Starting phenix.real_space_refine on Mon Jul 28 05:11:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d3w_27166/07_2025/8d3w_27166_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d3w_27166/07_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_27166/07_2025/8d3w_27166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d3w_27166/07_2025/8d3w_27166.map" model { file = "/net/cci-nas-00/data/ceres_data/8d3w_27166/07_2025/8d3w_27166_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d3w_27166/07_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-5711/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: 8.92, per 1000 atoms: 0.89 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: 2.30 Conformation dependent library (CDL) restraints added in 2.1 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: 1.13 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: 3.36 Time building geometry restraints manager: 2.75 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.890 Find NCS groups from input model: 0.100 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 1.306 10257 Z= 0.472 Angle : 0.840 43.794 13913 Z= 0.453 Chirality : 0.043 0.359 1575 Planarity : 0.005 0.120 1787 Dihedral : 17.167 97.183 3811 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.09 % Allowed : 25.23 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.17680 ( 441) hydrogen bonds : angle 5.91296 ( 1236) SS BOND : bond 0.00048 ( 2) SS BOND : angle 0.45771 ( 4) covalent geometry : bond 0.01442 (10255) covalent geometry : angle 0.84037 (13909) *********************** 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 : 1.034 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: 0.2309 time to fit residues: 40.6775 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 : 1.476 ------------------------------------------------------------------------------- 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 = 0.127036 restraints weight = 28109.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.127436 restraints weight = 41173.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.128729 restraints weight = 10002.040| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3364 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 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 = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3364 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 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 10257 Z= 0.186 Angle : 0.607 9.863 13913 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 Details of bonding type rmsd hydrogen bonds : bond 0.04676 ( 441) hydrogen bonds : angle 4.61499 ( 1236) SS BOND : bond 0.00176 ( 2) SS BOND : angle 0.60392 ( 4) covalent geometry : bond 0.00468 (10255) covalent geometry : angle 0.60672 (13909) *********************** 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 : 1.074 Fit side-chains REVERT: A 132 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8403 (mp) REVERT: A 434 LYS cc_start: 0.9056 (ttpp) cc_final: 0.8774 (ttpp) REVERT: B 110 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6697 (tp30) REVERT: B 177 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8793 (mp) outliers start: 31 outliers final: 19 residues processed: 157 average time/residue: 0.2366 time to fit residues: 52.0889 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 : 1.201 ------------------------------------------------------------------------------- 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: 9.9990 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 50 optimal weight: 30.0000 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 = 0.3722 r_free = 0.3722 target = 0.156266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.126546 restraints weight = 23360.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.126785 restraints weight = 42079.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.127817 restraints weight = 11218.603| |-----------------------------------------------------------------------------| 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 = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 10257 Z= 0.168 Angle : 0.576 7.467 13913 Z= 0.301 Chirality : 0.043 0.144 1575 Planarity : 0.005 0.048 1787 Dihedral : 7.747 101.144 1412 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.66 % Allowed : 22.85 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.24 (0.24), residues: 1273 helix: 1.17 (0.23), residues: 526 sheet: -1.21 (0.41), residues: 142 loop : -1.08 (0.25), residues: 605 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 0.014 0.001 TYR A 859 ARG 0.003 0.000 ARG B 118 Details of bonding type rmsd hydrogen bonds : bond 0.04323 ( 441) hydrogen bonds : angle 4.41983 ( 1236) SS BOND : bond 0.00126 ( 2) SS BOND : angle 0.40653 ( 4) covalent geometry : bond 0.00415 (10255) covalent geometry : angle 0.57583 (13909) *********************** 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 163 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.979 Fit side-chains REVERT: A 132 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8427 (mt) REVERT: A 434 LYS cc_start: 0.9057 (ttpp) cc_final: 0.8795 (ttpp) REVERT: B 110 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6809 (tp30) REVERT: B 177 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8746 (mp) outliers start: 40 outliers final: 25 residues processed: 155 average time/residue: 0.2918 time to fit residues: 66.2564 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 : 1.158 ------------------------------------------------------------------------------- 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: 0.3980 chunk 38 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 45 optimal weight: 0.0570 chunk 6 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 overall best weight: 1.2502 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.158468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.122565 restraints weight = 16959.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.113366 restraints weight = 19199.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.112615 restraints weight = 15602.771| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 10257 Z= 0.138 Angle : 0.546 7.299 13913 Z= 0.286 Chirality : 0.042 0.145 1575 Planarity : 0.004 0.046 1787 Dihedral : 7.599 100.644 1412 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.93 % Allowed : 22.85 % Favored : 73.22 % 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: 1.30 (0.24), residues: 526 sheet: -1.32 (0.39), residues: 151 loop : -1.03 (0.25), residues: 596 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 0.016 0.001 TYR A 478 ARG 0.002 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03919 ( 441) hydrogen bonds : angle 4.30371 ( 1236) SS BOND : bond 0.00404 ( 2) SS BOND : angle 0.41270 ( 4) covalent geometry : bond 0.00344 (10255) covalent geometry : angle 0.54644 (13909) *********************** 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 170 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 127 time to evaluate : 1.913 Fit side-chains REVERT: A 132 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8435 (mt) REVERT: A 434 LYS cc_start: 0.9140 (ttpp) cc_final: 0.8891 (ttpp) REVERT: B 110 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6855 (tp30) REVERT: B 177 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8781 (mp) outliers start: 43 outliers final: 28 residues processed: 161 average time/residue: 0.3245 time to fit residues: 77.3367 Evaluate side-chains 148 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 1.486 ------------------------------------------------------------------------------- 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 631 VAL 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: 6.9990 chunk 82 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 41 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.157777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.126962 restraints weight = 28298.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.126666 restraints weight = 44284.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.129733 restraints weight = 11671.571| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 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 = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 10257 Z= 0.180 Angle : 0.580 7.675 13913 Z= 0.303 Chirality : 0.044 0.238 1575 Planarity : 0.004 0.048 1787 Dihedral : 7.636 102.948 1412 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 4.57 % Allowed : 22.67 % Favored : 72.76 % 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: 1.21 (0.23), residues: 526 sheet: -1.36 (0.39), residues: 151 loop : -1.08 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 307 HIS 0.011 0.001 HIS A 675 PHE 0.013 0.001 PHE A 297 TYR 0.016 0.001 TYR A 478 ARG 0.002 0.000 ARG A 995 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 441) hydrogen bonds : angle 4.34394 ( 1236) SS BOND : bond 0.00155 ( 2) SS BOND : angle 0.49687 ( 4) covalent geometry : bond 0.00450 (10255) covalent geometry : angle 0.58000 (13909) *********************** 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 173 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 123 time to evaluate : 1.112 Fit side-chains REVERT: A 132 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8432 (mt) REVERT: A 412 SER cc_start: 0.8067 (OUTLIER) cc_final: 0.7789 (t) REVERT: A 434 LYS cc_start: 0.9116 (ttpp) cc_final: 0.8868 (ttpp) REVERT: A 557 LYS cc_start: 0.5215 (mttt) cc_final: 0.4600 (mttm) REVERT: B 110 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6822 (tp30) REVERT: B 177 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8741 (mp) REVERT: B 275 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7769 (tt0) outliers start: 50 outliers final: 33 residues processed: 162 average time/residue: 0.2156 time to fit residues: 50.0370 Evaluate side-chains 154 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 183 ILE 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 322 VAL 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 533 LEU Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 674 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 115 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 77 optimal weight: 0.0770 chunk 43 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 overall best weight: 0.7942 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.159699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.128543 restraints weight = 33411.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.128439 restraints weight = 42218.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.130190 restraints weight = 10393.534| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10257 Z= 0.116 Angle : 0.550 9.475 13913 Z= 0.286 Chirality : 0.042 0.213 1575 Planarity : 0.004 0.046 1787 Dihedral : 7.511 101.968 1412 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.11 % Allowed : 24.13 % Favored : 72.76 % 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: 1.42 (0.24), residues: 526 sheet: -1.32 (0.38), residues: 150 loop : -0.99 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 307 HIS 0.009 0.001 HIS A 675 PHE 0.013 0.001 PHE A 297 TYR 0.015 0.001 TYR A 478 ARG 0.002 0.000 ARG A 637 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 441) hydrogen bonds : angle 4.22377 ( 1236) SS BOND : bond 0.00062 ( 2) SS BOND : angle 0.40033 ( 4) covalent geometry : bond 0.00276 (10255) covalent geometry : angle 0.55051 (13909) *********************** 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 155 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 1.119 Fit side-chains REVERT: A 132 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8459 (mt) REVERT: A 434 LYS cc_start: 0.9132 (ttpp) cc_final: 0.8910 (ttpp) REVERT: A 677 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6897 (mt-10) REVERT: B 177 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8705 (mp) outliers start: 34 outliers final: 25 residues processed: 147 average time/residue: 0.2009 time to fit residues: 43.5623 Evaluate side-chains 141 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 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 677 GLU 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 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 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: 0.6980 chunk 88 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 A 872 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.157233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.126622 restraints weight = 27412.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.126831 restraints weight = 44132.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.128394 restraints weight = 10997.004| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10257 Z= 0.163 Angle : 0.581 8.493 13913 Z= 0.301 Chirality : 0.043 0.211 1575 Planarity : 0.004 0.047 1787 Dihedral : 7.567 103.504 1412 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 4.02 % Allowed : 23.95 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.13 (0.24), residues: 1273 helix: 1.34 (0.23), residues: 526 sheet: -1.34 (0.38), residues: 150 loop : -1.03 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 155 HIS 0.008 0.001 HIS A 675 PHE 0.013 0.001 PHE A 297 TYR 0.024 0.001 TYR A 478 ARG 0.005 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03963 ( 441) hydrogen bonds : angle 4.20834 ( 1236) SS BOND : bond 0.00118 ( 2) SS BOND : angle 0.43305 ( 4) covalent geometry : bond 0.00405 (10255) covalent geometry : angle 0.58055 (13909) *********************** 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 161 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 117 time to evaluate : 1.310 Fit side-chains REVERT: A 132 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8451 (mt) REVERT: A 412 SER cc_start: 0.8088 (OUTLIER) cc_final: 0.7848 (t) REVERT: A 434 LYS cc_start: 0.9117 (ttpp) cc_final: 0.8886 (ttpp) REVERT: A 677 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6883 (mt-10) REVERT: B 110 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6806 (tp30) REVERT: B 177 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8700 (mp) REVERT: B 241 GLN cc_start: 0.9344 (OUTLIER) cc_final: 0.8683 (pt0) REVERT: B 275 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7783 (tt0) outliers start: 44 outliers final: 33 residues processed: 152 average time/residue: 0.1976 time to fit residues: 44.5904 Evaluate side-chains 154 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 114 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 183 ILE 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 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 B residue 241 GLN 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: 0.6980 chunk 63 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 1 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.159262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.129268 restraints weight = 25765.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.129753 restraints weight = 44233.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.130802 restraints weight = 10954.531| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3387 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3387 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10257 Z= 0.116 Angle : 0.547 8.874 13913 Z= 0.284 Chirality : 0.042 0.199 1575 Planarity : 0.004 0.047 1787 Dihedral : 7.482 102.706 1412 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.47 % Allowed : 25.23 % Favored : 71.30 % 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: 0.03 (0.24), residues: 1273 helix: 1.50 (0.24), residues: 526 sheet: -1.27 (0.38), residues: 150 loop : -0.98 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 79 HIS 0.008 0.001 HIS A 675 PHE 0.013 0.001 PHE A 297 TYR 0.022 0.001 TYR A 478 ARG 0.004 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 441) hydrogen bonds : angle 4.14259 ( 1236) SS BOND : bond 0.00057 ( 2) SS BOND : angle 0.34877 ( 4) covalent geometry : bond 0.00275 (10255) covalent geometry : angle 0.54727 (13909) *********************** 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 155 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 1.205 Fit side-chains REVERT: A 132 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8443 (mt) REVERT: A 412 SER cc_start: 0.8101 (OUTLIER) cc_final: 0.7885 (t) REVERT: A 434 LYS cc_start: 0.9106 (ttpp) cc_final: 0.8888 (ttpp) REVERT: A 518 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7258 (tm-30) REVERT: A 677 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6947 (mt-10) REVERT: B 110 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6855 (tp30) REVERT: B 177 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8645 (mp) outliers start: 38 outliers final: 30 residues processed: 148 average time/residue: 0.2155 time to fit residues: 46.8680 Evaluate side-chains 150 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 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 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 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: 0.3980 chunk 30 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 116 optimal weight: 0.0670 chunk 49 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.0924 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.159276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.128465 restraints weight = 30608.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.128673 restraints weight = 41739.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.130525 restraints weight = 10374.481| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3302 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10257 Z= 0.127 Angle : 0.553 8.548 13913 Z= 0.286 Chirality : 0.042 0.195 1575 Planarity : 0.004 0.046 1787 Dihedral : 7.461 102.916 1412 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.66 % Allowed : 24.86 % Favored : 71.48 % 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: 0.03 (0.24), residues: 1273 helix: 1.51 (0.24), residues: 526 sheet: -1.26 (0.38), residues: 150 loop : -0.98 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 155 HIS 0.005 0.001 HIS A 675 PHE 0.013 0.001 PHE A 297 TYR 0.022 0.001 TYR A 478 ARG 0.004 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 441) hydrogen bonds : angle 4.11679 ( 1236) SS BOND : bond 0.00065 ( 2) SS BOND : angle 0.37586 ( 4) covalent geometry : bond 0.00310 (10255) covalent geometry : angle 0.55298 (13909) *********************** 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 : 1.372 Fit side-chains REVERT: A 132 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8447 (mt) REVERT: A 518 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7274 (tm-30) REVERT: A 677 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6961 (mt-10) REVERT: B 110 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6839 (tp30) REVERT: B 177 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8681 (mp) outliers start: 40 outliers final: 30 residues processed: 150 average time/residue: 0.1995 time to fit residues: 44.1474 Evaluate side-chains 146 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 1.226 ------------------------------------------------------------------------------- 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 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 504 ILE 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 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: 7.9990 chunk 1 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 112 optimal weight: 0.0770 chunk 46 optimal weight: 20.0000 chunk 73 optimal weight: 0.5980 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 ASN A 674 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.160033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.130909 restraints weight = 24962.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.130971 restraints weight = 43022.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.131076 restraints weight = 11923.079| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 10257 Z= 0.131 Angle : 0.570 8.523 13913 Z= 0.295 Chirality : 0.042 0.188 1575 Planarity : 0.004 0.046 1787 Dihedral : 7.459 103.075 1412 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.56 % Allowed : 24.86 % Favored : 71.57 % 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: 0.03 (0.24), residues: 1273 helix: 1.50 (0.24), residues: 525 sheet: -1.25 (0.39), residues: 150 loop : -0.97 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 155 HIS 0.007 0.001 HIS A 675 PHE 0.013 0.001 PHE A 297 TYR 0.021 0.001 TYR A 478 ARG 0.003 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 441) hydrogen bonds : angle 4.14658 ( 1236) SS BOND : bond 0.00066 ( 2) SS BOND : angle 0.36480 ( 4) covalent geometry : bond 0.00323 (10255) covalent geometry : angle 0.56982 (13909) ********************** 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 156 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 1.162 Fit side-chains REVERT: A 132 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8441 (mt) REVERT: A 518 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7292 (tm-30) REVERT: A 519 PRO cc_start: 0.6857 (Cg_exo) cc_final: 0.6594 (Cg_endo) REVERT: A 677 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6837 (mt-10) REVERT: B 98 TYR cc_start: 0.8406 (p90) cc_final: 0.8160 (p90) REVERT: B 110 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6894 (tp30) REVERT: B 177 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8692 (mp) REVERT: B 241 GLN cc_start: 0.9328 (OUTLIER) cc_final: 0.8662 (pt0) outliers start: 39 outliers final: 29 residues processed: 151 average time/residue: 0.2010 time to fit residues: 45.1321 Evaluate side-chains 147 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 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 504 ILE 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 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 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 B residue 241 GLN 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 107 optimal weight: 2.9990 chunk 17 optimal weight: 0.0470 chunk 117 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 3 optimal weight: 0.0970 chunk 49 optimal weight: 2.9990 overall best weight: 0.5676 ------------------------------------------------------------------------------- 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 = 0.3795 r_free = 0.3795 target = 0.162737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.131337 restraints weight = 35348.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.131417 restraints weight = 41741.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.133537 restraints weight = 10260.714| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10257 Z= 0.108 Angle : 0.555 8.868 13913 Z= 0.285 Chirality : 0.041 0.162 1575 Planarity : 0.004 0.047 1787 Dihedral : 7.322 101.577 1412 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.93 % Allowed : 25.50 % Favored : 71.57 % 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: 0.19 (0.24), residues: 1273 helix: 1.62 (0.24), residues: 527 sheet: -1.26 (0.40), residues: 142 loop : -0.86 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 155 HIS 0.004 0.001 HIS G 31 PHE 0.014 0.001 PHE A 297 TYR 0.021 0.001 TYR A 478 ARG 0.004 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.03306 ( 441) hydrogen bonds : angle 4.05878 ( 1236) SS BOND : bond 0.00030 ( 2) SS BOND : angle 0.30167 ( 4) covalent geometry : bond 0.00256 (10255) covalent geometry : angle 0.55500 (13909) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4045.33 seconds wall clock time: 72 minutes 28.21 seconds (4348.21 seconds total)