Starting phenix.real_space_refine on Fri Feb 14 09:44:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d3w_27166/02_2025/8d3w_27166_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d3w_27166/02_2025/8d3w_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d3w_27166/02_2025/8d3w_27166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d3w_27166/02_2025/8d3w_27166.map" model { file = "/net/cci-nas-00/data/ceres_data/8d3w_27166/02_2025/8d3w_27166_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d3w_27166/02_2025/8d3w_27166_neut.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'PHE:plan': 3, 'GLU:plan': 3, 'ASN:plan1': 1, '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: {'PHE:plan': 3, 'GLU:plan': 3, 'ASN:plan1': 1, '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: 9.26, per 1000 atoms: 0.92 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: 2.65 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 1.23 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: 3.44 Time building geometry restraints manager: 2.92 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 30.040 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.060 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.190 ------------------------------------------------------------------------------- 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 10255 Z= 0.879 Angle : 0.840 43.794 13909 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (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 TRP 0.023 0.001 TRP A 307 HIS 0.004 0.001 HIS G 31 PHE 0.013 0.001 PHE A 297 TYR 0.012 0.001 TYR A 478 ARG 0.004 0.000 ARG B 107 *********************** 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 : 1.176 Fit side-chains REVERT: A 434 LYS cc_start: 0.9072 (ttpp) cc_final: 0.8782 (ttpp) REVERT: A 923 ASP cc_start: 0.8605 (t0) cc_final: 0.8220 (t0) outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.2320 time to fit residues: 40.8407 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 : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 51 optimal weight: 0.0050 chunk 99 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.157365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.126974 restraints weight = 28109.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.127389 restraints weight = 41171.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.128674 restraints weight = 9986.885| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 10255 Z= 0.296 Angle : 0.607 9.863 13909 Z= 0.319 Chirality : 0.044 0.143 1575 Planarity : 0.005 0.066 1787 Dihedral : 7.858 101.055 1412 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.83 % Allowed : 23.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.24), residues: 1273 helix: 1.11 (0.23), residues: 530 sheet: -1.19 (0.41), residues: 143 loop : -1.11 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 307 HIS 0.003 0.001 HIS G 31 PHE 0.013 0.001 PHE A 297 TYR 0.014 0.001 TYR A 859 ARG 0.003 0.000 ARG A 254 *********************** 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 165 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 1.005 Fit side-chains REVERT: A 132 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8404 (mp) REVERT: A 434 LYS cc_start: 0.9056 (ttpp) cc_final: 0.8774 (ttpp) REVERT: B 110 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6701 (tp30) REVERT: B 177 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8794 (mp) outliers start: 31 outliers final: 19 residues processed: 157 average time/residue: 0.2416 time to fit residues: 53.1592 Evaluate side-chains 137 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.279 ------------------------------------------------------------------------------- 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 272 THR Chi-restraints excluded: chain A residue 290 VAL 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 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 631 VAL 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 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 62 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 199 HIS A 223 HIS A 674 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.156733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.126961 restraints weight = 23389.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.127406 restraints weight = 42708.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.128240 restraints weight = 11051.412| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10255 Z= 0.267 Angle : 0.576 7.506 13909 Z= 0.301 Chirality : 0.043 0.144 1575 Planarity : 0.005 0.048 1787 Dihedral : 7.752 101.151 1412 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.56 % Allowed : 22.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.24), residues: 1273 helix: 1.12 (0.23), residues: 532 sheet: -1.21 (0.41), residues: 142 loop : -1.10 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 307 HIS 0.003 0.001 HIS G 31 PHE 0.013 0.001 PHE A 297 TYR 0.015 0.001 TYR A 859 ARG 0.003 0.000 ARG B 118 *********************** 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 161 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 122 time to evaluate : 1.164 Fit side-chains REVERT: A 132 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8430 (mt) REVERT: A 434 LYS cc_start: 0.9053 (ttpp) cc_final: 0.8792 (ttpp) REVERT: B 110 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6810 (tp30) REVERT: B 177 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8745 (mp) outliers start: 39 outliers final: 25 residues processed: 153 average time/residue: 0.2238 time to fit residues: 49.5545 Evaluate side-chains 147 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 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 494 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 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 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 167 TYR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 227 VAL 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 101 optimal weight: 2.9990 chunk 50 optimal weight: 0.0970 chunk 38 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 overall best weight: 1.1180 ------------------------------------------------------------------------------- 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 674 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.159441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.127272 restraints weight = 16945.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.117700 restraints weight = 19366.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.116796 restraints weight = 19770.483| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 10255 Z= 0.201 Angle : 0.542 7.274 13909 Z= 0.284 Chirality : 0.042 0.146 1575 Planarity : 0.004 0.045 1787 Dihedral : 7.587 100.290 1412 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.84 % Allowed : 22.76 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.24), residues: 1273 helix: 1.27 (0.23), residues: 532 sheet: -1.29 (0.39), residues: 151 loop : -1.04 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 307 HIS 0.003 0.001 HIS G 31 PHE 0.013 0.001 PHE A 297 TYR 0.015 0.001 TYR A 478 ARG 0.002 0.000 ARG A 586 *********************** 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 168 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 1.059 Fit side-chains REVERT: A 132 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8441 (mt) REVERT: A 434 LYS cc_start: 0.9094 (ttpp) cc_final: 0.8850 (ttpp) REVERT: A 872 ASN cc_start: 0.7967 (p0) cc_final: 0.7744 (p0) REVERT: B 110 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6851 (tp30) REVERT: B 177 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8822 (mp) outliers start: 42 outliers final: 27 residues processed: 160 average time/residue: 0.2107 time to fit residues: 48.8312 Evaluate side-chains 147 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 1.137 ------------------------------------------------------------------------------- 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 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 494 LEU 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 674 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 737 ASP 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 G residue 46 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 26 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 82 optimal weight: 0.3980 chunk 103 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 41 optimal weight: 20.0000 chunk 16 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 674 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.160869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.130886 restraints weight = 28246.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.130892 restraints weight = 44207.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.133459 restraints weight = 11447.116| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10255 Z= 0.172 Angle : 0.532 7.231 13909 Z= 0.279 Chirality : 0.042 0.225 1575 Planarity : 0.004 0.044 1787 Dihedral : 7.471 100.267 1412 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.47 % Allowed : 23.58 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.24), residues: 1273 helix: 1.42 (0.24), residues: 526 sheet: -1.24 (0.39), residues: 151 loop : -0.98 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 307 HIS 0.010 0.001 HIS A 675 PHE 0.013 0.001 PHE A 297 TYR 0.014 0.001 TYR A 478 ARG 0.002 0.000 ARG A 995 *********************** 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 163 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 1.136 Fit side-chains REVERT: A 132 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8458 (mt) REVERT: A 434 LYS cc_start: 0.9110 (ttpp) cc_final: 0.8868 (ttpp) REVERT: B 110 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6822 (tp30) REVERT: B 177 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8670 (mp) REVERT: B 275 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7735 (tt0) outliers start: 38 outliers final: 26 residues processed: 154 average time/residue: 0.2159 time to fit residues: 47.6528 Evaluate side-chains 143 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 209 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 321 ASN 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 494 LEU 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 674 ASN Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 737 ASP 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 275 GLU 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 115 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 87 optimal weight: 0.1980 chunk 78 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.162561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.131379 restraints weight = 33363.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.131397 restraints weight = 41871.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.133300 restraints weight = 10295.266| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 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 = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10255 Z= 0.167 Angle : 0.532 7.212 13909 Z= 0.278 Chirality : 0.042 0.211 1575 Planarity : 0.004 0.046 1787 Dihedral : 7.381 100.185 1412 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.93 % Allowed : 23.13 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.24), residues: 1273 helix: 1.54 (0.24), residues: 526 sheet: -1.20 (0.39), residues: 150 loop : -0.92 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 307 HIS 0.008 0.001 HIS A 675 PHE 0.013 0.001 PHE A 297 TYR 0.016 0.001 TYR A 138 ARG 0.001 0.000 ARG A 637 *********************** 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 163 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 120 time to evaluate : 1.110 Fit side-chains REVERT: A 132 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8442 (mt) REVERT: A 412 SER cc_start: 0.8062 (OUTLIER) cc_final: 0.7794 (t) REVERT: A 434 LYS cc_start: 0.9112 (ttpp) cc_final: 0.8872 (ttpp) REVERT: A 518 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7303 (tm-30) REVERT: A 677 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6928 (mt-10) REVERT: B 177 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8699 (mp) outliers start: 43 outliers final: 31 residues processed: 154 average time/residue: 0.1992 time to fit residues: 45.1578 Evaluate side-chains 148 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 278 ILE Chi-restraints excluded: chain A residue 290 VAL 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 494 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 674 ASN 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 737 ASP Chi-restraints excluded: chain A residue 743 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 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 20 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 122 optimal weight: 0.0010 chunk 7 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN A 674 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.156702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.126118 restraints weight = 27468.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.126369 restraints weight = 44982.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.127873 restraints weight = 10924.833| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 10255 Z= 0.333 Angle : 0.603 8.402 13909 Z= 0.315 Chirality : 0.045 0.223 1575 Planarity : 0.005 0.048 1787 Dihedral : 7.583 103.815 1412 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 4.20 % Allowed : 22.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.24), residues: 1273 helix: 1.29 (0.23), residues: 526 sheet: -1.22 (0.40), residues: 143 loop : -1.06 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 155 HIS 0.010 0.001 HIS A 675 PHE 0.012 0.002 PHE A 783 TYR 0.024 0.002 TYR A 478 ARG 0.003 0.000 ARG A 995 *********************** 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 168 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 122 time to evaluate : 1.057 Fit side-chains REVERT: A 79 TRP cc_start: 0.6493 (p90) cc_final: 0.6128 (p-90) REVERT: A 132 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8464 (mt) REVERT: A 412 SER cc_start: 0.8081 (OUTLIER) cc_final: 0.7795 (t) REVERT: A 434 LYS cc_start: 0.9126 (ttpp) cc_final: 0.8896 (ttpp) REVERT: A 480 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.6950 (mm) REVERT: A 677 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6748 (mt-10) REVERT: B 110 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6818 (tp30) REVERT: B 177 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8719 (mp) REVERT: B 275 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7746 (tt0) outliers start: 46 outliers final: 33 residues processed: 158 average time/residue: 0.2023 time to fit residues: 47.0032 Evaluate side-chains 158 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 118 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 209 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 290 VAL 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 480 LEU Chi-restraints excluded: chain A residue 494 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 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 A residue 994 ILE 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 B residue 222 ASP Chi-restraints excluded: chain B residue 275 GLU 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 25 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 36 optimal weight: 0.3980 chunk 68 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.158162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.128433 restraints weight = 25704.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.128955 restraints weight = 44436.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.130244 restraints weight = 10963.185| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10255 Z= 0.195 Angle : 0.558 9.826 13909 Z= 0.289 Chirality : 0.042 0.197 1575 Planarity : 0.004 0.044 1787 Dihedral : 7.507 102.841 1412 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.66 % Allowed : 24.13 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.24), residues: 1273 helix: 1.44 (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 TRP 0.020 0.001 TRP B 155 HIS 0.009 0.001 HIS A 675 PHE 0.013 0.001 PHE A 297 TYR 0.021 0.001 TYR A 478 ARG 0.005 0.000 ARG B 107 *********************** 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 158 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 118 time to evaluate : 1.094 Fit side-chains REVERT: A 79 TRP cc_start: 0.6496 (p90) cc_final: 0.6128 (p-90) REVERT: A 132 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8446 (mt) REVERT: A 412 SER cc_start: 0.8061 (OUTLIER) cc_final: 0.7825 (t) REVERT: A 434 LYS cc_start: 0.9105 (ttpp) cc_final: 0.8881 (ttpp) REVERT: A 480 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7088 (mm) REVERT: A 677 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6824 (mt-10) REVERT: B 110 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6820 (tp30) REVERT: B 177 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8691 (mp) outliers start: 40 outliers final: 31 residues processed: 149 average time/residue: 0.2115 time to fit residues: 46.1009 Evaluate side-chains 149 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 290 VAL 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 480 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 504 ILE 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 674 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 674 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.157925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.127836 restraints weight = 30630.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.127900 restraints weight = 42868.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.130307 restraints weight = 11142.441| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10255 Z= 0.248 Angle : 0.577 9.049 13909 Z= 0.298 Chirality : 0.043 0.195 1575 Planarity : 0.004 0.045 1787 Dihedral : 7.522 103.502 1412 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.66 % Allowed : 24.22 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.24), residues: 1273 helix: 1.40 (0.23), residues: 526 sheet: -1.22 (0.40), residues: 143 loop : -1.04 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 155 HIS 0.009 0.001 HIS A 675 PHE 0.013 0.001 PHE A 297 TYR 0.021 0.001 TYR A 478 ARG 0.002 0.000 ARG B 146 *********************** 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 158 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 118 time to evaluate : 1.151 Fit side-chains REVERT: A 79 TRP cc_start: 0.6540 (p90) cc_final: 0.6197 (p-90) REVERT: A 132 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8453 (mt) REVERT: A 412 SER cc_start: 0.8095 (OUTLIER) cc_final: 0.7866 (t) REVERT: A 434 LYS cc_start: 0.9120 (ttpp) cc_final: 0.8887 (ttpp) REVERT: A 480 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7081 (mm) REVERT: A 677 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6731 (mt-10) REVERT: B 110 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6851 (tp30) REVERT: B 177 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8707 (mp) outliers start: 40 outliers final: 30 residues processed: 149 average time/residue: 0.2061 time to fit residues: 45.4613 Evaluate side-chains 152 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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 290 VAL 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 480 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 504 ILE 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 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 34 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 73 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 674 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.159911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.130542 restraints weight = 24907.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.130946 restraints weight = 43617.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.133362 restraints weight = 11585.424| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10255 Z= 0.176 Angle : 0.560 9.503 13909 Z= 0.286 Chirality : 0.042 0.174 1575 Planarity : 0.004 0.047 1787 Dihedral : 7.407 102.160 1412 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.29 % Allowed : 24.50 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.24), residues: 1273 helix: 1.58 (0.24), residues: 526 sheet: -1.23 (0.38), residues: 150 loop : -0.96 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 155 HIS 0.004 0.001 HIS G 31 PHE 0.014 0.001 PHE A 297 TYR 0.020 0.001 TYR A 478 ARG 0.003 0.000 ARG B 107 ********************** 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 153 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 1.220 Fit side-chains REVERT: A 132 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8424 (mt) REVERT: A 412 SER cc_start: 0.8124 (OUTLIER) cc_final: 0.7897 (t) REVERT: A 434 LYS cc_start: 0.9083 (ttpp) cc_final: 0.8820 (ttpp) REVERT: A 518 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7354 (tm-30) REVERT: A 677 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6781 (mt-10) REVERT: B 98 TYR cc_start: 0.8367 (p90) cc_final: 0.8127 (p90) REVERT: B 177 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8660 (mp) REVERT: B 275 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7811 (tt0) outliers start: 36 outliers final: 27 residues processed: 147 average time/residue: 0.2031 time to fit residues: 44.0324 Evaluate side-chains 144 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 209 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 290 VAL 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 494 LEU Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 518 GLN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 674 ASN 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 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 B residue 275 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 117 optimal weight: 0.0470 chunk 79 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 21 optimal weight: 0.2980 chunk 3 optimal weight: 0.0970 chunk 49 optimal weight: 0.0980 overall best weight: 0.2676 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.161391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.129712 restraints weight = 35412.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.129770 restraints weight = 40557.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.131616 restraints weight = 10052.264| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.193 10255 Z= 0.245 Angle : 0.872 59.195 13909 Z= 0.521 Chirality : 0.043 0.460 1575 Planarity : 0.004 0.047 1787 Dihedral : 7.485 102.142 1412 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.12 % Favored : 94.80 % Rotamer: Outliers : 3.38 % Allowed : 24.41 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.24), residues: 1273 helix: 1.59 (0.24), residues: 526 sheet: -1.23 (0.38), residues: 150 loop : -0.95 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 307 HIS 0.003 0.001 HIS G 31 PHE 0.013 0.001 PHE A 297 TYR 0.018 0.001 TYR A 478 ARG 0.002 0.000 ARG B 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3409.08 seconds wall clock time: 61 minutes 56.36 seconds (3716.36 seconds total)