Starting phenix.real_space_refine on Wed Jan 14 09:49:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z8k_14555/01_2026/7z8k_14555.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z8k_14555/01_2026/7z8k_14555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z8k_14555/01_2026/7z8k_14555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z8k_14555/01_2026/7z8k_14555.map" model { file = "/net/cci-nas-00/data/ceres_data/7z8k_14555/01_2026/7z8k_14555.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z8k_14555/01_2026/7z8k_14555.cif" } resolution = 4.37 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= 0.001 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: 3 Type Number sf(0) Gaussians C 8638 2.51 5 N 2918 2.21 5 O 2918 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14474 Number of models: 1 Model: "" Number of chains: 9 Chain: "e" Number of atoms: 4237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 854, 4237 Classifications: {'peptide': 854} Incomplete info: {'truncation_to_alanine': 769} Link IDs: {'PTRANS': 28, 'TRANS': 825} Chain breaks: 2 Unresolved chain link angles: 28 Unresolved non-hydrogen bonds: 2923 Unresolved non-hydrogen angles: 3729 Unresolved non-hydrogen dihedrals: 2426 Unresolved non-hydrogen chiralities: 253 Planarities with less than four sites: {'HIS:plan': 17, 'ASN:plan1': 35, 'GLN:plan1': 50, 'TYR:plan': 28, 'GLU:plan': 74, 'ARG:plan': 66, 'ASP:plan': 49, 'PHE:plan': 29, 'TRP:plan': 15} Unresolved non-hydrogen planarities: 1668 Chain: "i" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1160 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 213} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 813 Unresolved non-hydrogen angles: 1039 Unresolved non-hydrogen dihedrals: 694 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'ARG:plan': 9, 'ASN:plan1': 4, 'TRP:plan': 4, 'ASP:plan': 17, 'TYR:plan': 9, 'HIS:plan': 9, 'PHE:plan': 12, 'GLU:plan': 21, 'GLN:plan1': 8} Unresolved non-hydrogen planarities: 440 Chain: "f" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 2488 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 450} Link IDs: {'PTRANS': 15, 'TRANS': 485} Chain breaks: 2 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1737 Unresolved non-hydrogen angles: 2203 Unresolved non-hydrogen dihedrals: 1444 Unresolved non-hydrogen chiralities: 141 Planarities with less than four sites: {'HIS:plan': 11, 'ASN:plan1': 20, 'GLN:plan1': 31, 'TYR:plan': 11, 'GLU:plan': 38, 'ARG:plan': 47, 'ASP:plan': 34, 'PHE:plan': 20, 'TRP:plan': 9} Unresolved non-hydrogen planarities: 1006 Chain: "h" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 1767 Classifications: {'peptide': 358} Incomplete info: {'truncation_to_alanine': 309} Link IDs: {'PTRANS': 17, 'TRANS': 340} Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1121 Unresolved non-hydrogen angles: 1464 Unresolved non-hydrogen dihedrals: 965 Unresolved non-hydrogen chiralities: 93 Planarities with less than four sites: {'ASN:plan1': 22, 'ARG:plan': 14, 'GLN:plan1': 11, 'PHE:plan': 14, 'ASP:plan': 20, 'GLU:plan': 18, 'TRP:plan': 11, 'HIS:plan': 16, 'TYR:plan': 11} Unresolved non-hydrogen planarities: 652 Chain: "X" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 683 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'TRANS': 136} Unresolved non-hydrogen bonds: 467 Unresolved non-hydrogen angles: 585 Unresolved non-hydrogen dihedrals: 363 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 19, 'ASP:plan': 9, 'GLU:plan': 20, 'ARG:plan': 14, 'HIS:plan': 6, 'ASN:plan1': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 301 Chain: "x" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 673 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'TRANS': 134} Unresolved non-hydrogen bonds: 460 Unresolved non-hydrogen angles: 576 Unresolved non-hydrogen dihedrals: 358 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 18, 'ASP:plan': 9, 'GLU:plan': 20, 'ARG:plan': 14, 'HIS:plan': 6, 'ASN:plan1': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 297 Chain: "F" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 1822 Classifications: {'peptide': 370} Incomplete info: {'truncation_to_alanine': 318} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1204 Unresolved non-hydrogen angles: 1535 Unresolved non-hydrogen dihedrals: 1020 Unresolved non-hydrogen chiralities: 98 Planarities with less than four sites: {'ASN:plan1': 9, 'GLN:plan1': 10, 'ASP:plan': 20, 'PHE:plan': 20, 'TYR:plan': 14, 'ARG:plan': 25, 'HIS:plan': 9, 'GLU:plan': 30, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 671 Chain: "W" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 822 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 154} Link IDs: {'TRANS': 164} Unresolved non-hydrogen bonds: 587 Unresolved non-hydrogen angles: 729 Unresolved non-hydrogen dihedrals: 471 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'ARG:plan': 20, 'GLN:plan1': 17, 'GLU:plan': 28, 'ASP:plan': 9, 'ASN:plan1': 5, 'TYR:plan': 1, 'HIS:plan': 6, 'PHE:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 380 Chain: "w" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 822 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 154} Link IDs: {'TRANS': 164} Unresolved non-hydrogen bonds: 587 Unresolved non-hydrogen angles: 729 Unresolved non-hydrogen dihedrals: 471 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'ARG:plan': 20, 'GLN:plan1': 17, 'GLU:plan': 28, 'ASP:plan': 9, 'ASN:plan1': 5, 'TYR:plan': 1, 'HIS:plan': 6, 'PHE:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 380 Time building chain proxies: 3.89, per 1000 atoms: 0.27 Number of scatterers: 14474 At special positions: 0 Unit cell: (243.922, 156.807, 201.609, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2918 8.00 N 2918 7.00 C 8638 6.00 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=0, symmetry=0 Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 818.1 milliseconds 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5604 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 16 sheets defined 69.9% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'e' and resid 210 through 223 Processing helix chain 'e' and resid 228 through 237 removed outlier: 6.958A pdb=" N ASP e 234 " --> pdb=" O ASP e 231 " (cutoff:3.500A) Processing helix chain 'e' and resid 238 through 261 Processing helix chain 'e' and resid 270 through 293 Processing helix chain 'e' and resid 294 through 307 Processing helix chain 'e' and resid 309 through 319 removed outlier: 3.647A pdb=" N THR e 313 " --> pdb=" O ARG e 309 " (cutoff:3.500A) Processing helix chain 'e' and resid 321 through 338 Proline residue: e 334 - end of helix removed outlier: 3.628A pdb=" N ASP e 338 " --> pdb=" O PRO e 334 " (cutoff:3.500A) Processing helix chain 'e' and resid 340 through 347 removed outlier: 3.885A pdb=" N LEU e 344 " --> pdb=" O PRO e 340 " (cutoff:3.500A) Processing helix chain 'e' and resid 349 through 366 Processing helix chain 'e' and resid 367 through 370 Processing helix chain 'e' and resid 373 through 400 removed outlier: 3.583A pdb=" N ARG e 399 " --> pdb=" O VAL e 395 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS e 400 " --> pdb=" O LEU e 396 " (cutoff:3.500A) Processing helix chain 'e' and resid 405 through 441 Processing helix chain 'e' and resid 455 through 484 removed outlier: 4.130A pdb=" N LEU e 459 " --> pdb=" O ALA e 455 " (cutoff:3.500A) Processing helix chain 'e' and resid 513 through 532 removed outlier: 3.530A pdb=" N GLU e 532 " --> pdb=" O GLU e 528 " (cutoff:3.500A) Processing helix chain 'e' and resid 539 through 575 removed outlier: 3.670A pdb=" N LEU e 572 " --> pdb=" O LEU e 568 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR e 574 " --> pdb=" O ASP e 570 " (cutoff:3.500A) Processing helix chain 'e' and resid 577 through 588 removed outlier: 3.521A pdb=" N ILE e 584 " --> pdb=" O GLU e 580 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE e 588 " --> pdb=" O ILE e 584 " (cutoff:3.500A) Processing helix chain 'e' and resid 589 through 593 removed outlier: 3.758A pdb=" N PHE e 592 " --> pdb=" O ASN e 589 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL e 593 " --> pdb=" O ALA e 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 589 through 593' Processing helix chain 'e' and resid 596 through 625 removed outlier: 3.766A pdb=" N TYR e 604 " --> pdb=" O ALA e 600 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N THR e 606 " --> pdb=" O ARG e 602 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N GLN e 607 " --> pdb=" O GLU e 603 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN e 610 " --> pdb=" O THR e 606 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL e 625 " --> pdb=" O ASP e 621 " (cutoff:3.500A) Processing helix chain 'e' and resid 630 through 639 removed outlier: 3.871A pdb=" N LYS e 634 " --> pdb=" O SER e 630 " (cutoff:3.500A) Processing helix chain 'e' and resid 642 through 670 removed outlier: 3.667A pdb=" N ILE e 654 " --> pdb=" O TRP e 650 " (cutoff:3.500A) Processing helix chain 'e' and resid 672 through 675 Processing helix chain 'e' and resid 676 through 693 Processing helix chain 'e' and resid 695 through 710 removed outlier: 3.546A pdb=" N ASP e 701 " --> pdb=" O GLU e 697 " (cutoff:3.500A) Processing helix chain 'e' and resid 741 through 757 removed outlier: 3.981A pdb=" N THR e 745 " --> pdb=" O PRO e 741 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER e 747 " --> pdb=" O ILE e 743 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP e 755 " --> pdb=" O ARG e 751 " (cutoff:3.500A) Processing helix chain 'e' and resid 761 through 798 removed outlier: 3.572A pdb=" N ALA e 771 " --> pdb=" O LYS e 767 " (cutoff:3.500A) Proline residue: e 776 - end of helix removed outlier: 3.543A pdb=" N SER e 784 " --> pdb=" O SER e 780 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS e 794 " --> pdb=" O ARG e 790 " (cutoff:3.500A) Processing helix chain 'e' and resid 799 through 803 removed outlier: 4.003A pdb=" N LEU e 803 " --> pdb=" O THR e 800 " (cutoff:3.500A) Processing helix chain 'e' and resid 805 through 820 removed outlier: 3.534A pdb=" N VAL e 812 " --> pdb=" O LEU e 808 " (cutoff:3.500A) Processing helix chain 'e' and resid 828 through 867 removed outlier: 3.989A pdb=" N GLU e 865 " --> pdb=" O VAL e 861 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR e 866 " --> pdb=" O ARG e 862 " (cutoff:3.500A) Processing helix chain 'e' and resid 870 through 891 Processing helix chain 'e' and resid 895 through 927 Processing helix chain 'e' and resid 932 through 936 Processing helix chain 'e' and resid 974 through 995 removed outlier: 4.277A pdb=" N VAL e 993 " --> pdb=" O TRP e 989 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER e 995 " --> pdb=" O MET e 991 " (cutoff:3.500A) Processing helix chain 'e' and resid 1013 through 1018 Processing helix chain 'e' and resid 1021 through 1025 Processing helix chain 'e' and resid 1030 through 1057 removed outlier: 3.562A pdb=" N VAL e1040 " --> pdb=" O SER e1036 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TRP e1054 " --> pdb=" O TYR e1050 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR e1057 " --> pdb=" O VAL e1053 " (cutoff:3.500A) Processing helix chain 'e' and resid 1058 through 1061 Processing helix chain 'e' and resid 1109 through 1120 removed outlier: 3.601A pdb=" N LYS e1115 " --> pdb=" O LYS e1111 " (cutoff:3.500A) Processing helix chain 'i' and resid 112 through 117 removed outlier: 4.963A pdb=" N GLY i 117 " --> pdb=" O TYR i 114 " (cutoff:3.500A) Processing helix chain 'i' and resid 118 through 123 removed outlier: 3.503A pdb=" N ALA i 122 " --> pdb=" O LEU i 118 " (cutoff:3.500A) Processing helix chain 'i' and resid 141 through 143 No H-bonds generated for 'chain 'i' and resid 141 through 143' Processing helix chain 'i' and resid 144 through 164 removed outlier: 3.893A pdb=" N LYS i 164 " --> pdb=" O ILE i 160 " (cutoff:3.500A) Processing helix chain 'i' and resid 166 through 183 Processing helix chain 'i' and resid 233 through 235 No H-bonds generated for 'chain 'i' and resid 233 through 235' Processing helix chain 'i' and resid 236 through 244 Processing helix chain 'i' and resid 247 through 266 Processing helix chain 'i' and resid 279 through 293 Processing helix chain 'i' and resid 316 through 327 removed outlier: 4.196A pdb=" N ILE i 322 " --> pdb=" O LYS i 318 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LEU i 323 " --> pdb=" O LYS i 319 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N HIS i 324 " --> pdb=" O ILE i 320 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU i 325 " --> pdb=" O ALA i 321 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASN i 326 " --> pdb=" O ILE i 322 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE i 327 " --> pdb=" O LEU i 323 " (cutoff:3.500A) Processing helix chain 'i' and resid 335 through 340 Processing helix chain 'i' and resid 358 through 373 removed outlier: 3.617A pdb=" N GLN i 373 " --> pdb=" O LEU i 369 " (cutoff:3.500A) Processing helix chain 'f' and resid 211 through 223 Processing helix chain 'f' and resid 228 through 237 removed outlier: 6.268A pdb=" N ASP f 234 " --> pdb=" O ASP f 231 " (cutoff:3.500A) Processing helix chain 'f' and resid 238 through 261 Processing helix chain 'f' and resid 270 through 293 Processing helix chain 'f' and resid 294 through 307 Processing helix chain 'f' and resid 309 through 319 removed outlier: 3.880A pdb=" N THR f 313 " --> pdb=" O ARG f 309 " (cutoff:3.500A) Processing helix chain 'f' and resid 321 through 337 Proline residue: f 334 - end of helix Processing helix chain 'f' and resid 340 through 347 Processing helix chain 'f' and resid 349 through 366 Processing helix chain 'f' and resid 367 through 370 Processing helix chain 'f' and resid 373 through 400 Processing helix chain 'f' and resid 405 through 441 Processing helix chain 'f' and resid 455 through 484 removed outlier: 4.324A pdb=" N LEU f 459 " --> pdb=" O ALA f 455 " (cutoff:3.500A) Processing helix chain 'f' and resid 513 through 533 removed outlier: 3.556A pdb=" N ALA f 517 " --> pdb=" O ASP f 513 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL f 533 " --> pdb=" O ASN f 529 " (cutoff:3.500A) Processing helix chain 'f' and resid 539 through 575 removed outlier: 3.867A pdb=" N VAL f 560 " --> pdb=" O ARG f 556 " (cutoff:3.500A) Processing helix chain 'f' and resid 577 through 588 removed outlier: 3.895A pdb=" N PHE f 588 " --> pdb=" O ILE f 584 " (cutoff:3.500A) Processing helix chain 'f' and resid 589 through 593 removed outlier: 3.732A pdb=" N PHE f 592 " --> pdb=" O ASN f 589 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL f 593 " --> pdb=" O ALA f 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 589 through 593' Processing helix chain 'f' and resid 596 through 625 removed outlier: 3.755A pdb=" N ALA f 600 " --> pdb=" O HIS f 596 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR f 606 " --> pdb=" O ARG f 602 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLN f 607 " --> pdb=" O GLU f 603 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL f 625 " --> pdb=" O ASP f 621 " (cutoff:3.500A) Processing helix chain 'f' and resid 630 through 639 removed outlier: 3.780A pdb=" N LYS f 634 " --> pdb=" O SER f 630 " (cutoff:3.500A) Processing helix chain 'f' and resid 642 through 670 Processing helix chain 'f' and resid 672 through 675 Processing helix chain 'f' and resid 676 through 693 Processing helix chain 'f' and resid 695 through 709 Processing helix chain 'f' and resid 745 through 756 removed outlier: 3.550A pdb=" N TRP f 755 " --> pdb=" O ARG f 751 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU f 756 " --> pdb=" O ASN f 752 " (cutoff:3.500A) Processing helix chain 'f' and resid 761 through 767 Processing helix chain 'h' and resid 600 through 605 Processing helix chain 'h' and resid 609 through 621 Processing helix chain 'X' and resid 180 through 315 Processing helix chain 'x' and resid 180 through 313 Processing helix chain 'F' and resid 59 through 65 removed outlier: 3.564A pdb=" N HIS F 65 " --> pdb=" O LYS F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.544A pdb=" N TYR F 94 " --> pdb=" O TRP F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 131 removed outlier: 3.633A pdb=" N ARG F 121 " --> pdb=" O PRO F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 151 Processing helix chain 'F' and resid 177 through 180 Processing helix chain 'F' and resid 186 through 201 Processing helix chain 'F' and resid 207 through 221 removed outlier: 4.014A pdb=" N GLU F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE F 213 " --> pdb=" O SER F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 234 Processing helix chain 'F' and resid 253 through 258 Processing helix chain 'F' and resid 259 through 264 removed outlier: 4.256A pdb=" N PHE F 263 " --> pdb=" O PRO F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 286 removed outlier: 3.569A pdb=" N SER F 286 " --> pdb=" O ALA F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 297 Processing helix chain 'F' and resid 302 through 307 removed outlier: 3.793A pdb=" N PHE F 307 " --> pdb=" O SER F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 322 Processing helix chain 'F' and resid 338 through 350 Processing helix chain 'F' and resid 352 through 357 Processing helix chain 'F' and resid 360 through 367 Processing helix chain 'F' and resid 367 through 374 removed outlier: 3.841A pdb=" N ILE F 371 " --> pdb=" O GLY F 367 " (cutoff:3.500A) Processing helix chain 'W' and resid 106 through 269 Processing helix chain 'w' and resid 106 through 269 Processing sheet with id=AA1, first strand: chain 'e' and resid 721 through 723 removed outlier: 3.970A pdb=" N GLU e 721 " --> pdb=" O LYS e 734 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'e' and resid 969 through 971 removed outlier: 6.218A pdb=" N VAL e 958 " --> pdb=" O VAL e1106 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ASP e1108 " --> pdb=" O VAL e 958 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N HIS e 960 " --> pdb=" O ASP e1108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'i' and resid 133 through 138 removed outlier: 6.616A pdb=" N VAL i 133 " --> pdb=" O LEU i 228 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N VAL i 230 " --> pdb=" O VAL i 133 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N PHE i 135 " --> pdb=" O VAL i 230 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR i 232 " --> pdb=" O PHE i 135 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA i 137 " --> pdb=" O THR i 232 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'h' and resid 265 through 271 removed outlier: 6.867A pdb=" N ILE h 596 " --> pdb=" O ASN h 268 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLN h 270 " --> pdb=" O ILE h 594 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE h 594 " --> pdb=" O GLN h 270 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'h' and resid 282 through 287 removed outlier: 4.235A pdb=" N CYS h 284 " --> pdb=" O SER h 298 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'h' and resid 335 through 340 Processing sheet with id=AA7, first strand: chain 'h' and resid 384 through 391 removed outlier: 3.950A pdb=" N CYS h 386 " --> pdb=" O ILE h 401 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LYS h 406 " --> pdb=" O SER h 402 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'h' and resid 434 through 438 Processing sheet with id=AA9, first strand: chain 'h' and resid 479 through 484 Processing sheet with id=AB1, first strand: chain 'h' and resid 527 through 532 removed outlier: 4.059A pdb=" N ARG h 548 " --> pdb=" O ASP h 544 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 33 through 36 removed outlier: 3.662A pdb=" N THR F 111 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASN F 16 " --> pdb=" O THR F 111 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 57 through 58 Processing sheet with id=AB4, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.608A pdb=" N ILE F 79 " --> pdb=" O GLU F 76 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 174 through 175 Processing sheet with id=AB6, first strand: chain 'F' and resid 174 through 175 removed outlier: 6.913A pdb=" N VAL F 299 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL F 156 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N SER F 301 " --> pdb=" O VAL F 156 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU F 158 " --> pdb=" O SER F 301 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE F 298 " --> pdb=" O SER F 331 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 240 through 242 1721 hydrogen bonds defined for protein. 5025 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.99 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 2918 1.28 - 1.35: 2891 1.35 - 1.41: 13 1.41 - 1.48: 2892 1.48 - 1.55: 5746 Bond restraints: 14460 Sorted by residual: bond pdb=" C ASN h 570 " pdb=" O ASN h 570 " ideal model delta sigma weight residual 1.235 1.252 -0.017 4.70e-03 4.53e+04 1.28e+01 bond pdb=" N ILE e 969 " pdb=" CA ILE e 969 " ideal model delta sigma weight residual 1.459 1.496 -0.038 1.24e-02 6.50e+03 9.16e+00 bond pdb=" N VAL e 959 " pdb=" CA VAL e 959 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.14e-02 7.69e+03 9.15e+00 bond pdb=" N ASN h 570 " pdb=" CA ASN h 570 " ideal model delta sigma weight residual 1.458 1.436 0.022 7.40e-03 1.83e+04 8.96e+00 bond pdb=" N HIS e 960 " pdb=" CA HIS e 960 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.77e+00 ... (remaining 14455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 19679 1.65 - 3.29: 417 3.29 - 4.94: 46 4.94 - 6.58: 8 6.58 - 8.23: 2 Bond angle restraints: 20152 Sorted by residual: angle pdb=" N PRO e 973 " pdb=" CA PRO e 973 " pdb=" C PRO e 973 " ideal model delta sigma weight residual 110.70 102.47 8.23 1.22e+00 6.72e-01 4.55e+01 angle pdb=" N HIS e 596 " pdb=" CA HIS e 596 " pdb=" C HIS e 596 " ideal model delta sigma weight residual 112.93 106.97 5.96 1.33e+00 5.65e-01 2.01e+01 angle pdb=" N GLU f 617 " pdb=" CA GLU f 617 " pdb=" CB GLU f 617 " ideal model delta sigma weight residual 110.28 116.53 -6.25 1.55e+00 4.16e-01 1.63e+01 angle pdb=" N GLU f 382 " pdb=" CA GLU f 382 " pdb=" CB GLU f 382 " ideal model delta sigma weight residual 110.22 116.27 -6.05 1.54e+00 4.22e-01 1.54e+01 angle pdb=" C ARG e 639 " pdb=" N ASP e 640 " pdb=" CA ASP e 640 " ideal model delta sigma weight residual 122.46 127.67 -5.21 1.41e+00 5.03e-01 1.36e+01 ... (remaining 20147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 3.89: 7354 3.89 - 7.78: 879 7.78 - 11.67: 210 11.67 - 15.56: 56 15.56 - 19.45: 9 Dihedral angle restraints: 8508 sinusoidal: 0 harmonic: 8508 Sorted by residual: dihedral pdb=" CA GLU h 453 " pdb=" C GLU h 453 " pdb=" N GLY h 454 " pdb=" CA GLY h 454 " ideal model delta harmonic sigma weight residual -180.00 -160.55 -19.45 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA LEU F 69 " pdb=" C LEU F 69 " pdb=" N SER F 70 " pdb=" CA SER F 70 " ideal model delta harmonic sigma weight residual 180.00 161.13 18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA GLU F 219 " pdb=" C GLU F 219 " pdb=" N ARG F 220 " pdb=" CA ARG F 220 " ideal model delta harmonic sigma weight residual -180.00 -161.71 -18.29 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 8505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2125 0.044 - 0.087: 491 0.087 - 0.131: 153 0.131 - 0.175: 31 0.175 - 0.218: 2 Chirality restraints: 2802 Sorted by residual: chirality pdb=" CA LEU e 962 " pdb=" N LEU e 962 " pdb=" C LEU e 962 " pdb=" CB LEU e 962 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ILE e 975 " pdb=" N ILE e 975 " pdb=" C ILE e 975 " pdb=" CB ILE e 975 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA GLU f 617 " pdb=" N GLU f 617 " pdb=" C GLU f 617 " pdb=" CB GLU f 617 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.40e-01 ... (remaining 2799 not shown) Planarity restraints: 2904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN f 472 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.54e+00 pdb=" C GLN f 472 " 0.053 2.00e-02 2.50e+03 pdb=" O GLN f 472 " -0.020 2.00e-02 2.50e+03 pdb=" N HIS f 473 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG f 467 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.81e+00 pdb=" C ARG f 467 " 0.051 2.00e-02 2.50e+03 pdb=" O ARG f 467 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS f 468 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET f 466 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.44e+00 pdb=" C MET f 466 " -0.050 2.00e-02 2.50e+03 pdb=" O MET f 466 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG f 467 " 0.017 2.00e-02 2.50e+03 ... (remaining 2901 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 5376 2.84 - 3.35: 15466 3.35 - 3.87: 22513 3.87 - 4.38: 21467 4.38 - 4.90: 35241 Nonbonded interactions: 100063 Sorted by model distance: nonbonded pdb=" O SER i 273 " pdb=" N GLU i 277 " model vdw 2.323 3.120 nonbonded pdb=" O ARG h 280 " pdb=" N GLY h 592 " model vdw 2.387 3.120 nonbonded pdb=" O SER h 409 " pdb=" N GLN h 419 " model vdw 2.392 3.120 nonbonded pdb=" O VAL e 958 " pdb=" N VAL e1106 " model vdw 2.393 3.120 nonbonded pdb=" O PRO F 60 " pdb=" N GLU F 63 " model vdw 2.434 3.120 ... (remaining 100058 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 Found NCS groups: ncs_group { reference = chain 'W' selection = chain 'w' } ncs_group { reference = (chain 'X' and resid 179 through 313) selection = chain 'x' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 34.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.280 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 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 0.038 14460 Z= 0.234 Angle : 0.620 8.227 20152 Z= 0.436 Chirality : 0.043 0.218 2802 Planarity : 0.003 0.031 2904 Dihedral : 4.762 19.453 2904 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 0.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.01 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.15), residues: 2890 helix: 1.66 (0.11), residues: 1860 sheet: -0.85 (0.31), residues: 258 loop : 0.38 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR e 221 PHE 0.000 0.000 PHE e 232 TRP 0.000 0.000 TRP e 252 Details of bonding type rmsd covalent geometry : bond 0.00305 (14460) covalent geometry : angle 0.62028 (20152) hydrogen bonds : bond 0.14778 ( 1719) hydrogen bonds : angle 5.67953 ( 5025) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.464 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0614 time to fit residues: 8.0820 Evaluate side-chains 63 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.084028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.049440 restraints weight = 111817.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.048090 restraints weight = 149220.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.047755 restraints weight = 171427.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.048077 restraints weight = 145286.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.048135 restraints weight = 115441.926| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14460 Z= 0.406 Angle : 0.666 10.727 20152 Z= 0.460 Chirality : 0.043 0.155 2802 Planarity : 0.005 0.024 2904 Dihedral : 6.055 29.668 2904 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.32 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.15), residues: 2890 helix: 0.83 (0.11), residues: 1861 sheet: -1.58 (0.32), residues: 232 loop : -0.68 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR e 221 PHE 0.000 0.000 PHE e 232 TRP 0.000 0.000 TRP e 252 Details of bonding type rmsd covalent geometry : bond 0.00541 (14460) covalent geometry : angle 0.66570 (20152) hydrogen bonds : bond 0.06725 ( 1719) hydrogen bonds : angle 6.10563 ( 5025) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.503 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0575 time to fit residues: 7.8508 Evaluate side-chains 63 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 177 optimal weight: 0.9990 chunk 214 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 220 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 284 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 154 optimal weight: 7.9990 chunk 87 optimal weight: 0.0980 chunk 271 optimal weight: 1.9990 chunk 199 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.059034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.050395 restraints weight = 154877.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.050022 restraints weight = 334224.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.049997 restraints weight = 250268.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.050016 restraints weight = 169994.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.050039 restraints weight = 178573.128| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14460 Z= 0.212 Angle : 0.425 9.012 20152 Z= 0.287 Chirality : 0.038 0.133 2802 Planarity : 0.002 0.012 2904 Dihedral : 4.561 19.983 2904 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.15), residues: 2890 helix: 2.02 (0.11), residues: 1856 sheet: -1.82 (0.34), residues: 218 loop : -0.80 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR e 221 PHE 0.000 0.000 PHE e 232 TRP 0.000 0.000 TRP e 252 Details of bonding type rmsd covalent geometry : bond 0.00284 (14460) covalent geometry : angle 0.42516 (20152) hydrogen bonds : bond 0.04711 ( 1719) hydrogen bonds : angle 4.64924 ( 5025) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.543 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0613 time to fit residues: 8.0053 Evaluate side-chains 63 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 235 optimal weight: 1.9990 chunk 245 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 120 optimal weight: 0.9990 chunk 240 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 218 optimal weight: 8.9990 chunk 176 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 167 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.057650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.049319 restraints weight = 155407.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.049301 restraints weight = 358398.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.049321 restraints weight = 219121.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.049251 restraints weight = 164604.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.049259 restraints weight = 173319.208| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.6182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14460 Z= 0.378 Angle : 0.626 14.445 20152 Z= 0.426 Chirality : 0.042 0.141 2802 Planarity : 0.004 0.019 2904 Dihedral : 6.032 29.252 2904 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.33 % Favored : 93.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.15), residues: 2890 helix: 0.52 (0.11), residues: 1863 sheet: -2.22 (0.36), residues: 199 loop : -1.61 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR e 221 PHE 0.000 0.000 PHE e 232 TRP 0.000 0.000 TRP e 252 Details of bonding type rmsd covalent geometry : bond 0.00510 (14460) covalent geometry : angle 0.62639 (20152) hydrogen bonds : bond 0.06437 ( 1719) hydrogen bonds : angle 6.24331 ( 5025) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.594 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0582 time to fit residues: 7.6941 Evaluate side-chains 63 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 173 optimal weight: 0.1980 chunk 267 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 226 optimal weight: 0.0870 chunk 247 optimal weight: 3.9990 chunk 274 optimal weight: 9.9990 chunk 157 optimal weight: 4.9990 chunk 235 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 overall best weight: 1.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.082184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.048663 restraints weight = 113224.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.048009 restraints weight = 139190.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.047729 restraints weight = 143930.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.047903 restraints weight = 126069.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.047934 restraints weight = 120986.251| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.6402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14460 Z= 0.245 Angle : 0.469 11.014 20152 Z= 0.316 Chirality : 0.039 0.142 2802 Planarity : 0.003 0.015 2904 Dihedral : 4.972 22.751 2904 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.15), residues: 2890 helix: 1.49 (0.11), residues: 1847 sheet: -2.16 (0.36), residues: 197 loop : -1.66 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR e 221 PHE 0.000 0.000 PHE e 232 TRP 0.000 0.000 TRP e 252 Details of bonding type rmsd covalent geometry : bond 0.00329 (14460) covalent geometry : angle 0.46882 (20152) hydrogen bonds : bond 0.04884 ( 1719) hydrogen bonds : angle 5.11036 ( 5025) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.578 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0617 time to fit residues: 8.1936 Evaluate side-chains 63 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 98 optimal weight: 0.6980 chunk 123 optimal weight: 0.1980 chunk 68 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 196 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 chunk 148 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.081875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.048736 restraints weight = 111973.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.047169 restraints weight = 150524.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.047082 restraints weight = 182694.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.047155 restraints weight = 157972.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.047217 restraints weight = 122002.727| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.7226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14460 Z= 0.319 Angle : 0.570 13.143 20152 Z= 0.387 Chirality : 0.040 0.138 2802 Planarity : 0.004 0.017 2904 Dihedral : 5.821 28.928 2904 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.89 % Favored : 92.04 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.15), residues: 2890 helix: 0.73 (0.11), residues: 1835 sheet: -2.36 (0.37), residues: 193 loop : -1.99 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR e 221 PHE 0.000 0.000 PHE e 232 TRP 0.000 0.000 TRP e 252 Details of bonding type rmsd covalent geometry : bond 0.00430 (14460) covalent geometry : angle 0.56969 (20152) hydrogen bonds : bond 0.05921 ( 1719) hydrogen bonds : angle 6.02404 ( 5025) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.489 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0614 time to fit residues: 8.0609 Evaluate side-chains 63 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 182 optimal weight: 9.9990 chunk 179 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 141 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 112 optimal weight: 0.0980 chunk 70 optimal weight: 10.0000 chunk 118 optimal weight: 0.5980 chunk 280 optimal weight: 9.9990 chunk 235 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.081559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.048483 restraints weight = 112035.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.047388 restraints weight = 168071.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.047248 restraints weight = 156474.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.047443 restraints weight = 136850.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.047634 restraints weight = 114799.958| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.7047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 14460 Z= 0.150 Angle : 0.376 9.818 20152 Z= 0.249 Chirality : 0.037 0.127 2802 Planarity : 0.002 0.015 2904 Dihedral : 4.495 19.057 2904 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.16), residues: 2890 helix: 2.13 (0.11), residues: 1842 sheet: -2.19 (0.35), residues: 212 loop : -1.70 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR e 221 PHE 0.000 0.000 PHE e 232 TRP 0.000 0.000 TRP e 252 Details of bonding type rmsd covalent geometry : bond 0.00197 (14460) covalent geometry : angle 0.37596 (20152) hydrogen bonds : bond 0.04234 ( 1719) hydrogen bonds : angle 4.62949 ( 5025) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.532 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0628 time to fit residues: 8.2632 Evaluate side-chains 63 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 264 optimal weight: 7.9990 chunk 66 optimal weight: 0.0670 chunk 176 optimal weight: 7.9990 chunk 279 optimal weight: 8.9990 chunk 269 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 77 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 205 optimal weight: 0.6980 overall best weight: 1.3920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.081510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.048126 restraints weight = 112129.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.047585 restraints weight = 147209.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.047246 restraints weight = 137425.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.047326 restraints weight = 123963.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.047871 restraints weight = 113781.408| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.7337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14460 Z= 0.208 Angle : 0.432 11.440 20152 Z= 0.289 Chirality : 0.038 0.128 2802 Planarity : 0.002 0.016 2904 Dihedral : 4.757 22.543 2904 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.16), residues: 2890 helix: 1.98 (0.11), residues: 1858 sheet: -2.09 (0.38), residues: 198 loop : -1.86 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR e 221 PHE 0.000 0.000 PHE e 232 TRP 0.000 0.000 TRP e 252 Details of bonding type rmsd covalent geometry : bond 0.00277 (14460) covalent geometry : angle 0.43221 (20152) hydrogen bonds : bond 0.04677 ( 1719) hydrogen bonds : angle 4.95685 ( 5025) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.594 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0626 time to fit residues: 8.2141 Evaluate side-chains 63 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 239 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 chunk 177 optimal weight: 6.9990 chunk 204 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.081516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.048658 restraints weight = 112862.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.047784 restraints weight = 138226.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.047476 restraints weight = 138825.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.047168 restraints weight = 168311.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.047244 restraints weight = 158343.415| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.8238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 14460 Z= 0.447 Angle : 0.713 16.020 20152 Z= 0.488 Chirality : 0.043 0.163 2802 Planarity : 0.005 0.020 2904 Dihedral : 6.649 31.210 2904 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.15), residues: 2890 helix: -0.16 (0.11), residues: 1841 sheet: -2.81 (0.39), residues: 174 loop : -2.53 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR e 221 PHE 0.000 0.000 PHE e 232 TRP 0.000 0.000 TRP e 252 Details of bonding type rmsd covalent geometry : bond 0.00604 (14460) covalent geometry : angle 0.71327 (20152) hydrogen bonds : bond 0.07015 ( 1719) hydrogen bonds : angle 6.99279 ( 5025) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.585 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0610 time to fit residues: 8.0523 Evaluate side-chains 63 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 142 optimal weight: 8.9990 chunk 172 optimal weight: 7.9990 chunk 260 optimal weight: 10.0000 chunk 274 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 chunk 223 optimal weight: 0.0270 chunk 4 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 242 optimal weight: 0.5980 chunk 268 optimal weight: 10.0000 overall best weight: 1.7244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.081194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.049059 restraints weight = 112382.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.047630 restraints weight = 154203.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.047434 restraints weight = 178700.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.047428 restraints weight = 173542.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.047463 restraints weight = 152795.443| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.8153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14460 Z= 0.254 Angle : 0.494 11.952 20152 Z= 0.333 Chirality : 0.039 0.138 2802 Planarity : 0.003 0.017 2904 Dihedral : 5.453 25.041 2904 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.16), residues: 2890 helix: 0.91 (0.12), residues: 1849 sheet: -2.66 (0.36), residues: 201 loop : -2.34 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR e 221 PHE 0.000 0.000 PHE e 232 TRP 0.000 0.000 TRP e 252 Details of bonding type rmsd covalent geometry : bond 0.00342 (14460) covalent geometry : angle 0.49400 (20152) hydrogen bonds : bond 0.05120 ( 1719) hydrogen bonds : angle 5.67398 ( 5025) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.613 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0591 time to fit residues: 7.7457 Evaluate side-chains 63 residues out of total 2623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 1 optimal weight: 0.9990 chunk 131 optimal weight: 8.9990 chunk 220 optimal weight: 4.9990 chunk 198 optimal weight: 6.9990 chunk 0 optimal weight: 0.7980 chunk 273 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 274 optimal weight: 5.9990 chunk 225 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 137 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.081000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.049019 restraints weight = 112166.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.047401 restraints weight = 131144.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.047277 restraints weight = 174617.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.047313 restraints weight = 164249.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.047312 restraints weight = 148424.345| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.8533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14460 Z= 0.296 Angle : 0.543 13.402 20152 Z= 0.367 Chirality : 0.040 0.140 2802 Planarity : 0.003 0.017 2904 Dihedral : 5.845 28.143 2904 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.15), residues: 2890 helix: 0.64 (0.11), residues: 1847 sheet: -2.94 (0.38), residues: 174 loop : -2.46 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR e 221 PHE 0.000 0.000 PHE e 232 TRP 0.000 0.000 TRP e 252 Details of bonding type rmsd covalent geometry : bond 0.00399 (14460) covalent geometry : angle 0.54317 (20152) hydrogen bonds : bond 0.05616 ( 1719) hydrogen bonds : angle 6.05806 ( 5025) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3557.12 seconds wall clock time: 61 minutes 20.51 seconds (3680.51 seconds total)