Starting phenix.real_space_refine on Wed Mar 4 07:24:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gjg_51391/03_2026/9gjg_51391.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gjg_51391/03_2026/9gjg_51391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gjg_51391/03_2026/9gjg_51391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gjg_51391/03_2026/9gjg_51391.map" model { file = "/net/cci-nas-00/data/ceres_data/9gjg_51391/03_2026/9gjg_51391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gjg_51391/03_2026/9gjg_51391.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.047 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: 4 Type Number sf(0) Gaussians S 106 5.16 5 C 7133 2.51 5 N 1936 2.21 5 O 2300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11475 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 7396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 938, 7396 Classifications: {'peptide': 938} Link IDs: {'PTRANS': 25, 'TRANS': 912} Chain breaks: 1 Chain: "L" Number of atoms: 2270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2270 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 16, 'TRANS': 258} Chain: "A" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1726 Classifications: {'peptide': 226} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 215} Chain breaks: 1 Chain: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 2.64, per 1000 atoms: 0.23 Number of scatterers: 11475 At special positions: 0 Unit cell: (101.504, 110.656, 188.864, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 106 16.00 O 2300 8.00 N 1936 7.00 C 7133 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS H 69 " - pdb=" SG CYS H 78 " distance=2.03 Simple disulfide: pdb=" SG CYS H 104 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 169 " distance=2.03 Simple disulfide: pdb=" SG CYS H 395 " - pdb=" SG CYS H 404 " distance=2.03 Simple disulfide: pdb=" SG CYS H 400 " - pdb=" SG CYS H 410 " distance=2.03 Simple disulfide: pdb=" SG CYS H 412 " - pdb=" SG CYS H 425 " distance=2.03 Simple disulfide: pdb=" SG CYS H 415 " - pdb=" SG CYS L 75 " distance=2.03 Simple disulfide: pdb=" SG CYS H 416 " - pdb=" SG CYS H 432 " distance=2.03 Simple disulfide: pdb=" SG CYS H 420 " - pdb=" SG CYS H 456 " distance=2.03 Simple disulfide: pdb=" SG CYS H 446 " - pdb=" SG CYS H 462 " distance=2.03 Simple disulfide: pdb=" SG CYS H 450 " - pdb=" SG CYS H 482 " distance=2.03 Simple disulfide: pdb=" SG CYS H 471 " - pdb=" SG CYS H 492 " distance=2.03 Simple disulfide: pdb=" SG CYS H 477 " - pdb=" SG CYS H 515 " distance=2.03 Simple disulfide: pdb=" SG CYS H 498 " - pdb=" SG CYS H 522 " distance=2.03 Simple disulfide: pdb=" SG CYS H 510 " - pdb=" SG CYS H 544 " distance=2.02 Simple disulfide: pdb=" SG CYS H 532 " - pdb=" SG CYS H 550 " distance=2.03 Simple disulfide: pdb=" SG CYS H 539 " - pdb=" SG CYS H 573 " distance=2.03 Simple disulfide: pdb=" SG CYS H 557 " - pdb=" SG CYS H 580 " distance=2.02 Simple disulfide: pdb=" SG CYS H 568 " - pdb=" SG CYS H 603 " distance=2.03 Simple disulfide: pdb=" SG CYS H 586 " - pdb=" SG CYS H 611 " distance=2.03 Simple disulfide: pdb=" SG CYS H 592 " - pdb=" SG CYS H 630 " distance=2.03 Simple disulfide: pdb=" SG CYS H 601 " - pdb=" SG CYS H 613 " distance=2.04 Simple disulfide: pdb=" SG CYS H 622 " - pdb=" SG CYS H 639 " distance=2.03 Simple disulfide: pdb=" SG CYS H 644 " - pdb=" SG CYS H 658 " distance=2.03 Simple disulfide: pdb=" SG CYS H 653 " - pdb=" SG CYS H 697 " distance=2.04 Simple disulfide: pdb=" SG CYS H 672 " - pdb=" SG CYS H 702 " distance=2.03 Simple disulfide: pdb=" SG CYS H 689 " - pdb=" SG CYS H 718 " distance=2.03 Simple disulfide: pdb=" SG CYS H 715 " - pdb=" SG CYS H 746 " distance=2.03 Simple disulfide: pdb=" SG CYS H 732 " - pdb=" SG CYS H 756 " distance=2.03 Simple disulfide: pdb=" SG CYS H 739 " - pdb=" SG CYS H 775 " distance=2.03 Simple disulfide: pdb=" SG CYS H 772 " - pdb=" SG CYS H 798 " distance=2.03 Simple disulfide: pdb=" SG CYS H 780 " - pdb=" SG CYS H 811 " distance=2.02 Simple disulfide: pdb=" SG CYS H 808 " - pdb=" SG CYS H 845 " distance=2.03 Simple disulfide: pdb=" SG CYS H 820 " - pdb=" SG CYS H 850 " distance=2.03 Simple disulfide: pdb=" SG CYS H 858 " - pdb=" SG CYS H 914 " distance=2.03 Simple disulfide: pdb=" SG CYS H 875 " - pdb=" SG CYS H 926 " distance=2.03 Simple disulfide: pdb=" SG CYS H 923 " - pdb=" SG CYS H 954 " distance=2.03 Simple disulfide: pdb=" SG CYS H 941 " - pdb=" SG CYS H 959 " distance=2.03 Simple disulfide: pdb=" SG CYS L 71 " - pdb=" SG CYS L 74 " distance=2.03 Simple disulfide: pdb=" SG CYS L 241 " - pdb=" SG CYS L 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 230 " 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 Links applied ALPHA1-2 " MAN B 4 " - " MAN B 5 " " MAN B 5 " - " MAN B 6 " ALPHA1-3 " BMA B 3 " - " MAN B 4 " ALPHA1-6 " BMA B 3 " - " MAN B 7 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG B 1 " - " ASN H 390 " Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 514.6 milliseconds 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2716 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 33 sheets defined 16.0% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.742A pdb=" N ILE H 94 " --> pdb=" O VAL H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 122 removed outlier: 3.502A pdb=" N VAL H 122 " --> pdb=" O TRP H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 129 Processing helix chain 'H' and resid 188 through 196 removed outlier: 4.162A pdb=" N ILE H 192 " --> pdb=" O ASN H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 235 Processing helix chain 'H' and resid 236 through 241 removed outlier: 3.608A pdb=" N LEU H 241 " --> pdb=" O LEU H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 274 removed outlier: 3.879A pdb=" N LYS H 274 " --> pdb=" O ASP H 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 299 Processing helix chain 'H' and resid 328 through 333 Processing helix chain 'H' and resid 350 through 358 removed outlier: 3.613A pdb=" N THR H 354 " --> pdb=" O ASP H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 363 through 365 No H-bonds generated for 'chain 'H' and resid 363 through 365' Processing helix chain 'H' and resid 375 through 390 Processing helix chain 'H' and resid 560 through 564 Processing helix chain 'H' and resid 586 through 590 Processing helix chain 'H' and resid 604 through 608 Processing helix chain 'H' and resid 671 through 675 removed outlier: 4.208A pdb=" N ASN H 674 " --> pdb=" O ASP H 671 " (cutoff:3.500A) Processing helix chain 'H' and resid 684 through 688 Processing helix chain 'H' and resid 689 through 691 No H-bonds generated for 'chain 'H' and resid 689 through 691' Processing helix chain 'H' and resid 767 through 776 removed outlier: 4.048A pdb=" N ALA H 773 " --> pdb=" O ASN H 769 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU H 774 " --> pdb=" O ASP H 770 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N CYS H 775 " --> pdb=" O ILE H 771 " (cutoff:3.500A) Processing helix chain 'H' and resid 865 through 872 Processing helix chain 'H' and resid 873 through 876 removed outlier: 3.705A pdb=" N GLN H 876 " --> pdb=" O LEU H 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 873 through 876' Processing helix chain 'H' and resid 890 through 896 Processing helix chain 'H' and resid 901 through 912 removed outlier: 3.871A pdb=" N MET H 905 " --> pdb=" O SER H 901 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU H 907 " --> pdb=" O GLU H 903 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASP H 909 " --> pdb=" O MET H 905 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LYS H 910 " --> pdb=" O LYS H 906 " (cutoff:3.500A) Processing helix chain 'H' and resid 940 through 949 Processing helix chain 'L' and resid 92 through 99 Processing helix chain 'L' and resid 111 through 115 removed outlier: 3.705A pdb=" N VAL L 115 " --> pdb=" O LYS L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 138 Processing helix chain 'L' and resid 182 through 187 removed outlier: 3.596A pdb=" N ASN L 187 " --> pdb=" O PRO L 183 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 201 Processing helix chain 'L' and resid 222 through 226 Processing helix chain 'L' and resid 278 through 281 Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.741A pdb=" N PHE A 225 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 104 through 108 removed outlier: 3.816A pdb=" N HIS H 63 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N CYS H 169 " --> pdb=" O PHE H 181 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TYR H 152 " --> pdb=" O CYS H 169 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N MET H 171 " --> pdb=" O TYR H 150 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N TYR H 150 " --> pdb=" O MET H 171 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N PHE H 173 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU H 148 " --> pdb=" O PHE H 173 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 214 through 215 removed outlier: 5.454A pdb=" N HIS H 215 " --> pdb=" O THR H 314 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE H 316 " --> pdb=" O HIS H 215 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE H 219 " --> pdb=" O LEU H 318 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LEU H 252 " --> pdb=" O PHE H 220 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL H 260 " --> pdb=" O LEU H 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 214 through 215 removed outlier: 5.454A pdb=" N HIS H 215 " --> pdb=" O THR H 314 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE H 316 " --> pdb=" O HIS H 215 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLY H 313 " --> pdb=" O SER H 339 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N HIS H 341 " --> pdb=" O GLY H 313 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N MET H 315 " --> pdb=" O HIS H 341 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL H 343 " --> pdb=" O MET H 315 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL H 317 " --> pdb=" O VAL H 343 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU H 345 " --> pdb=" O VAL H 317 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N MET H 319 " --> pdb=" O LEU H 345 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N HIS H 368 " --> pdb=" O VAL H 340 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N THR H 342 " --> pdb=" O HIS H 368 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N PHE H 370 " --> pdb=" O THR H 342 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL H 344 " --> pdb=" O PHE H 370 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'H' and resid 403 through 404 Processing sheet with id=AA5, first strand: chain 'H' and resid 423 through 425 Processing sheet with id=AA6, first strand: chain 'H' and resid 452 through 457 removed outlier: 7.029A pdb=" N SER H 453 " --> pdb=" O THR H 465 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 478 through 481 Processing sheet with id=AA8, first strand: chain 'H' and resid 512 through 515 removed outlier: 6.431A pdb=" N SER H 512 " --> pdb=" O ASP H 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 540 through 544 Processing sheet with id=AB1, first strand: chain 'H' and resid 569 through 573 Processing sheet with id=AB2, first strand: chain 'H' and resid 601 through 602 removed outlier: 3.989A pdb=" N LYS H 602 " --> pdb=" O GLN H 612 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN H 612 " --> pdb=" O LYS H 602 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'H' and resid 628 through 631 removed outlier: 3.541A pdb=" N GLN H 638 " --> pdb=" O ASP H 631 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 650 through 651 Processing sheet with id=AB5, first strand: chain 'H' and resid 693 through 698 removed outlier: 3.698A pdb=" N VAL H 703 " --> pdb=" O THR H 696 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 717 through 720 Processing sheet with id=AB7, first strand: chain 'H' and resid 745 through 749 removed outlier: 3.684A pdb=" N GLY H 749 " --> pdb=" O SER H 753 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 787 through 791 Processing sheet with id=AB9, first strand: chain 'H' and resid 809 through 811 Processing sheet with id=AC1, first strand: chain 'H' and resid 824 through 830 Processing sheet with id=AC2, first strand: chain 'H' and resid 879 through 883 Processing sheet with id=AC3, first strand: chain 'H' and resid 924 through 928 Processing sheet with id=AC4, first strand: chain 'H' and resid 953 through 955 Processing sheet with id=AC5, first strand: chain 'L' and resid 41 through 42 removed outlier: 6.375A pdb=" N PHE L 41 " --> pdb=" O ASN L 261 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'L' and resid 77 through 81 Processing sheet with id=AC7, first strand: chain 'L' and resid 83 through 84 Processing sheet with id=AC8, first strand: chain 'L' and resid 103 through 107 removed outlier: 4.631A pdb=" N GLN L 124 " --> pdb=" O ILE L 172 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LEU L 170 " --> pdb=" O ILE L 126 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 140 through 143 removed outlier: 3.542A pdb=" N THR L 149 " --> pdb=" O GLU L 141 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET L 147 " --> pdb=" O ALA L 143 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 191 through 192 removed outlier: 5.367A pdb=" N PHE L 230 " --> pdb=" O TYR L 242 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU L 240 " --> pdb=" O LEU L 232 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 207 through 212 Processing sheet with id=AD3, first strand: chain 'A' and resid 6 through 10 Processing sheet with id=AD4, first strand: chain 'A' and resid 14 through 15 removed outlier: 6.899A pdb=" N ILE A 37 " --> pdb=" O ARG A 53 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ARG A 53 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP A 39 " --> pdb=" O VAL A 51 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 146 through 149 removed outlier: 3.525A pdb=" N VAL A 161 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 152 through 154 removed outlier: 6.633A pdb=" N LEU A 175 " --> pdb=" O TYR A 191 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR A 191 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TRP A 177 " --> pdb=" O LEU A 189 " (cutoff:3.500A) 325 hydrogen bonds defined for protein. 801 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: 2.24 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3722 1.34 - 1.46: 2753 1.46 - 1.58: 5107 1.58 - 1.70: 0 1.70 - 1.82: 128 Bond restraints: 11710 Sorted by residual: bond pdb=" N ASN H 390 " pdb=" CA ASN H 390 " ideal model delta sigma weight residual 1.455 1.494 -0.038 1.25e-02 6.40e+03 9.37e+00 bond pdb=" N CYS H 811 " pdb=" CA CYS H 811 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.18e-02 7.18e+03 8.21e+00 bond pdb=" N ILE H 629 " pdb=" CA ILE H 629 " ideal model delta sigma weight residual 1.457 1.488 -0.032 1.15e-02 7.56e+03 7.58e+00 bond pdb=" N ASP H 631 " pdb=" CA ASP H 631 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.15e-02 7.56e+03 6.84e+00 bond pdb=" N LYS H 681 " pdb=" CA LYS H 681 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.19e-02 7.06e+03 6.82e+00 ... (remaining 11705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 15425 1.51 - 3.01: 336 3.01 - 4.52: 62 4.52 - 6.02: 15 6.02 - 7.53: 5 Bond angle restraints: 15843 Sorted by residual: angle pdb=" C ASN H 750 " pdb=" CA ASN H 750 " pdb=" CB ASN H 750 " ideal model delta sigma weight residual 116.54 110.78 5.76 1.15e+00 7.56e-01 2.51e+01 angle pdb=" N TYR H 632 " pdb=" CA TYR H 632 " pdb=" C TYR H 632 " ideal model delta sigma weight residual 114.64 109.28 5.36 1.52e+00 4.33e-01 1.24e+01 angle pdb=" C PRO H 781 " pdb=" CA PRO H 781 " pdb=" CB PRO H 781 " ideal model delta sigma weight residual 112.55 107.49 5.06 1.50e+00 4.44e-01 1.14e+01 angle pdb=" CA LEU H 778 " pdb=" C LEU H 778 " pdb=" O LEU H 778 " ideal model delta sigma weight residual 121.87 118.21 3.66 1.10e+00 8.26e-01 1.11e+01 angle pdb=" CA CYS H 715 " pdb=" CB CYS H 715 " pdb=" SG CYS H 715 " ideal model delta sigma weight residual 114.40 121.93 -7.53 2.30e+00 1.89e-01 1.07e+01 ... (remaining 15838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 6353 17.59 - 35.18: 701 35.18 - 52.77: 177 52.77 - 70.36: 35 70.36 - 87.95: 24 Dihedral angle restraints: 7290 sinusoidal: 3048 harmonic: 4242 Sorted by residual: dihedral pdb=" CB CYS H 420 " pdb=" SG CYS H 420 " pdb=" SG CYS H 456 " pdb=" CB CYS H 456 " ideal model delta sinusoidal sigma weight residual -86.00 -167.74 81.74 1 1.00e+01 1.00e-02 8.22e+01 dihedral pdb=" CB CYS H 477 " pdb=" SG CYS H 477 " pdb=" SG CYS H 515 " pdb=" CB CYS H 515 " ideal model delta sinusoidal sigma weight residual 93.00 30.81 62.19 1 1.00e+01 1.00e-02 5.12e+01 dihedral pdb=" CB CYS H 780 " pdb=" SG CYS H 780 " pdb=" SG CYS H 811 " pdb=" CB CYS H 811 " ideal model delta sinusoidal sigma weight residual -86.00 -144.20 58.20 1 1.00e+01 1.00e-02 4.54e+01 ... (remaining 7287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.337: 1739 0.337 - 0.674: 0 0.674 - 1.012: 0 1.012 - 1.349: 0 1.349 - 1.686: 1 Chirality restraints: 1740 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN H 390 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.71 -1.69 2.00e-01 2.50e+01 7.11e+01 chirality pdb=" CA ILE H 629 " pdb=" N ILE H 629 " pdb=" C ILE H 629 " pdb=" CB ILE H 629 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA VAL H 810 " pdb=" N VAL H 810 " pdb=" C VAL H 810 " pdb=" CB VAL H 810 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.19 2.00e-01 2.50e+01 9.41e-01 ... (remaining 1737 not shown) Planarity restraints: 2044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS H 780 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C CYS H 780 " 0.038 2.00e-02 2.50e+03 pdb=" O CYS H 780 " -0.014 2.00e-02 2.50e+03 pdb=" N PRO H 781 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP L 223 " -0.035 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO L 224 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO L 224 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO L 224 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS H 439 " 0.011 2.00e-02 2.50e+03 2.10e-02 4.40e+00 pdb=" C LYS H 439 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS H 439 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO H 440 " 0.012 2.00e-02 2.50e+03 ... (remaining 2041 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 590 2.72 - 3.27: 11166 3.27 - 3.81: 18505 3.81 - 4.36: 23807 4.36 - 4.90: 40231 Nonbonded interactions: 94299 Sorted by model distance: nonbonded pdb=" O LYS L 222 " pdb=" OG1 THR L 225 " model vdw 2.179 3.040 nonbonded pdb=" O ARG H 657 " pdb=" OG1 THR H 665 " model vdw 2.189 3.040 nonbonded pdb=" OG1 THR L 15 " pdb=" OD1 ASP L 17 " model vdw 2.189 3.040 nonbonded pdb=" O PRO H 951 " pdb=" OH TYR A 109 " model vdw 2.198 3.040 nonbonded pdb=" ND2 ASN H 211 " pdb=" O GLU H 393 " model vdw 2.215 3.120 ... (remaining 94294 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 29.550 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.940 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 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 : 0.004 0.038 11759 Z= 0.181 Angle : 0.588 10.938 15948 Z= 0.325 Chirality : 0.060 1.686 1740 Planarity : 0.004 0.053 2043 Dihedral : 15.946 87.952 4448 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.72 % Allowed : 16.49 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.23), residues: 1429 helix: -0.85 (0.44), residues: 145 sheet: 0.24 (0.26), residues: 404 loop : -0.08 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 235 TYR 0.034 0.001 TYR H 717 PHE 0.024 0.001 PHE H 742 TRP 0.017 0.001 TRP L 223 HIS 0.002 0.001 HIS L 158 Details of bonding type rmsd covalent geometry : bond 0.00360 (11710) covalent geometry : angle 0.57281 (15843) SS BOND : bond 0.00349 ( 42) SS BOND : angle 0.99912 ( 84) hydrogen bonds : bond 0.23286 ( 325) hydrogen bonds : angle 8.93085 ( 801) link_ALPHA1-2 : bond 0.00309 ( 2) link_ALPHA1-2 : angle 1.46143 ( 6) link_ALPHA1-3 : bond 0.00428 ( 1) link_ALPHA1-3 : angle 1.54981 ( 3) link_ALPHA1-6 : bond 0.00032 ( 1) link_ALPHA1-6 : angle 1.51477 ( 3) link_BETA1-4 : bond 0.00469 ( 2) link_BETA1-4 : angle 1.20546 ( 6) link_NAG-ASN : bond 0.01625 ( 1) link_NAG-ASN : angle 7.92959 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 65 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 484 ASN cc_start: 0.6249 (t0) cc_final: 0.5859 (m-40) outliers start: 35 outliers final: 29 residues processed: 98 average time/residue: 0.4682 time to fit residues: 50.8244 Evaluate side-chains 90 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 61 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 187 GLU Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 275 TYR Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain H residue 315 MET Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 456 CYS Chi-restraints excluded: chain H residue 465 THR Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 482 CYS Chi-restraints excluded: chain H residue 515 CYS Chi-restraints excluded: chain H residue 536 THR Chi-restraints excluded: chain H residue 607 THR Chi-restraints excluded: chain H residue 710 VAL Chi-restraints excluded: chain H residue 725 ILE Chi-restraints excluded: chain H residue 751 ASP Chi-restraints excluded: chain H residue 793 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 217 VAL Chi-restraints excluded: chain L residue 220 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 234 ASN H 341 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.214302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.179393 restraints weight = 14567.188| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 1.92 r_work: 0.3905 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3850 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.0701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11759 Z= 0.156 Angle : 0.574 7.023 15948 Z= 0.306 Chirality : 0.045 0.214 1740 Planarity : 0.004 0.049 2043 Dihedral : 8.145 69.479 1760 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.34 % Allowed : 15.09 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.23), residues: 1429 helix: -0.82 (0.43), residues: 158 sheet: 0.10 (0.25), residues: 414 loop : -0.09 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 102 TYR 0.020 0.001 TYR H 27 PHE 0.017 0.002 PHE H 742 TRP 0.016 0.001 TRP L 223 HIS 0.003 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00359 (11710) covalent geometry : angle 0.56709 (15843) SS BOND : bond 0.00722 ( 42) SS BOND : angle 1.11830 ( 84) hydrogen bonds : bond 0.04101 ( 325) hydrogen bonds : angle 6.55546 ( 801) link_ALPHA1-2 : bond 0.00363 ( 2) link_ALPHA1-2 : angle 1.46105 ( 6) link_ALPHA1-3 : bond 0.00838 ( 1) link_ALPHA1-3 : angle 1.67822 ( 3) link_ALPHA1-6 : bond 0.00012 ( 1) link_ALPHA1-6 : angle 2.05915 ( 3) link_BETA1-4 : bond 0.00321 ( 2) link_BETA1-4 : angle 2.09758 ( 6) link_NAG-ASN : bond 0.00808 ( 1) link_NAG-ASN : angle 0.69775 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 76 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 52 VAL cc_start: 0.8892 (OUTLIER) cc_final: 0.8500 (t) REVERT: H 101 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.6361 (pt0) REVERT: H 467 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.6595 (m-80) REVERT: H 484 ASN cc_start: 0.6282 (t0) cc_final: 0.5771 (t160) REVERT: H 905 MET cc_start: 0.3353 (OUTLIER) cc_final: 0.0513 (mpt) outliers start: 43 outliers final: 20 residues processed: 111 average time/residue: 0.5501 time to fit residues: 66.7428 Evaluate side-chains 87 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 465 THR Chi-restraints excluded: chain H residue 467 TYR Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 482 CYS Chi-restraints excluded: chain H residue 536 THR Chi-restraints excluded: chain H residue 710 VAL Chi-restraints excluded: chain H residue 725 ILE Chi-restraints excluded: chain H residue 905 MET Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 217 VAL Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 251 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 74 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 127 optimal weight: 0.4980 chunk 54 optimal weight: 0.3980 chunk 126 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 39 optimal weight: 0.3980 chunk 83 optimal weight: 7.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 234 ASN H 240 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.214488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.179367 restraints weight = 14719.831| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 1.96 r_work: 0.3905 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3857 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11759 Z= 0.151 Angle : 0.557 6.977 15948 Z= 0.295 Chirality : 0.044 0.185 1740 Planarity : 0.004 0.048 2043 Dihedral : 7.505 62.220 1744 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.58 % Allowed : 15.09 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.22), residues: 1429 helix: -0.91 (0.41), residues: 165 sheet: 0.09 (0.25), residues: 408 loop : -0.12 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 177 TYR 0.019 0.001 TYR H 27 PHE 0.015 0.002 PHE H 64 TRP 0.014 0.001 TRP L 223 HIS 0.003 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00356 (11710) covalent geometry : angle 0.54807 (15843) SS BOND : bond 0.00352 ( 42) SS BOND : angle 1.12187 ( 84) hydrogen bonds : bond 0.03390 ( 325) hydrogen bonds : angle 5.99888 ( 801) link_ALPHA1-2 : bond 0.00338 ( 2) link_ALPHA1-2 : angle 1.51448 ( 6) link_ALPHA1-3 : bond 0.00733 ( 1) link_ALPHA1-3 : angle 1.85752 ( 3) link_ALPHA1-6 : bond 0.00126 ( 1) link_ALPHA1-6 : angle 2.17495 ( 3) link_BETA1-4 : bond 0.00450 ( 2) link_BETA1-4 : angle 2.46907 ( 6) link_NAG-ASN : bond 0.00108 ( 1) link_NAG-ASN : angle 1.21275 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 67 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: H 52 VAL cc_start: 0.8928 (OUTLIER) cc_final: 0.8491 (t) REVERT: H 358 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8500 (mp) REVERT: H 467 TYR cc_start: 0.7073 (OUTLIER) cc_final: 0.6631 (m-80) REVERT: H 523 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8195 (ptpp) REVERT: L 278 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6714 (tp30) outliers start: 46 outliers final: 19 residues processed: 104 average time/residue: 0.5504 time to fit residues: 62.7031 Evaluate side-chains 86 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 465 THR Chi-restraints excluded: chain H residue 467 TYR Chi-restraints excluded: chain H residue 482 CYS Chi-restraints excluded: chain H residue 523 LYS Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain H residue 665 THR Chi-restraints excluded: chain H residue 747 ILE Chi-restraints excluded: chain H residue 771 ILE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 251 ARG Chi-restraints excluded: chain L residue 278 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 125 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 126 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 234 ASN H 620 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.212661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.176619 restraints weight = 14632.376| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 2.00 r_work: 0.3882 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3827 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11759 Z= 0.222 Angle : 0.598 7.711 15948 Z= 0.315 Chirality : 0.046 0.204 1740 Planarity : 0.005 0.051 2043 Dihedral : 7.491 58.727 1736 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.81 % Allowed : 16.17 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.22), residues: 1429 helix: -0.97 (0.41), residues: 165 sheet: -0.07 (0.25), residues: 411 loop : -0.18 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 177 TYR 0.023 0.002 TYR H 27 PHE 0.017 0.002 PHE H 64 TRP 0.015 0.002 TRP L 223 HIS 0.003 0.001 HIS H 87 Details of bonding type rmsd covalent geometry : bond 0.00530 (11710) covalent geometry : angle 0.58607 (15843) SS BOND : bond 0.00471 ( 42) SS BOND : angle 1.37258 ( 84) hydrogen bonds : bond 0.03343 ( 325) hydrogen bonds : angle 5.91967 ( 801) link_ALPHA1-2 : bond 0.00234 ( 2) link_ALPHA1-2 : angle 1.62708 ( 6) link_ALPHA1-3 : bond 0.00518 ( 1) link_ALPHA1-3 : angle 1.99073 ( 3) link_ALPHA1-6 : bond 0.00231 ( 1) link_ALPHA1-6 : angle 2.24159 ( 3) link_BETA1-4 : bond 0.00520 ( 2) link_BETA1-4 : angle 2.80546 ( 6) link_NAG-ASN : bond 0.00113 ( 1) link_NAG-ASN : angle 1.93212 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 60 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: H 47 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7449 (mm-30) REVERT: H 52 VAL cc_start: 0.9099 (OUTLIER) cc_final: 0.8772 (m) REVERT: H 358 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8327 (mp) REVERT: H 467 TYR cc_start: 0.7055 (OUTLIER) cc_final: 0.6656 (m-80) REVERT: H 484 ASN cc_start: 0.6342 (t0) cc_final: 0.5979 (m-40) REVERT: H 523 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8196 (ptpp) REVERT: H 531 MET cc_start: 0.7046 (OUTLIER) cc_final: 0.6697 (ttm) REVERT: H 905 MET cc_start: 0.3442 (OUTLIER) cc_final: 0.0757 (mpt) REVERT: L 278 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.6761 (tp30) outliers start: 49 outliers final: 18 residues processed: 101 average time/residue: 0.5365 time to fit residues: 59.4959 Evaluate side-chains 83 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 465 THR Chi-restraints excluded: chain H residue 467 TYR Chi-restraints excluded: chain H residue 482 CYS Chi-restraints excluded: chain H residue 523 LYS Chi-restraints excluded: chain H residue 531 MET Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain H residue 905 MET Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 251 ARG Chi-restraints excluded: chain L residue 278 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 4 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 110 optimal weight: 0.0870 chunk 34 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 234 ASN H 620 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.213887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.179287 restraints weight = 14620.102| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 1.91 r_work: 0.3905 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3849 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11759 Z= 0.153 Angle : 0.554 7.218 15948 Z= 0.290 Chirality : 0.045 0.182 1740 Planarity : 0.004 0.050 2043 Dihedral : 7.059 55.560 1736 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.19 % Allowed : 17.03 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.22), residues: 1429 helix: -0.91 (0.41), residues: 165 sheet: -0.04 (0.25), residues: 411 loop : -0.14 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 177 TYR 0.017 0.001 TYR H 27 PHE 0.016 0.002 PHE H 64 TRP 0.016 0.001 TRP L 223 HIS 0.002 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00362 (11710) covalent geometry : angle 0.54421 (15843) SS BOND : bond 0.00361 ( 42) SS BOND : angle 1.05851 ( 84) hydrogen bonds : bond 0.02950 ( 325) hydrogen bonds : angle 5.69377 ( 801) link_ALPHA1-2 : bond 0.00321 ( 2) link_ALPHA1-2 : angle 1.54705 ( 6) link_ALPHA1-3 : bond 0.00891 ( 1) link_ALPHA1-3 : angle 1.96628 ( 3) link_ALPHA1-6 : bond 0.00058 ( 1) link_ALPHA1-6 : angle 2.10558 ( 3) link_BETA1-4 : bond 0.00580 ( 2) link_BETA1-4 : angle 2.77307 ( 6) link_NAG-ASN : bond 0.00168 ( 1) link_NAG-ASN : angle 2.24966 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 63 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: H 52 VAL cc_start: 0.9041 (OUTLIER) cc_final: 0.8571 (t) REVERT: H 358 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8233 (mm) REVERT: H 467 TYR cc_start: 0.7059 (OUTLIER) cc_final: 0.6710 (m-80) REVERT: H 531 MET cc_start: 0.6929 (OUTLIER) cc_final: 0.6651 (ttm) REVERT: H 905 MET cc_start: 0.3397 (OUTLIER) cc_final: 0.0726 (mpt) REVERT: L 278 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.6695 (tp30) outliers start: 41 outliers final: 19 residues processed: 96 average time/residue: 0.5399 time to fit residues: 56.9598 Evaluate side-chains 82 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 57 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 292 ASP Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 467 TYR Chi-restraints excluded: chain H residue 482 CYS Chi-restraints excluded: chain H residue 531 MET Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain H residue 725 ILE Chi-restraints excluded: chain H residue 771 ILE Chi-restraints excluded: chain H residue 905 MET Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 251 ARG Chi-restraints excluded: chain L residue 278 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 106 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 234 ASN H 620 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.213824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.178194 restraints weight = 14579.162| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 1.91 r_work: 0.3900 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3851 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11759 Z= 0.160 Angle : 0.560 7.863 15948 Z= 0.293 Chirality : 0.045 0.178 1740 Planarity : 0.004 0.050 2043 Dihedral : 6.885 53.448 1733 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.50 % Allowed : 17.03 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.22), residues: 1429 helix: -0.89 (0.41), residues: 165 sheet: -0.01 (0.25), residues: 411 loop : -0.15 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 177 TYR 0.026 0.001 TYR H 717 PHE 0.018 0.002 PHE H 742 TRP 0.015 0.001 TRP L 223 HIS 0.003 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00380 (11710) covalent geometry : angle 0.54983 (15843) SS BOND : bond 0.00363 ( 42) SS BOND : angle 1.12547 ( 84) hydrogen bonds : bond 0.02924 ( 325) hydrogen bonds : angle 5.60895 ( 801) link_ALPHA1-2 : bond 0.00306 ( 2) link_ALPHA1-2 : angle 1.56786 ( 6) link_ALPHA1-3 : bond 0.00896 ( 1) link_ALPHA1-3 : angle 2.06541 ( 3) link_ALPHA1-6 : bond 0.00083 ( 1) link_ALPHA1-6 : angle 1.94502 ( 3) link_BETA1-4 : bond 0.00589 ( 2) link_BETA1-4 : angle 2.85241 ( 6) link_NAG-ASN : bond 0.00232 ( 1) link_NAG-ASN : angle 2.44702 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 65 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 52 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8572 (t) REVERT: H 358 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8484 (mp) REVERT: H 467 TYR cc_start: 0.7107 (OUTLIER) cc_final: 0.6780 (m-80) REVERT: H 484 ASN cc_start: 0.6207 (t0) cc_final: 0.5699 (m-40) REVERT: H 531 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6712 (ttm) REVERT: H 905 MET cc_start: 0.3301 (OUTLIER) cc_final: 0.0633 (mpt) REVERT: L 278 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.6686 (tp30) outliers start: 45 outliers final: 22 residues processed: 102 average time/residue: 0.5737 time to fit residues: 63.9018 Evaluate side-chains 86 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 467 TYR Chi-restraints excluded: chain H residue 482 CYS Chi-restraints excluded: chain H residue 491 VAL Chi-restraints excluded: chain H residue 531 MET Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain H residue 695 THR Chi-restraints excluded: chain H residue 710 VAL Chi-restraints excluded: chain H residue 725 ILE Chi-restraints excluded: chain H residue 905 MET Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 251 ARG Chi-restraints excluded: chain L residue 278 GLU Chi-restraints excluded: chain A residue 6 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 139 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 96 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 22 optimal weight: 0.0970 chunk 114 optimal weight: 0.5980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 234 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.210671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.175990 restraints weight = 14600.547| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 1.92 r_work: 0.3865 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3817 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 11759 Z= 0.349 Angle : 0.708 8.620 15948 Z= 0.371 Chirality : 0.051 0.273 1740 Planarity : 0.005 0.054 2043 Dihedral : 7.818 58.691 1733 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.73 % Allowed : 17.42 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.22), residues: 1429 helix: -1.13 (0.41), residues: 164 sheet: -0.16 (0.26), residues: 405 loop : -0.33 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 177 TYR 0.032 0.002 TYR H 717 PHE 0.019 0.003 PHE L 287 TRP 0.014 0.002 TRP H 66 HIS 0.006 0.002 HIS H 729 Details of bonding type rmsd covalent geometry : bond 0.00837 (11710) covalent geometry : angle 0.69107 (15843) SS BOND : bond 0.00606 ( 42) SS BOND : angle 1.86262 ( 84) hydrogen bonds : bond 0.03621 ( 325) hydrogen bonds : angle 5.91766 ( 801) link_ALPHA1-2 : bond 0.00128 ( 2) link_ALPHA1-2 : angle 1.83169 ( 6) link_ALPHA1-3 : bond 0.00296 ( 1) link_ALPHA1-3 : angle 2.55994 ( 3) link_ALPHA1-6 : bond 0.00220 ( 1) link_ALPHA1-6 : angle 2.20774 ( 3) link_BETA1-4 : bond 0.00611 ( 2) link_BETA1-4 : angle 3.35260 ( 6) link_NAG-ASN : bond 0.00179 ( 1) link_NAG-ASN : angle 2.89898 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 58 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 47 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7501 (mm-30) REVERT: H 52 VAL cc_start: 0.9130 (OUTLIER) cc_final: 0.8814 (m) REVERT: H 358 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8345 (mt) REVERT: H 467 TYR cc_start: 0.7158 (OUTLIER) cc_final: 0.6817 (m-80) REVERT: H 484 ASN cc_start: 0.6200 (t0) cc_final: 0.5834 (m-40) REVERT: H 531 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6671 (ttm) REVERT: H 905 MET cc_start: 0.3130 (OUTLIER) cc_final: 0.0491 (mpt) REVERT: L 278 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.6800 (tp30) outliers start: 48 outliers final: 24 residues processed: 100 average time/residue: 0.4805 time to fit residues: 53.2289 Evaluate side-chains 85 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 55 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 464 VAL Chi-restraints excluded: chain H residue 465 THR Chi-restraints excluded: chain H residue 467 TYR Chi-restraints excluded: chain H residue 482 CYS Chi-restraints excluded: chain H residue 531 MET Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain H residue 695 THR Chi-restraints excluded: chain H residue 710 VAL Chi-restraints excluded: chain H residue 838 LYS Chi-restraints excluded: chain H residue 905 MET Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 251 ARG Chi-restraints excluded: chain L residue 264 SER Chi-restraints excluded: chain L residue 278 GLU Chi-restraints excluded: chain A residue 236 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 78 optimal weight: 9.9990 chunk 49 optimal weight: 0.4980 chunk 84 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 115 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 85 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 87 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 234 ASN A 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.213388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.177704 restraints weight = 14605.555| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 2.00 r_work: 0.3890 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3835 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11759 Z= 0.150 Angle : 0.587 7.313 15948 Z= 0.306 Chirality : 0.044 0.178 1740 Planarity : 0.004 0.052 2043 Dihedral : 7.238 58.292 1733 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.50 % Allowed : 18.12 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.22), residues: 1429 helix: -1.01 (0.41), residues: 165 sheet: -0.05 (0.26), residues: 403 loop : -0.21 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 553 TYR 0.034 0.001 TYR H 717 PHE 0.020 0.002 PHE H 742 TRP 0.019 0.001 TRP L 223 HIS 0.007 0.001 HIS H 729 Details of bonding type rmsd covalent geometry : bond 0.00356 (11710) covalent geometry : angle 0.57593 (15843) SS BOND : bond 0.00389 ( 42) SS BOND : angle 1.19145 ( 84) hydrogen bonds : bond 0.02897 ( 325) hydrogen bonds : angle 5.68578 ( 801) link_ALPHA1-2 : bond 0.00388 ( 2) link_ALPHA1-2 : angle 1.69955 ( 6) link_ALPHA1-3 : bond 0.00888 ( 1) link_ALPHA1-3 : angle 1.97047 ( 3) link_ALPHA1-6 : bond 0.00034 ( 1) link_ALPHA1-6 : angle 1.99306 ( 3) link_BETA1-4 : bond 0.00746 ( 2) link_BETA1-4 : angle 2.97757 ( 6) link_NAG-ASN : bond 0.00191 ( 1) link_NAG-ASN : angle 3.02358 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 60 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: H 52 VAL cc_start: 0.9056 (OUTLIER) cc_final: 0.8612 (t) REVERT: H 358 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8397 (mp) REVERT: H 467 TYR cc_start: 0.7111 (OUTLIER) cc_final: 0.6822 (m-80) REVERT: H 484 ASN cc_start: 0.6116 (t0) cc_final: 0.5684 (m-40) REVERT: H 531 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.6586 (ttm) REVERT: H 905 MET cc_start: 0.3105 (OUTLIER) cc_final: 0.0360 (mpt) REVERT: L 278 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.6684 (tp30) outliers start: 45 outliers final: 23 residues processed: 98 average time/residue: 0.5088 time to fit residues: 54.9725 Evaluate side-chains 87 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 58 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 462 CYS Chi-restraints excluded: chain H residue 465 THR Chi-restraints excluded: chain H residue 467 TYR Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 482 CYS Chi-restraints excluded: chain H residue 531 MET Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain H residue 695 THR Chi-restraints excluded: chain H residue 710 VAL Chi-restraints excluded: chain H residue 747 ILE Chi-restraints excluded: chain H residue 905 MET Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 251 ARG Chi-restraints excluded: chain L residue 278 GLU Chi-restraints excluded: chain A residue 236 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 138 optimal weight: 20.0000 chunk 117 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 234 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.210680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.174094 restraints weight = 14439.496| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 1.98 r_work: 0.3842 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3778 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 11759 Z= 0.253 Angle : 0.645 7.909 15948 Z= 0.336 Chirality : 0.047 0.226 1740 Planarity : 0.005 0.053 2043 Dihedral : 7.483 58.907 1733 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.88 % Allowed : 18.58 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.22), residues: 1429 helix: -1.04 (0.42), residues: 164 sheet: -0.09 (0.26), residues: 405 loop : -0.25 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 177 TYR 0.031 0.002 TYR H 717 PHE 0.016 0.002 PHE L 287 TRP 0.015 0.002 TRP H 66 HIS 0.006 0.001 HIS H 729 Details of bonding type rmsd covalent geometry : bond 0.00608 (11710) covalent geometry : angle 0.63096 (15843) SS BOND : bond 0.00497 ( 42) SS BOND : angle 1.48667 ( 84) hydrogen bonds : bond 0.03216 ( 325) hydrogen bonds : angle 5.75882 ( 801) link_ALPHA1-2 : bond 0.00183 ( 2) link_ALPHA1-2 : angle 1.77946 ( 6) link_ALPHA1-3 : bond 0.00512 ( 1) link_ALPHA1-3 : angle 2.29965 ( 3) link_ALPHA1-6 : bond 0.00008 ( 1) link_ALPHA1-6 : angle 1.95887 ( 3) link_BETA1-4 : bond 0.00608 ( 2) link_BETA1-4 : angle 3.22887 ( 6) link_NAG-ASN : bond 0.00207 ( 1) link_NAG-ASN : angle 3.09096 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 56 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 47 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7393 (mm-30) REVERT: H 52 VAL cc_start: 0.9112 (OUTLIER) cc_final: 0.8796 (m) REVERT: H 358 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8386 (mt) REVERT: H 467 TYR cc_start: 0.7208 (OUTLIER) cc_final: 0.6902 (m-80) REVERT: H 531 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6748 (ttm) REVERT: H 905 MET cc_start: 0.3063 (OUTLIER) cc_final: 0.0431 (mpt) REVERT: L 278 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.6772 (tp30) outliers start: 37 outliers final: 22 residues processed: 86 average time/residue: 0.4943 time to fit residues: 46.8364 Evaluate side-chains 82 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 54 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 462 CYS Chi-restraints excluded: chain H residue 465 THR Chi-restraints excluded: chain H residue 467 TYR Chi-restraints excluded: chain H residue 482 CYS Chi-restraints excluded: chain H residue 531 MET Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain H residue 695 THR Chi-restraints excluded: chain H residue 710 VAL Chi-restraints excluded: chain H residue 838 LYS Chi-restraints excluded: chain H residue 905 MET Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 251 ARG Chi-restraints excluded: chain L residue 278 GLU Chi-restraints excluded: chain A residue 236 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 136 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 125 optimal weight: 20.0000 chunk 106 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 129 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 234 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.211730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.175721 restraints weight = 14522.556| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 1.96 r_work: 0.3868 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 11759 Z= 0.244 Angle : 0.640 7.622 15948 Z= 0.334 Chirality : 0.047 0.220 1740 Planarity : 0.005 0.053 2043 Dihedral : 7.464 59.537 1733 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.72 % Allowed : 19.05 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.22), residues: 1429 helix: -1.08 (0.42), residues: 164 sheet: -0.07 (0.26), residues: 405 loop : -0.29 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 177 TYR 0.032 0.002 TYR H 717 PHE 0.020 0.002 PHE H 742 TRP 0.016 0.002 TRP L 223 HIS 0.007 0.001 HIS H 729 Details of bonding type rmsd covalent geometry : bond 0.00587 (11710) covalent geometry : angle 0.62683 (15843) SS BOND : bond 0.00482 ( 42) SS BOND : angle 1.42407 ( 84) hydrogen bonds : bond 0.03136 ( 325) hydrogen bonds : angle 5.73063 ( 801) link_ALPHA1-2 : bond 0.00217 ( 2) link_ALPHA1-2 : angle 1.76615 ( 6) link_ALPHA1-3 : bond 0.00626 ( 1) link_ALPHA1-3 : angle 2.23162 ( 3) link_ALPHA1-6 : bond 0.00076 ( 1) link_ALPHA1-6 : angle 1.97941 ( 3) link_BETA1-4 : bond 0.00613 ( 2) link_BETA1-4 : angle 3.17096 ( 6) link_NAG-ASN : bond 0.00246 ( 1) link_NAG-ASN : angle 3.28660 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 56 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 47 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7474 (mm-30) REVERT: H 52 VAL cc_start: 0.9095 (OUTLIER) cc_final: 0.8773 (m) REVERT: H 358 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8352 (mt) REVERT: H 467 TYR cc_start: 0.7198 (OUTLIER) cc_final: 0.6936 (m-80) REVERT: H 484 ASN cc_start: 0.6348 (t0) cc_final: 0.5655 (t160) REVERT: H 531 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6684 (ttm) REVERT: H 905 MET cc_start: 0.3014 (OUTLIER) cc_final: 0.0375 (mpt) REVERT: L 278 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.6750 (tp30) outliers start: 35 outliers final: 23 residues processed: 86 average time/residue: 0.5361 time to fit residues: 50.8442 Evaluate side-chains 83 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 54 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 462 CYS Chi-restraints excluded: chain H residue 465 THR Chi-restraints excluded: chain H residue 467 TYR Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 482 CYS Chi-restraints excluded: chain H residue 531 MET Chi-restraints excluded: chain H residue 573 CYS Chi-restraints excluded: chain H residue 695 THR Chi-restraints excluded: chain H residue 710 VAL Chi-restraints excluded: chain H residue 838 LYS Chi-restraints excluded: chain H residue 905 MET Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 206 SER Chi-restraints excluded: chain L residue 220 THR Chi-restraints excluded: chain L residue 251 ARG Chi-restraints excluded: chain L residue 278 GLU Chi-restraints excluded: chain A residue 236 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 0 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 chunk 116 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 chunk 115 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 234 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.213085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.177113 restraints weight = 14593.182| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 1.99 r_work: 0.3886 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3831 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11759 Z= 0.165 Angle : 0.586 7.188 15948 Z= 0.307 Chirality : 0.044 0.193 1740 Planarity : 0.004 0.052 2043 Dihedral : 7.071 58.973 1733 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.57 % Allowed : 19.28 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.22), residues: 1429 helix: -1.03 (0.42), residues: 165 sheet: -0.01 (0.26), residues: 403 loop : -0.25 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 553 TYR 0.031 0.001 TYR H 717 PHE 0.015 0.002 PHE H 64 TRP 0.018 0.001 TRP L 223 HIS 0.007 0.001 HIS H 729 Details of bonding type rmsd covalent geometry : bond 0.00392 (11710) covalent geometry : angle 0.57463 (15843) SS BOND : bond 0.00396 ( 42) SS BOND : angle 1.15705 ( 84) hydrogen bonds : bond 0.02833 ( 325) hydrogen bonds : angle 5.58517 ( 801) link_ALPHA1-2 : bond 0.00333 ( 2) link_ALPHA1-2 : angle 1.67870 ( 6) link_ALPHA1-3 : bond 0.00845 ( 1) link_ALPHA1-3 : angle 2.06318 ( 3) link_ALPHA1-6 : bond 0.00091 ( 1) link_ALPHA1-6 : angle 1.89482 ( 3) link_BETA1-4 : bond 0.00547 ( 2) link_BETA1-4 : angle 3.01349 ( 6) link_NAG-ASN : bond 0.00227 ( 1) link_NAG-ASN : angle 3.24927 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4330.33 seconds wall clock time: 74 minutes 53.18 seconds (4493.18 seconds total)