Starting phenix.real_space_refine on Tue Aug 26 12:14:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hfl_52115/08_2025/9hfl_52115_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hfl_52115/08_2025/9hfl_52115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hfl_52115/08_2025/9hfl_52115.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hfl_52115/08_2025/9hfl_52115.map" model { file = "/net/cci-nas-00/data/ceres_data/9hfl_52115/08_2025/9hfl_52115_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hfl_52115/08_2025/9hfl_52115_trim.cif" } resolution = 2.62 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= 0.004 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: 7 Type Number sf(0) Gaussians P 7 5.49 5 Mg 1 5.21 5 S 104 5.16 5 C 11365 2.51 5 N 3034 2.21 5 O 3291 1.98 5 H 17699 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35501 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 16951 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1037, 16882 Classifications: {'peptide': 1037} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 1001} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 1037, 16882 Classifications: {'peptide': 1037} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 1001} Chain breaks: 1 bond proxies already assigned to first conformer: 16982 Chain: "B" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2823 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain: "C" Number of atoms: 12224 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 747, 12207 Classifications: {'peptide': 747} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 706} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 747, 12207 Classifications: {'peptide': 747} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 706} Chain breaks: 2 bond proxies already assigned to first conformer: 12343 Chain: "D" Number of atoms: 2430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2430 Classifications: {'peptide': 152} Link IDs: {'TRANS': 151} Chain: "N" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 98 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Chain: "P" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 826 Classifications: {'peptide': 51} Link IDs: {'TRANS': 50} Chain: "R" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Classifications: {'RNA': 1} Modifications used: {'rna3p_pur': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'GTA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "R" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ATYR A 469 " occ=0.50 ... (40 atoms not shown) pdb=" HH BTYR A 469 " occ=0.50 residue: pdb=" N AARG A 765 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG A 765 " occ=0.50 residue: pdb=" N AARG A 887 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG A 887 " occ=0.50 residue: pdb=" N AGLN C 748 " occ=0.50 ... (32 atoms not shown) pdb="HE22BGLN C 748 " occ=0.50 Time building chain proxies: 9.87, per 1000 atoms: 0.28 Number of scatterers: 35501 At special positions: 0 Unit cell: (91.56, 112.56, 173.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 104 16.00 P 7 15.00 Mg 1 11.99 O 3291 8.00 N 3034 7.00 C 11365 6.00 H 17699 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4168 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 4 sheets defined 75.9% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 8 through 18 Processing helix chain 'A' and resid 24 through 38 Processing helix chain 'A' and resid 40 through 56 removed outlier: 3.973A pdb=" N ARG A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 70 removed outlier: 3.550A pdb=" N VAL A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP A 64 " --> pdb=" O TRP A 60 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N THR A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 91 removed outlier: 3.676A pdb=" N TRP A 91 " --> pdb=" O ILE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 116 removed outlier: 3.726A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 Processing helix chain 'A' and resid 124 through 142 Processing helix chain 'A' and resid 148 through 160 Processing helix chain 'A' and resid 160 through 180 Processing helix chain 'A' and resid 187 through 201 Processing helix chain 'A' and resid 201 through 216 removed outlier: 4.049A pdb=" N ILE A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 245 through 254 Processing helix chain 'A' and resid 260 through 274 removed outlier: 3.698A pdb=" N VAL A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 298 Processing helix chain 'A' and resid 303 through 311 Processing helix chain 'A' and resid 312 through 339 removed outlier: 6.683A pdb=" N GLN A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 343 through 359 Processing helix chain 'A' and resid 362 through 384 Processing helix chain 'A' and resid 403 through 423 Proline residue: A 411 - end of helix removed outlier: 4.411A pdb=" N PHE A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LYS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 468 Processing helix chain 'A' and resid 468 through 486 removed outlier: 4.063A pdb=" N THR A 472 " --> pdb=" O ASP A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 504 removed outlier: 3.686A pdb=" N ILE A 504 " --> pdb=" O ALA A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 531 Processing helix chain 'A' and resid 533 through 550 Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 558 through 573 Processing helix chain 'A' and resid 579 through 595 Processing helix chain 'A' and resid 596 through 599 Processing helix chain 'A' and resid 609 through 617 removed outlier: 3.560A pdb=" N GLU A 613 " --> pdb=" O PRO A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 622 Processing helix chain 'A' and resid 626 through 643 removed outlier: 3.716A pdb=" N ALA A 643 " --> pdb=" O TYR A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 658 Processing helix chain 'A' and resid 658 through 675 removed outlier: 3.612A pdb=" N VAL A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 680 Processing helix chain 'A' and resid 681 through 703 Processing helix chain 'A' and resid 706 through 736 removed outlier: 5.467A pdb=" N LEU A 715 " --> pdb=" O GLY A 711 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ASP A 716 " --> pdb=" O ARG A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 741 Processing helix chain 'A' and resid 742 through 766 Processing helix chain 'A' and resid 768 through 776 Processing helix chain 'A' and resid 776 through 784 removed outlier: 3.653A pdb=" N LEU A 780 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP A 782 " --> pdb=" O PRO A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 791 Processing helix chain 'A' and resid 792 through 797 removed outlier: 6.081A pdb=" N GLU A 797 " --> pdb=" O ALA A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 812 removed outlier: 3.512A pdb=" N SER A 802 " --> pdb=" O PRO A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 817 removed outlier: 3.779A pdb=" N THR A 816 " --> pdb=" O GLY A 813 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ALA A 817 " --> pdb=" O HIS A 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 813 through 817' Processing helix chain 'A' and resid 818 through 832 removed outlier: 5.709A pdb=" N GLU A 828 " --> pdb=" O ASP A 824 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N CYS A 829 " --> pdb=" O ALA A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 859 Processing helix chain 'A' and resid 859 through 865 removed outlier: 3.737A pdb=" N PHE A 863 " --> pdb=" O CYS A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 883 Processing helix chain 'A' and resid 886 through 907 Processing helix chain 'A' and resid 907 through 931 removed outlier: 4.219A pdb=" N GLN A 912 " --> pdb=" O GLU A 908 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N SER A 913 " --> pdb=" O ALA A 909 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N CYS A 920 " --> pdb=" O GLN A 916 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ASP A 921 " --> pdb=" O THR A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 937 removed outlier: 3.585A pdb=" N THR A 936 " --> pdb=" O THR A 933 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ALA A 937 " --> pdb=" O SER A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 955 Processing helix chain 'A' and resid 969 through 986 Processing helix chain 'A' and resid 990 through 1004 Processing helix chain 'A' and resid 1007 through 1022 Processing helix chain 'A' and resid 1034 through 1055 Processing helix chain 'B' and resid 22 through 33 Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'B' and resid 94 through 100 removed outlier: 3.770A pdb=" N TYR B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 112 removed outlier: 3.954A pdb=" N VAL B 111 " --> pdb=" O ASP B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 removed outlier: 3.803A pdb=" N ILE B 136 " --> pdb=" O ALA B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 143 removed outlier: 4.450A pdb=" N LYS B 141 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS B 142 " --> pdb=" O PHE B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 170 Processing helix chain 'C' and resid 26 through 38 removed outlier: 3.523A pdb=" N VAL C 38 " --> pdb=" O LEU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 61 Processing helix chain 'C' and resid 64 through 79 Processing helix chain 'C' and resid 82 through 97 removed outlier: 3.562A pdb=" N LEU C 89 " --> pdb=" O ILE C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 118 Processing helix chain 'C' and resid 120 through 137 removed outlier: 3.660A pdb=" N ASN C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 155 removed outlier: 3.516A pdb=" N MET C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 162 through 176 removed outlier: 3.819A pdb=" N ARG C 166 " --> pdb=" O PRO C 162 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 188 removed outlier: 6.350A pdb=" N LYS C 182 " --> pdb=" O PRO C 178 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N GLU C 183 " --> pdb=" O TRP C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 205 removed outlier: 3.636A pdb=" N ARG C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 215 Processing helix chain 'C' and resid 227 through 242 Processing helix chain 'C' and resid 251 through 255 Processing helix chain 'C' and resid 256 through 262 removed outlier: 3.918A pdb=" N GLU C 262 " --> pdb=" O SER C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 308 through 325 removed outlier: 3.518A pdb=" N PHE C 312 " --> pdb=" O SER C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 338 Processing helix chain 'C' and resid 346 through 360 Processing helix chain 'C' and resid 368 through 383 removed outlier: 3.944A pdb=" N TYR C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR C 373 " --> pdb=" O ASP C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 401 Processing helix chain 'C' and resid 406 through 423 Processing helix chain 'C' and resid 429 through 439 removed outlier: 4.966A pdb=" N ASP C 435 " --> pdb=" O ASP C 432 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN C 439 " --> pdb=" O CYS C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 459 Processing helix chain 'C' and resid 461 through 469 removed outlier: 3.686A pdb=" N VAL C 469 " --> pdb=" O ILE C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 477 removed outlier: 4.691A pdb=" N ALA C 475 " --> pdb=" O THR C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 495 removed outlier: 4.223A pdb=" N SER C 494 " --> pdb=" O SER C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 510 Processing helix chain 'C' and resid 513 through 522 Processing helix chain 'C' and resid 540 through 555 Processing helix chain 'C' and resid 558 through 569 Processing helix chain 'C' and resid 569 through 577 Processing helix chain 'C' and resid 579 through 594 Processing helix chain 'C' and resid 597 through 611 Processing helix chain 'C' and resid 615 through 624 removed outlier: 3.596A pdb=" N PHE C 624 " --> pdb=" O ALA C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 674 removed outlier: 4.028A pdb=" N TRP C 638 " --> pdb=" O ARG C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 732 Processing helix chain 'C' and resid 737 through 754 removed outlier: 3.630A pdb=" N HIS C 754 " --> pdb=" O ILE C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 760 removed outlier: 4.110A pdb=" N GLN C 760 " --> pdb=" O GLN C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 768 Processing helix chain 'C' and resid 775 through 788 removed outlier: 4.003A pdb=" N VAL C 781 " --> pdb=" O HIS C 777 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE C 782 " --> pdb=" O ILE C 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 11 Processing helix chain 'D' and resid 12 through 16 removed outlier: 3.562A pdb=" N GLU D 16 " --> pdb=" O SER D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 38 removed outlier: 3.620A pdb=" N LYS D 38 " --> pdb=" O LYS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 61 Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.510A pdb=" N ALA D 94 " --> pdb=" O SER D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 139 Processing helix chain 'D' and resid 143 through 147 removed outlier: 3.652A pdb=" N GLY D 147 " --> pdb=" O ALA D 144 " (cutoff:3.500A) Processing helix chain 'P' and resid 116 through 136 Processing helix chain 'P' and resid 147 through 151 Processing helix chain 'P' and resid 153 through 162 Processing sheet with id=AA1, first strand: chain 'A' and resid 430 through 434 Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 54 removed outlier: 3.532A pdb=" N GLY B 57 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N PHE B 11 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N TRP B 64 " --> pdb=" O PHE B 11 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU B 13 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR B 66 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU B 15 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 9.245A pdb=" N CYS B 85 " --> pdb=" O GLN B 10 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LYS B 12 " --> pdb=" O CYS B 85 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE B 87 " --> pdb=" O LYS B 12 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL B 14 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N MET B 89 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL B 16 " --> pdb=" O MET B 89 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N ASP B 91 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA B 86 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N CYS B 120 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE B 88 " --> pdb=" O CYS B 120 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ASN B 122 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N PHE B 90 " --> pdb=" O ASN B 122 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE B 117 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N TYR B 147 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU B 119 " --> pdb=" O TYR B 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 66 through 73 removed outlier: 4.977A pdb=" N PHE D 83 " --> pdb=" O GLY D 72 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N THR D 41 " --> pdb=" O ASP D 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 105 through 106 1155 hydrogen bonds defined for protein. 3359 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: 9.07 Time building geometry restraints manager: 4.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17655 1.03 - 1.23: 49 1.23 - 1.42: 7585 1.42 - 1.62: 10413 1.62 - 1.81: 165 Bond restraints: 35867 Sorted by residual: bond pdb=" C5 GTA R 101 " pdb=" C6 GTA R 101 " ideal model delta sigma weight residual 1.422 1.332 0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C2C GTA R 101 " pdb=" N3C GTA R 101 " ideal model delta sigma weight residual 1.322 1.396 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C5C GTA R 101 " pdb=" C6C GTA R 101 " ideal model delta sigma weight residual 1.404 1.331 0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C2C GTA R 101 " pdb=" N1C GTA R 101 " ideal model delta sigma weight residual 1.331 1.395 -0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" O23 GTA R 101 " pdb=" P2 GTA R 101 " ideal model delta sigma weight residual 1.658 1.602 0.056 2.00e-02 2.50e+03 7.91e+00 ... (remaining 35862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 64716 2.65 - 5.30: 130 5.30 - 7.95: 12 7.95 - 10.61: 9 10.61 - 13.26: 5 Bond angle restraints: 64872 Sorted by residual: angle pdb=" PB GTP B 301 " pdb=" O3B GTP B 301 " pdb=" PG GTP B 301 " ideal model delta sigma weight residual 120.50 133.76 -13.26 3.00e+00 1.11e-01 1.95e+01 angle pdb=" PA GTP B 301 " pdb=" O3A GTP B 301 " pdb=" PB GTP B 301 " ideal model delta sigma weight residual 120.50 133.13 -12.63 3.00e+00 1.11e-01 1.77e+01 angle pdb=" C1' GTP B 301 " pdb=" C2' GTP B 301 " pdb=" C3' GTP B 301 " ideal model delta sigma weight residual 111.00 99.09 11.91 3.00e+00 1.11e-01 1.58e+01 angle pdb=" C2' GTP B 301 " pdb=" C3' GTP B 301 " pdb=" C4' GTP B 301 " ideal model delta sigma weight residual 111.00 99.75 11.25 3.00e+00 1.11e-01 1.41e+01 angle pdb=" O1B GTP B 301 " pdb=" PB GTP B 301 " pdb=" O2B GTP B 301 " ideal model delta sigma weight residual 109.50 120.18 -10.68 3.00e+00 1.11e-01 1.27e+01 ... (remaining 64867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 16259 35.75 - 71.50: 531 71.50 - 107.25: 32 107.25 - 143.00: 1 143.00 - 178.74: 2 Dihedral angle restraints: 16825 sinusoidal: 9181 harmonic: 7644 Sorted by residual: dihedral pdb=" C8 GTP B 301 " pdb=" C1' GTP B 301 " pdb=" N9 GTP B 301 " pdb=" O4' GTP B 301 " ideal model delta sinusoidal sigma weight residual 104.59 -74.15 178.74 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O3B GTP B 301 " pdb=" O3A GTP B 301 " pdb=" PB GTP B 301 " pdb=" PA GTP B 301 " ideal model delta sinusoidal sigma weight residual -68.92 85.47 -154.39 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" O3A GTP B 301 " pdb=" O3B GTP B 301 " pdb=" PB GTP B 301 " pdb=" PG GTP B 301 " ideal model delta sinusoidal sigma weight residual -56.21 -172.36 116.15 1 2.00e+01 2.50e-03 3.46e+01 ... (remaining 16822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2410 0.054 - 0.108: 297 0.108 - 0.162: 32 0.162 - 0.217: 2 0.217 - 0.271: 3 Chirality restraints: 2744 Sorted by residual: chirality pdb=" C3' GTP B 301 " pdb=" C2' GTP B 301 " pdb=" C4' GTP B 301 " pdb=" O3' GTP B 301 " both_signs ideal model delta sigma weight residual False -2.47 -2.74 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C1B GTA R 101 " pdb=" C2B GTA R 101 " pdb=" N9C GTA R 101 " pdb=" O4B GTA R 101 " both_signs ideal model delta sigma weight residual False 2.34 2.57 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C4B GTA R 101 " pdb=" C3B GTA R 101 " pdb=" C5B GTA R 101 " pdb=" O4B GTA R 101 " both_signs ideal model delta sigma weight residual False -2.53 -2.75 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2741 not shown) Planarity restraints: 5211 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 947 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.98e+00 pdb=" C ALA A 947 " -0.030 2.00e-02 2.50e+03 pdb=" O ALA A 947 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR A 948 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 440 " -0.023 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO C 441 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 441 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 441 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 948 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" C TYR A 948 " 0.024 2.00e-02 2.50e+03 pdb=" O TYR A 948 " -0.009 2.00e-02 2.50e+03 pdb=" N MET A 949 " -0.008 2.00e-02 2.50e+03 ... (remaining 5208 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1185 2.16 - 2.77: 68331 2.77 - 3.38: 104029 3.38 - 3.99: 131899 3.99 - 4.60: 209839 Nonbonded interactions: 515283 Sorted by model distance: nonbonded pdb="HH22 ARG C 165 " pdb=" O PRO C 274 " model vdw 1.548 2.450 nonbonded pdb="HH12 ARG C 290 " pdb=" OE2 GLU C 315 " model vdw 1.589 2.450 nonbonded pdb=" O LEU A 298 " pdb=" HH TYR A 353 " model vdw 1.604 2.450 nonbonded pdb=" O LEU A 286 " pdb=" HG1 THR A 290 " model vdw 1.608 2.450 nonbonded pdb=" O ILE A 87 " pdb="HE21 GLN A 140 " model vdw 1.625 2.450 ... (remaining 515278 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.230 Extract box with map and model: 0.510 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 38.030 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 : 0.003 0.090 18169 Z= 0.155 Angle : 0.524 13.256 24609 Z= 0.248 Chirality : 0.036 0.271 2744 Planarity : 0.003 0.035 3127 Dihedral : 17.678 178.745 6835 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.19 % Allowed : 16.62 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 2.80 (0.19), residues: 2159 helix: 2.54 (0.14), residues: 1480 sheet: -0.22 (0.56), residues: 72 loop : 0.43 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1016 TYR 0.015 0.001 TYR A 372 PHE 0.021 0.001 PHE A 882 TRP 0.016 0.001 TRP A 762 HIS 0.006 0.001 HIS A 481 Details of bonding type rmsd covalent geometry : bond 0.00316 (18168) covalent geometry : angle 0.52389 (24609) hydrogen bonds : bond 0.11913 ( 1155) hydrogen bonds : angle 5.26486 ( 3359) Misc. bond : bond 0.04301 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 190 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Evaluate side-chains 407 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 365 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1017 ASP cc_start: 0.7828 (m-30) cc_final: 0.7451 (m-30) REVERT: C 572 VAL cc_start: 0.7903 (t) cc_final: 0.7648 (t) outliers start: 42 outliers final: 13 residues processed: 395 average time/residue: 1.2965 time to fit residues: 573.4376 Evaluate side-chains 229 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 216 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 481 HIS Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain N residue 56 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN A 483 GLN A 993 GLN A1021 GLN B 8 GLN C 348 ASN C 498 HIS C 724 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.122422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.088593 restraints weight = 132242.779| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.53 r_work: 0.3230 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18169 Z= 0.200 Angle : 0.576 8.966 24609 Z= 0.305 Chirality : 0.038 0.203 2744 Planarity : 0.005 0.058 3127 Dihedral : 8.933 177.283 2447 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.89 % Allowed : 23.05 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 2.81 (0.18), residues: 2159 helix: 2.59 (0.13), residues: 1496 sheet: -0.27 (0.58), residues: 69 loop : 0.27 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 231 TYR 0.018 0.002 TYR A 78 PHE 0.025 0.001 PHE A 882 TRP 0.019 0.002 TRP A 762 HIS 0.008 0.001 HIS C 30 Details of bonding type rmsd covalent geometry : bond 0.00444 (18168) covalent geometry : angle 0.57552 (24609) hydrogen bonds : bond 0.04579 ( 1155) hydrogen bonds : angle 4.43875 ( 3359) Misc. bond : bond 0.00074 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 190 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Evaluate side-chains 256 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8513 (mmt) cc_final: 0.8193 (mmt) REVERT: A 437 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.7146 (mp10) REVERT: A 1043 ARG cc_start: 0.7955 (tmm-80) cc_final: 0.7703 (tmm-80) REVERT: B 28 LYS cc_start: 0.9186 (mtpp) cc_final: 0.8967 (ttmm) REVERT: D 10 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7673 (tpp80) REVERT: D 16 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: P 143 ILE cc_start: 0.8528 (tt) cc_final: 0.8301 (tt) REVERT: P 144 ASP cc_start: 0.7455 (t0) cc_final: 0.7198 (t0) outliers start: 36 outliers final: 12 residues processed: 244 average time/residue: 1.1617 time to fit residues: 318.6263 Evaluate side-chains 209 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 194 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 655 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 539 PHE Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain D residue 10 ARG Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain N residue 56 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 24 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 189 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN A 481 HIS A 483 GLN B 8 GLN C 348 ASN C 498 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.120330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.085697 restraints weight = 131511.152| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.64 r_work: 0.3238 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18169 Z= 0.170 Angle : 0.538 8.092 24609 Z= 0.283 Chirality : 0.037 0.182 2744 Planarity : 0.004 0.043 3127 Dihedral : 8.179 176.283 2429 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.09 % Allowed : 22.49 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 2.82 (0.18), residues: 2159 helix: 2.65 (0.13), residues: 1483 sheet: -0.31 (0.57), residues: 69 loop : 0.17 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 231 TYR 0.022 0.001 TYR A 78 PHE 0.022 0.001 PHE A 882 TRP 0.019 0.001 TRP A 762 HIS 0.008 0.001 HIS C 30 Details of bonding type rmsd covalent geometry : bond 0.00383 (18168) covalent geometry : angle 0.53764 (24609) hydrogen bonds : bond 0.04230 ( 1155) hydrogen bonds : angle 4.28308 ( 3359) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 190 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Evaluate side-chains 247 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 207 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8472 (mmt) cc_final: 0.8182 (mmt) REVERT: C 606 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7951 (t0) REVERT: D 16 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: D 54 GLU cc_start: 0.8154 (mp0) cc_final: 0.7939 (mp0) REVERT: D 137 GLU cc_start: 0.8408 (pt0) cc_final: 0.7728 (pp20) REVERT: P 123 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8448 (tm-30) REVERT: P 144 ASP cc_start: 0.7686 (t0) cc_final: 0.7454 (t0) outliers start: 40 outliers final: 15 residues processed: 232 average time/residue: 1.2199 time to fit residues: 319.3872 Evaluate side-chains 206 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 481 HIS Chi-restraints excluded: chain A residue 655 GLU Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 539 PHE Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain N residue 56 HIS Chi-restraints excluded: chain P residue 123 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 190 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 184 optimal weight: 10.0000 chunk 205 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 483 GLN C 348 ASN C 498 HIS D 29 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.120624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.086405 restraints weight = 141782.389| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.71 r_work: 0.3251 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18169 Z= 0.132 Angle : 0.523 7.060 24609 Z= 0.274 Chirality : 0.036 0.166 2744 Planarity : 0.004 0.038 3127 Dihedral : 7.951 173.807 2429 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.73 % Allowed : 22.64 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 2.91 (0.18), residues: 2159 helix: 2.73 (0.13), residues: 1478 sheet: -0.44 (0.57), residues: 69 loop : 0.23 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 231 TYR 0.014 0.001 TYR A 78 PHE 0.021 0.001 PHE A 882 TRP 0.019 0.001 TRP A 762 HIS 0.032 0.001 HIS A 481 Details of bonding type rmsd covalent geometry : bond 0.00294 (18168) covalent geometry : angle 0.52341 (24609) hydrogen bonds : bond 0.03925 ( 1155) hydrogen bonds : angle 4.16584 ( 3359) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 190 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Evaluate side-chains 230 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8486 (mmt) cc_final: 0.8199 (mmt) REVERT: A 476 MET cc_start: 0.9125 (mtt) cc_final: 0.8910 (mtt) REVERT: C 606 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7953 (t0) REVERT: D 16 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: D 54 GLU cc_start: 0.8217 (mp0) cc_final: 0.7993 (mp0) REVERT: P 123 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8440 (tm-30) REVERT: P 144 ASP cc_start: 0.7743 (t0) cc_final: 0.7497 (t0) outliers start: 33 outliers final: 12 residues processed: 216 average time/residue: 1.3761 time to fit residues: 334.0463 Evaluate side-chains 203 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 247 ARG Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain N residue 56 HIS Chi-restraints excluded: chain P residue 123 GLN Chi-restraints excluded: chain P residue 156 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 90 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 195 optimal weight: 5.9990 chunk 211 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN D 29 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.121092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.087127 restraints weight = 138438.162| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.62 r_work: 0.3325 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18169 Z= 0.156 Angle : 0.523 6.914 24609 Z= 0.273 Chirality : 0.036 0.154 2744 Planarity : 0.004 0.053 3127 Dihedral : 7.858 173.964 2429 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.63 % Allowed : 22.90 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 2.89 (0.18), residues: 2159 helix: 2.74 (0.13), residues: 1476 sheet: -0.45 (0.57), residues: 69 loop : 0.15 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 10 TYR 0.015 0.001 TYR A 78 PHE 0.022 0.001 PHE A 882 TRP 0.019 0.001 TRP A 762 HIS 0.008 0.001 HIS C 30 Details of bonding type rmsd covalent geometry : bond 0.00352 (18168) covalent geometry : angle 0.52292 (24609) hydrogen bonds : bond 0.03850 ( 1155) hydrogen bonds : angle 4.13607 ( 3359) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 190 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Evaluate side-chains 224 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8509 (mmt) cc_final: 0.8225 (mmt) REVERT: A 217 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8305 (mp10) REVERT: A 437 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.6073 (mm-40) REVERT: A 989 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8349 (mp) REVERT: C 606 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7988 (t0) REVERT: D 16 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: D 54 GLU cc_start: 0.8311 (mp0) cc_final: 0.8070 (mp0) REVERT: P 123 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8460 (tm-30) REVERT: P 144 ASP cc_start: 0.7826 (t0) cc_final: 0.7560 (t0) outliers start: 31 outliers final: 15 residues processed: 211 average time/residue: 1.3721 time to fit residues: 328.2607 Evaluate side-chains 206 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain N residue 56 HIS Chi-restraints excluded: chain P residue 123 GLN Chi-restraints excluded: chain P residue 156 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 130 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 184 optimal weight: 9.9990 chunk 208 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 980 ASN D 29 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.118232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.083579 restraints weight = 133460.281| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.65 r_work: 0.3196 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18169 Z= 0.220 Angle : 0.565 8.681 24609 Z= 0.297 Chirality : 0.038 0.204 2744 Planarity : 0.004 0.062 3127 Dihedral : 8.054 178.151 2429 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.84 % Allowed : 22.44 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 2.65 (0.18), residues: 2159 helix: 2.54 (0.13), residues: 1486 sheet: -0.46 (0.57), residues: 69 loop : 0.05 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 76 TYR 0.017 0.002 TYR A 657 PHE 0.024 0.002 PHE A 882 TRP 0.019 0.002 TRP A 762 HIS 0.009 0.001 HIS C 30 Details of bonding type rmsd covalent geometry : bond 0.00497 (18168) covalent geometry : angle 0.56470 (24609) hydrogen bonds : bond 0.04151 ( 1155) hydrogen bonds : angle 4.22407 ( 3359) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 190 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Evaluate side-chains 222 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8518 (mmt) cc_final: 0.8259 (mmt) REVERT: A 217 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8346 (mp10) REVERT: A 412 MET cc_start: 0.7952 (pmm) cc_final: 0.7501 (pp-130) REVERT: A 437 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.5951 (mm-40) REVERT: C 226 GLU cc_start: 0.7555 (mp0) cc_final: 0.7327 (mp0) REVERT: D 16 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8074 (mp0) REVERT: D 54 GLU cc_start: 0.8318 (mp0) cc_final: 0.8085 (mp0) REVERT: P 123 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8468 (tm-30) REVERT: P 144 ASP cc_start: 0.7824 (t0) cc_final: 0.7602 (t0) outliers start: 35 outliers final: 17 residues processed: 209 average time/residue: 1.2550 time to fit residues: 297.6860 Evaluate side-chains 203 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain N residue 56 HIS Chi-restraints excluded: chain P residue 123 GLN Chi-restraints excluded: chain P residue 156 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 92 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 199 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 200 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.118652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.084184 restraints weight = 155805.312| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.86 r_work: 0.3209 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18169 Z= 0.161 Angle : 0.539 8.870 24609 Z= 0.281 Chirality : 0.036 0.173 2744 Planarity : 0.004 0.059 3127 Dihedral : 7.930 175.569 2429 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.78 % Allowed : 22.59 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 2.75 (0.18), residues: 2159 helix: 2.62 (0.13), residues: 1487 sheet: -0.43 (0.57), residues: 69 loop : 0.06 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 76 TYR 0.012 0.001 TYR C 121 PHE 0.021 0.001 PHE A 882 TRP 0.021 0.001 TRP A 762 HIS 0.009 0.001 HIS C 30 Details of bonding type rmsd covalent geometry : bond 0.00364 (18168) covalent geometry : angle 0.53851 (24609) hydrogen bonds : bond 0.03873 ( 1155) hydrogen bonds : angle 4.13158 ( 3359) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 190 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8516 (mmt) cc_final: 0.8264 (mmt) REVERT: A 217 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8336 (mp10) REVERT: A 412 MET cc_start: 0.7915 (pmm) cc_final: 0.7479 (pp-130) REVERT: A 437 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.5879 (mm-40) REVERT: A 1054 MET cc_start: 0.5539 (mpp) cc_final: 0.4831 (pp-130) REVERT: C 226 GLU cc_start: 0.7554 (mp0) cc_final: 0.7349 (mp0) REVERT: C 606 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7985 (t0) REVERT: D 16 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8052 (mp0) REVERT: D 54 GLU cc_start: 0.8366 (mp0) cc_final: 0.8083 (mp0) REVERT: D 121 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8315 (tp30) REVERT: P 144 ASP cc_start: 0.7825 (t0) cc_final: 0.7604 (t0) outliers start: 34 outliers final: 19 residues processed: 218 average time/residue: 1.1620 time to fit residues: 286.3986 Evaluate side-chains 210 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 606 ASP Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain N residue 56 HIS Chi-restraints excluded: chain P residue 156 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 90 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 169 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN ** D 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.119077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.085427 restraints weight = 133471.573| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.51 r_work: 0.3305 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3310 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18169 Z= 0.187 Angle : 0.555 9.168 24609 Z= 0.289 Chirality : 0.037 0.184 2744 Planarity : 0.004 0.065 3127 Dihedral : 7.932 176.429 2429 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.73 % Allowed : 22.85 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 2.68 (0.18), residues: 2159 helix: 2.58 (0.13), residues: 1489 sheet: -0.44 (0.57), residues: 69 loop : 0.01 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 76 TYR 0.014 0.001 TYR A 657 PHE 0.023 0.001 PHE A 882 TRP 0.020 0.001 TRP A 762 HIS 0.009 0.001 HIS C 30 Details of bonding type rmsd covalent geometry : bond 0.00424 (18168) covalent geometry : angle 0.55547 (24609) hydrogen bonds : bond 0.03946 ( 1155) hydrogen bonds : angle 4.15672 ( 3359) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 190 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8533 (mmt) cc_final: 0.8288 (mmt) REVERT: A 217 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8333 (mp10) REVERT: A 437 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.5980 (mm-40) REVERT: A 989 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8412 (mp) REVERT: A 1054 MET cc_start: 0.5496 (mpp) cc_final: 0.4786 (pp-130) REVERT: D 16 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: D 54 GLU cc_start: 0.8351 (mp0) cc_final: 0.8065 (mp0) REVERT: D 121 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8364 (tp30) REVERT: P 144 ASP cc_start: 0.7832 (t0) cc_final: 0.7599 (t0) outliers start: 33 outliers final: 18 residues processed: 209 average time/residue: 1.2002 time to fit residues: 282.2115 Evaluate side-chains 207 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain N residue 56 HIS Chi-restraints excluded: chain P residue 156 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 57 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 210 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.120498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.087924 restraints weight = 149795.726| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.59 r_work: 0.3307 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18169 Z= 0.167 Angle : 0.553 10.610 24609 Z= 0.287 Chirality : 0.036 0.176 2744 Planarity : 0.004 0.063 3127 Dihedral : 7.845 175.169 2429 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.27 % Allowed : 23.25 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 2.74 (0.18), residues: 2159 helix: 2.64 (0.13), residues: 1488 sheet: -0.46 (0.58), residues: 69 loop : -0.02 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 76 TYR 0.012 0.001 TYR A 657 PHE 0.022 0.001 PHE A 882 TRP 0.021 0.001 TRP A 762 HIS 0.009 0.001 HIS C 30 Details of bonding type rmsd covalent geometry : bond 0.00377 (18168) covalent geometry : angle 0.55329 (24609) hydrogen bonds : bond 0.03844 ( 1155) hydrogen bonds : angle 4.12506 ( 3359) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 190 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8511 (mmt) cc_final: 0.8270 (mmt) REVERT: A 217 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8380 (mp10) REVERT: A 286 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8625 (tp) REVERT: A 412 MET cc_start: 0.7960 (pmm) cc_final: 0.7408 (pp-130) REVERT: A 437 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.5858 (mm-40) REVERT: A 989 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8391 (mp) REVERT: A 1043 ARG cc_start: 0.8125 (tmm-80) cc_final: 0.7734 (tmm-80) REVERT: A 1054 MET cc_start: 0.5509 (mpp) cc_final: 0.4823 (pp-130) REVERT: D 16 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: D 54 GLU cc_start: 0.8294 (mp0) cc_final: 0.8005 (mp0) REVERT: D 121 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8336 (tp30) REVERT: P 144 ASP cc_start: 0.7796 (t0) cc_final: 0.7576 (t0) outliers start: 24 outliers final: 16 residues processed: 203 average time/residue: 1.2202 time to fit residues: 280.8381 Evaluate side-chains 205 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain N residue 56 HIS Chi-restraints excluded: chain P residue 156 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 213 optimal weight: 0.6980 chunk 76 optimal weight: 0.1980 chunk 162 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 78 optimal weight: 0.4980 chunk 186 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 190 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 570 HIS ** D 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.121956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.089687 restraints weight = 148633.983| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 3.57 r_work: 0.3345 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3363 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3363 r_free = 0.3363 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3363 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18169 Z= 0.113 Angle : 0.537 13.531 24609 Z= 0.274 Chirality : 0.035 0.135 2744 Planarity : 0.004 0.061 3127 Dihedral : 7.451 169.283 2428 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.02 % Allowed : 23.56 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 2.97 (0.18), residues: 2159 helix: 2.81 (0.13), residues: 1490 sheet: -0.40 (0.58), residues: 69 loop : 0.08 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 76 TYR 0.011 0.001 TYR A 372 PHE 0.021 0.001 PHE A 882 TRP 0.022 0.001 TRP A 762 HIS 0.009 0.001 HIS C 30 Details of bonding type rmsd covalent geometry : bond 0.00256 (18168) covalent geometry : angle 0.53705 (24609) hydrogen bonds : bond 0.03512 ( 1155) hydrogen bonds : angle 4.00220 ( 3359) Misc. bond : bond 0.00005 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4318 Ramachandran restraints generated. 2159 Oldfield, 0 Emsley, 2159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 190 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 568 is missing expected H atoms. Skipping. Residue THR 24 is missing expected H atoms. Skipping. Residue THR 42 is missing expected H atoms. Skipping. Residue LYS 208 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 MET cc_start: 0.8476 (mmt) cc_final: 0.8220 (mmt) REVERT: A 217 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8321 (mp10) REVERT: A 286 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8587 (tp) REVERT: A 412 MET cc_start: 0.7924 (pmm) cc_final: 0.7351 (pp-130) REVERT: A 437 GLN cc_start: 0.7207 (OUTLIER) cc_final: 0.5854 (mm-40) REVERT: A 1043 ARG cc_start: 0.8118 (tmm-80) cc_final: 0.7720 (tmm-80) REVERT: A 1054 MET cc_start: 0.5480 (mpp) cc_final: 0.4815 (pp-130) REVERT: D 16 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7986 (mp0) REVERT: D 54 GLU cc_start: 0.8312 (mp0) cc_final: 0.8034 (mp0) REVERT: D 121 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8315 (tp30) REVERT: P 144 ASP cc_start: 0.7803 (t0) cc_final: 0.7592 (t0) outliers start: 19 outliers final: 9 residues processed: 205 average time/residue: 1.1964 time to fit residues: 278.7045 Evaluate side-chains 198 residues out of total 1953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 184 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 217 GLN Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 437 GLN Chi-restraints excluded: chain A residue 885 THR Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain N residue 56 HIS Chi-restraints excluded: chain P residue 156 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 58 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 78 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 942 HIS ** D 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.120417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.086656 restraints weight = 143979.675| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.67 r_work: 0.3324 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18169 Z= 0.121 Angle : 0.540 12.823 24609 Z= 0.276 Chirality : 0.035 0.142 2744 Planarity : 0.004 0.087 3127 Dihedral : 7.319 167.246 2428 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.07 % Allowed : 23.61 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 3.01 (0.18), residues: 2159 helix: 2.83 (0.13), residues: 1491 sheet: -0.34 (0.58), residues: 69 loop : 0.10 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG P 161 TYR 0.014 0.001 TYR D 138 PHE 0.023 0.001 PHE A 882 TRP 0.020 0.001 TRP A 762 HIS 0.009 0.001 HIS C 30 Details of bonding type rmsd covalent geometry : bond 0.00275 (18168) covalent geometry : angle 0.54034 (24609) hydrogen bonds : bond 0.03500 ( 1155) hydrogen bonds : angle 3.99145 ( 3359) Misc. bond : bond 0.00008 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14002.41 seconds wall clock time: 236 minutes 55.54 seconds (14215.54 seconds total)