliers final: 23 residues processed: 145 average time/residue: 0.0911 time to fit residues: 19.6465 Evaluate side-chains 143 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain G residue 46 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 32 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 chunk 88 optimal weight: 0.0970 chunk 60 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.159010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.129834 restraints weight = 23236.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.129673 restraints weight = 42927.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.129880 restraints weight = 11782.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.130944 restraints weight = 6608.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.131230 restraints weight = 4860.743| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10257 Z= 0.116 Angle : 0.554 10.854 13913 Z= 0.285 Chirality : 0.042 0.200 1575 Planarity : 0.004 0.046 1787 Dihedral : 7.338 102.213 1412 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.74 % Allowed : 24.68 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.24), residues: 1273 helix: 1.58 (0.24), residues: 526 sheet: -1.22 (0.38), residues: 150 loop : -0.94 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 931 TYR 0.024 0.001 TYR A 478 PHE 0.013 0.001 PHE A 297 TRP 0.025 0.002 TRP A 79 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00279 (10255) covalent geometry : angle 0.55442 (13909) SS BOND : bond 0.00069 ( 2) SS BOND : angle 0.36818 ( 4) hydrogen bonds : bond 0.03469 ( 441) hydrogen bonds : angle 4.11866 ( 1236) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 132 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8430 (mt) REVERT: A 412 SER cc_start: 0.8225 (OUTLIER) cc_final: 0.7900 (t) REVERT: A 434 LYS cc_start: 0.9133 (ttpp) cc_final: 0.8877 (ttpp) REVERT: A 460 MET cc_start: 0.7853 (tmm) cc_final: 0.7317 (tmm) REVERT: A 518 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7250 (tm-30) REVERT: A 519 PRO cc_start: 0.6981 (Cg_exo) cc_final: 0.6715 (Cg_endo) REVERT: B 98 TYR cc_start: 0.8368 (p90) cc_final: 0.7812 (p90) REVERT: B 110 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6877 (tp30) REVERT: B 177 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8658 (mp) outliers start: 30 outliers final: 22 residues processed: 143 average time/residue: 0.0894 time to fit residues: 19.1147 Evaluate side-chains 142 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 167 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain G residue 46 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 56 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 53 optimal weight: 0.0570 chunk 82 optimal weight: 0.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.161745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.132528 restraints weight = 26000.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.132928 restraints weight = 43263.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.134803 restraints weight = 11291.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.135850 restraints weight = 6221.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.135533 restraints weight = 5116.797| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3441 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3441 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10257 Z= 0.107 Angle : 0.540 8.996 13913 Z= 0.277 Chirality : 0.041 0.185 1575 Planarity : 0.004 0.047 1787 Dihedral : 7.139 100.802 1412 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.56 % Allowed : 24.95 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.24), residues: 1273 helix: 1.71 (0.24), residues: 533 sheet: -1.12 (0.39), residues: 150 loop : -0.85 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 107 TYR 0.022 0.001 TYR A 478 PHE 0.013 0.001 PHE A 297 TRP 0.020 0.001 TRP B 155 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00253 (10255) covalent geometry : angle 0.53986 (13909) SS BOND : bond 0.00028 ( 2) SS BOND : angle 0.35109 ( 4) hydrogen bonds : bond 0.03274 ( 441) hydrogen bonds : angle 3.99313 ( 1236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1874.06 seconds wall clock time: 33 minutes 3.08 seconds (1983.08 seconds total)