Starting phenix.real_space_refine on Wed Mar 4 23:01:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xss_33433/03_2026/7xss_33433.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xss_33433/03_2026/7xss_33433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xss_33433/03_2026/7xss_33433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xss_33433/03_2026/7xss_33433.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xss_33433/03_2026/7xss_33433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xss_33433/03_2026/7xss_33433.map" } resolution = 3.2 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= 0.003 sd= 0.037 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 54 5.49 5 S 55 5.16 5 C 10509 2.51 5 N 2928 2.21 5 O 3297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16847 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 5361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5361 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 3 Chain: "A" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 438 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 13, 'rna3p_pyr': 3} Link IDs: {'rna2p': 4, 'rna3p': 15} Chain: "D" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 712 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 8, 'rna3p_pur': 2, 'rna3p_pyr': 13} Link IDs: {'rna2p': 19, 'rna3p': 14} Chain: "B" Number of atoms: 10332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1282, 10332 Classifications: {'peptide': 1282} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 60, 'TRANS': 1221} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10251 SG CYS B 491 51.531 61.380 43.574 1.00 60.61 S ATOM 10319 SG CYS B 501 52.869 59.111 41.007 1.00 78.43 S ATOM 10333 SG CYS B 503 50.624 62.101 39.975 1.00 63.44 S ATOM 10355 SG CYS B 506 54.129 62.759 41.028 1.00 61.94 S ATOM 12320 SG CYS B 750 37.086 68.987 69.699 1.00 82.00 S ATOM 12333 SG CYS B 752 35.703 72.353 68.473 1.00 76.41 S ATOM 12355 SG CYS B 755 39.381 71.473 67.865 1.00 66.60 S ATOM 14333 SG CYS B1018 40.584 94.375 98.167 1.00 72.20 S ATOM 14504 SG CYS B1406 40.785 90.807 97.058 1.00 61.86 S ATOM 14555 SG CYS B1414 37.418 92.784 96.977 1.00 67.22 S ATOM 14572 SG CYS B1417 40.053 93.446 94.418 1.00 58.03 S ATOM 7187 SG CYS B 88 73.014 51.784 19.001 1.00 75.41 S ATOM 7458 SG CYS B 121 75.863 50.427 16.716 1.00 90.38 S ATOM 7504 SG CYS B 127 75.564 54.021 17.405 1.00 77.54 S ATOM 7528 SG CYS B 130 76.582 51.697 20.272 1.00 72.67 S Time building chain proxies: 3.72, per 1000 atoms: 0.22 Number of scatterers: 16847 At special positions: 0 Unit cell: (107.67, 152.29, 132.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 55 16.00 P 54 15.00 O 3297 8.00 N 2928 7.00 C 10509 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: 1.42 Conformation dependent library (CDL) restraints added in 680.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1801 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 491 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 503 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 501 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 506 " pdb=" ZN B1802 " pdb="ZN ZN B1802 " - pdb=" ND1 HIS B 747 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 755 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 750 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 752 " pdb=" ZN B1803 " pdb="ZN ZN B1803 " - pdb=" SG CYS B1018 " pdb="ZN ZN B1803 " - pdb=" SG CYS B1414 " pdb="ZN ZN B1803 " - pdb=" SG CYS B1417 " pdb="ZN ZN B1803 " - pdb=" SG CYS B1406 " pdb=" ZN B1804 " pdb="ZN ZN B1804 " - pdb=" SG CYS B 127 " pdb="ZN ZN B1804 " - pdb=" SG CYS B 88 " pdb="ZN ZN B1804 " - pdb=" SG CYS B 121 " pdb="ZN ZN B1804 " - pdb=" SG CYS B 130 " Number of angles added : 21 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3594 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 18 sheets defined 39.4% alpha, 16.9% beta 5 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 2.01 Creating SS restraints... Processing helix chain 'C' and resid 21 through 33 removed outlier: 3.668A pdb=" N ASN C 33 " --> pdb=" O ASP C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 59 removed outlier: 4.053A pdb=" N ILE C 44 " --> pdb=" O ASP C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 81 removed outlier: 3.625A pdb=" N PHE C 68 " --> pdb=" O THR C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 110 removed outlier: 4.095A pdb=" N LYS C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS C 110 " --> pdb=" O ARG C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 136 Processing helix chain 'C' and resid 141 through 156 Processing helix chain 'C' and resid 163 through 177 removed outlier: 3.920A pdb=" N ILE C 167 " --> pdb=" O TYR C 163 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C 177 " --> pdb=" O LEU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 190 Processing helix chain 'C' and resid 194 through 205 Processing helix chain 'C' and resid 210 through 222 Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 230 through 246 removed outlier: 4.330A pdb=" N ASP C 234 " --> pdb=" O HIS C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 267 Processing helix chain 'C' and resid 270 through 277 Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 281 through 295 removed outlier: 3.674A pdb=" N GLN C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 320 removed outlier: 3.796A pdb=" N LYS C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C 307 " --> pdb=" O VAL C 303 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C 320 " --> pdb=" O ILE C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 328 Processing helix chain 'C' and resid 342 through 357 removed outlier: 3.543A pdb=" N LYS C 346 " --> pdb=" O ASN C 342 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN C 357 " --> pdb=" O VAL C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 448 Processing helix chain 'C' and resid 454 through 469 Processing helix chain 'C' and resid 470 through 474 removed outlier: 3.684A pdb=" N PHE C 473 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 500 removed outlier: 3.551A pdb=" N GLY C 499 " --> pdb=" O PRO C 496 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER C 500 " --> pdb=" O LEU C 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 496 through 500' Processing helix chain 'C' and resid 521 through 525 Processing helix chain 'C' and resid 566 through 572 removed outlier: 3.694A pdb=" N LEU C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 removed outlier: 3.744A pdb=" N LEU C 611 " --> pdb=" O TYR C 607 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL C 614 " --> pdb=" O ILE C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 653 removed outlier: 3.766A pdb=" N GLY C 653 " --> pdb=" O LEU C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 677 removed outlier: 3.570A pdb=" N THR C 669 " --> pdb=" O ARG C 665 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C 677 " --> pdb=" O ILE C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 692 removed outlier: 4.472A pdb=" N TRP C 687 " --> pdb=" O LYS C 683 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY C 692 " --> pdb=" O GLN C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 708 removed outlier: 3.652A pdb=" N PHE C 703 " --> pdb=" O HIS C 699 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA C 708 " --> pdb=" O TYR C 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 31 Processing helix chain 'B' and resid 32 through 38 Processing helix chain 'B' and resid 59 through 78 removed outlier: 3.682A pdb=" N VAL B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 127 through 134 Processing helix chain 'B' and resid 168 through 171 Processing helix chain 'B' and resid 216 through 225 removed outlier: 3.528A pdb=" N ALA B 222 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 287 removed outlier: 3.703A pdb=" N ASN B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 291 through 303 removed outlier: 4.565A pdb=" N ILE B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 338 through 350 Processing helix chain 'B' and resid 354 through 375 Processing helix chain 'B' and resid 471 through 488 Processing helix chain 'B' and resid 503 through 510 Processing helix chain 'B' and resid 569 through 580 Processing helix chain 'B' and resid 594 through 598 Processing helix chain 'B' and resid 617 through 624 Processing helix chain 'B' and resid 630 through 637 Processing helix chain 'B' and resid 688 through 692 Processing helix chain 'B' and resid 723 through 740 removed outlier: 3.523A pdb=" N HIS B 727 " --> pdb=" O LYS B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 744 Processing helix chain 'B' and resid 752 through 758 Processing helix chain 'B' and resid 776 through 780 removed outlier: 3.618A pdb=" N GLU B 779 " --> pdb=" O ASN B 776 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 780 " --> pdb=" O GLY B 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 776 through 780' Processing helix chain 'B' and resid 831 through 848 removed outlier: 3.840A pdb=" N GLY B 848 " --> pdb=" O ASP B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 859 removed outlier: 3.613A pdb=" N GLY B 859 " --> pdb=" O GLY B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 881 removed outlier: 3.790A pdb=" N ASN B 881 " --> pdb=" O LYS B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 914 removed outlier: 3.724A pdb=" N ASP B 914 " --> pdb=" O SER B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1016 removed outlier: 3.901A pdb=" N LEU B1003 " --> pdb=" O PRO B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1394 through 1399 removed outlier: 3.595A pdb=" N LYS B1398 " --> pdb=" O THR B1394 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B1399 " --> pdb=" O LEU B1395 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1394 through 1399' Processing helix chain 'B' and resid 1400 through 1404 Processing helix chain 'B' and resid 1414 through 1420 Processing helix chain 'B' and resid 1463 through 1468 removed outlier: 4.249A pdb=" N SER B1467 " --> pdb=" O ARG B1463 " (cutoff:3.500A) Processing helix chain 'B' and resid 1486 through 1493 removed outlier: 3.972A pdb=" N ILE B1490 " --> pdb=" O GLY B1486 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS B1493 " --> pdb=" O ILE B1489 " (cutoff:3.500A) Processing helix chain 'B' and resid 1493 through 1501 removed outlier: 4.147A pdb=" N GLU B1499 " --> pdb=" O LEU B1495 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B1501 " --> pdb=" O ILE B1497 " (cutoff:3.500A) Processing helix chain 'B' and resid 1528 through 1540 Processing helix chain 'B' and resid 1552 through 1556 Processing helix chain 'B' and resid 1583 through 1603 removed outlier: 3.558A pdb=" N GLY B1603 " --> pdb=" O ILE B1599 " (cutoff:3.500A) Processing helix chain 'B' and resid 1615 through 1618 removed outlier: 3.662A pdb=" N VAL B1618 " --> pdb=" O GLN B1615 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1615 through 1618' Processing helix chain 'B' and resid 1619 through 1629 Processing helix chain 'B' and resid 1673 through 1683 Processing sheet with id=AA1, first strand: chain 'C' and resid 425 through 431 Processing sheet with id=AA2, first strand: chain 'C' and resid 536 through 540 removed outlier: 6.355A pdb=" N LEU C 580 " --> pdb=" O ILE C 623 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N GLY C 625 " --> pdb=" O LEU C 580 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE C 582 " --> pdb=" O GLY C 625 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N CYS C 627 " --> pdb=" O ILE C 582 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N THR C 660 " --> pdb=" O LEU C 624 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA C 626 " --> pdb=" O THR C 660 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 173 through 181 removed outlier: 4.230A pdb=" N ASP B 190 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 13.679A pdb=" N ARG B 193 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N GLU B 22 " --> pdb=" O ARG B 193 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TRP B 195 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER B 56 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU B 158 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU B 11 " --> pdb=" O GLU B 238 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B 238 " --> pdb=" O GLU B 11 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 109 through 111 removed outlier: 6.268A pdb=" N THR B 110 " --> pdb=" O VAL B 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 512 through 514 removed outlier: 4.546A pdb=" N ARG B 421 " --> pdb=" O ASP B 606 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ASP B 606 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS B 423 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LEU B 604 " --> pdb=" O LYS B 423 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 512 through 514 removed outlier: 4.546A pdb=" N ARG B 421 " --> pdb=" O ASP B 606 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ASP B 606 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS B 423 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LEU B 604 " --> pdb=" O LYS B 423 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 431 through 432 removed outlier: 3.690A pdb=" N VAL B 432 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASN B 459 " --> pdb=" O VAL B 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 469 through 470 removed outlier: 3.579A pdb=" N SER B 517 " --> pdb=" O ILE B 470 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 526 through 533 removed outlier: 10.509A pdb=" N GLU B 526 " --> pdb=" O ASP B 547 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N ASP B 547 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 11.122A pdb=" N ARG B 528 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 9.831A pdb=" N LEU B 545 " --> pdb=" O ARG B 528 " (cutoff:3.500A) removed outlier: 10.648A pdb=" N ARG B 530 " --> pdb=" O GLY B 543 " (cutoff:3.500A) removed outlier: 9.537A pdb=" N GLY B 543 " --> pdb=" O ARG B 530 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ALA B 532 " --> pdb=" O GLU B 541 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 703 through 704 removed outlier: 5.917A pdb=" N PHE B 720 " --> pdb=" O LEU B 774 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 703 through 704 removed outlier: 5.917A pdb=" N PHE B 720 " --> pdb=" O LEU B 774 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY B 865 " --> pdb=" O GLU B 677 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 787 through 792 removed outlier: 6.446A pdb=" N ALA B 803 " --> pdb=" O ALA B 791 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 920 through 921 Processing sheet with id=AB5, first strand: chain 'B' and resid 924 through 927 Processing sheet with id=AB6, first strand: chain 'B' and resid 991 through 992 removed outlier: 3.604A pdb=" N GLU B 995 " --> pdb=" O ILE B 992 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU B 996 " --> pdb=" O TYR B1436 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR B1436 " --> pdb=" O LEU B 996 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL B1517 " --> pdb=" O GLU B1437 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 991 through 992 removed outlier: 3.604A pdb=" N GLU B 995 " --> pdb=" O ILE B 992 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU B 996 " --> pdb=" O TYR B1436 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR B1436 " --> pdb=" O LEU B 996 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL B1517 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN B1526 " --> pdb=" O LEU B 950 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU B 950 " --> pdb=" O ASN B1526 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER B 951 " --> pdb=" O THR B1569 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N THR B1569 " --> pdb=" O SER B 951 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS B 953 " --> pdb=" O LEU B1567 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU B1567 " --> pdb=" O LYS B 953 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN B 955 " --> pdb=" O ASP B1565 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 967 through 968 removed outlier: 4.449A pdb=" N LYS B 988 " --> pdb=" O ASP B 968 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N PHE B 989 " --> pdb=" O GLU B1510 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1421 through 1422 626 hydrogen bonds defined for protein. 1758 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 11 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 3.60 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5262 1.34 - 1.46: 3315 1.46 - 1.58: 8572 1.58 - 1.70: 107 1.70 - 1.82: 76 Bond restraints: 17332 Sorted by residual: bond pdb=" CA ASN B 973 " pdb=" CB ASN B 973 " ideal model delta sigma weight residual 1.528 1.576 -0.048 1.67e-02 3.59e+03 8.20e+00 bond pdb=" CB PRO B 86 " pdb=" CG PRO B 86 " ideal model delta sigma weight residual 1.492 1.627 -0.135 5.00e-02 4.00e+02 7.27e+00 bond pdb=" N ASN B1544 " pdb=" CA ASN B1544 " ideal model delta sigma weight residual 1.457 1.480 -0.022 1.29e-02 6.01e+03 2.96e+00 bond pdb=" C ARG B1644 " pdb=" N TYR B1645 " ideal model delta sigma weight residual 1.333 1.374 -0.041 2.74e-02 1.33e+03 2.26e+00 bond pdb=" CB ASP B1565 " pdb=" CG ASP B1565 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.89e+00 ... (remaining 17327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 23232 2.05 - 4.11: 340 4.11 - 6.16: 46 6.16 - 8.21: 6 8.21 - 10.27: 3 Bond angle restraints: 23627 Sorted by residual: angle pdb=" CA PRO B 86 " pdb=" N PRO B 86 " pdb=" CD PRO B 86 " ideal model delta sigma weight residual 112.00 102.06 9.94 1.40e+00 5.10e-01 5.04e+01 angle pdb=" N VAL B 377 " pdb=" CA VAL B 377 " pdb=" C VAL B 377 " ideal model delta sigma weight residual 113.10 109.69 3.41 9.70e-01 1.06e+00 1.24e+01 angle pdb=" CA GLU B1496 " pdb=" CB GLU B1496 " pdb=" CG GLU B1496 " ideal model delta sigma weight residual 114.10 121.03 -6.93 2.00e+00 2.50e-01 1.20e+01 angle pdb=" CA GLU C 268 " pdb=" CB GLU C 268 " pdb=" CG GLU C 268 " ideal model delta sigma weight residual 114.10 120.68 -6.58 2.00e+00 2.50e-01 1.08e+01 angle pdb=" CA ASP B1471 " pdb=" C ASP B1471 " pdb=" N GLU B1472 " ideal model delta sigma weight residual 116.84 122.20 -5.36 1.71e+00 3.42e-01 9.83e+00 ... (remaining 23622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 9980 35.92 - 71.83: 463 71.83 - 107.74: 34 107.74 - 143.66: 0 143.66 - 179.57: 4 Dihedral angle restraints: 10481 sinusoidal: 4888 harmonic: 5593 Sorted by residual: dihedral pdb=" O4' C D -7 " pdb=" C1' C D -7 " pdb=" N1 C D -7 " pdb=" C2 C D -7 " ideal model delta sinusoidal sigma weight residual 200.00 43.53 156.47 1 1.50e+01 4.44e-03 8.18e+01 dihedral pdb=" O4' U D -8 " pdb=" C1' U D -8 " pdb=" N1 U D -8 " pdb=" C2 U D -8 " ideal model delta sinusoidal sigma weight residual -128.00 51.57 -179.57 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U D -14 " pdb=" C1' U D -14 " pdb=" N1 U D -14 " pdb=" C2 U D -14 " ideal model delta sinusoidal sigma weight residual -128.00 47.29 -175.29 1 1.70e+01 3.46e-03 6.63e+01 ... (remaining 10478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1936 0.040 - 0.079: 473 0.079 - 0.119: 136 0.119 - 0.158: 18 0.158 - 0.198: 3 Chirality restraints: 2566 Sorted by residual: chirality pdb=" CG LEU C 27 " pdb=" CB LEU C 27 " pdb=" CD1 LEU C 27 " pdb=" CD2 LEU C 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.79e-01 chirality pdb=" C1' A D -16 " pdb=" O4' A D -16 " pdb=" C2' A D -16 " pdb=" N9 A D -16 " both_signs ideal model delta sigma weight residual False 2.46 2.27 0.19 2.00e-01 2.50e+01 8.87e-01 chirality pdb=" CA ASN B1544 " pdb=" N ASN B1544 " pdb=" C ASN B1544 " pdb=" CB ASN B1544 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.10e-01 ... (remaining 2563 not shown) Planarity restraints: 2844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 85 " -0.097 5.00e-02 4.00e+02 1.38e-01 3.06e+01 pdb=" N PRO B 86 " 0.239 5.00e-02 4.00e+02 pdb=" CA PRO B 86 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO B 86 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 439 " -0.056 5.00e-02 4.00e+02 8.58e-02 1.18e+01 pdb=" N PRO B 440 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 440 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 440 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 37 " 0.042 5.00e-02 4.00e+02 6.36e-02 6.48e+00 pdb=" N PRO C 38 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO C 38 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 38 " 0.035 5.00e-02 4.00e+02 ... (remaining 2841 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 452 2.69 - 3.25: 15678 3.25 - 3.80: 25665 3.80 - 4.35: 33989 4.35 - 4.90: 56432 Nonbonded interactions: 132216 Sorted by model distance: nonbonded pdb=" O ALA C 626 " pdb=" OG1 THR C 660 " model vdw 2.143 3.040 nonbonded pdb=" NZ LYS B1571 " pdb=" OD1 ASN B1573 " model vdw 2.145 3.120 nonbonded pdb=" OP2 U D 6 " pdb=" OG SER B 854 " model vdw 2.148 3.040 nonbonded pdb=" OH TYR B1436 " pdb=" OE2 GLU B1441 " model vdw 2.160 3.040 nonbonded pdb=" OH TYR B 191 " pdb=" OD2 ASP B 386 " model vdw 2.174 3.040 ... (remaining 132211 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.820 Find NCS groups from input model: 0.080 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 0.135 17348 Z= 0.127 Angle : 0.619 10.265 23648 Z= 0.347 Chirality : 0.039 0.198 2566 Planarity : 0.005 0.138 2844 Dihedral : 19.020 179.575 6887 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.72 % Favored : 94.18 % Rotamer: Outliers : 0.59 % Allowed : 27.57 % Favored : 71.85 % 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: -0.24 (0.19), residues: 1924 helix: 1.43 (0.21), residues: 630 sheet: 0.88 (0.32), residues: 270 loop : -1.57 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 273 TYR 0.021 0.001 TYR C 696 PHE 0.019 0.001 PHE B1570 TRP 0.013 0.001 TRP C 443 HIS 0.009 0.001 HIS B1621 Details of bonding type rmsd covalent geometry : bond 0.00271 (17332) covalent geometry : angle 0.61267 (23627) hydrogen bonds : bond 0.17429 ( 606) hydrogen bonds : angle 5.78758 ( 1780) metal coordination : bond 0.00428 ( 16) metal coordination : angle 2.96188 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 365 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 164 GLU cc_start: 0.6278 (tm-30) cc_final: 0.6020 (tm-30) REVERT: C 250 LEU cc_start: 0.8337 (tt) cc_final: 0.8129 (tp) REVERT: C 518 TYR cc_start: 0.7400 (t80) cc_final: 0.7196 (t80) REVERT: C 630 ASP cc_start: 0.5532 (OUTLIER) cc_final: 0.5300 (m-30) REVERT: B 744 LYS cc_start: 0.7806 (mtpt) cc_final: 0.7599 (mtpt) REVERT: B 836 LEU cc_start: 0.8269 (mp) cc_final: 0.7978 (mt) REVERT: B 973 ASN cc_start: 0.8289 (p0) cc_final: 0.8016 (p0) outliers start: 10 outliers final: 4 residues processed: 370 average time/residue: 0.1754 time to fit residues: 91.9641 Evaluate side-chains 349 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 344 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 348 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 514 HIS C 553 ASN C 612 ASN B 335 GLN B 668 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.126134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.110868 restraints weight = 24832.728| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.96 r_work: 0.3259 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17348 Z= 0.174 Angle : 0.588 6.347 23648 Z= 0.306 Chirality : 0.042 0.199 2566 Planarity : 0.005 0.084 2844 Dihedral : 15.227 179.944 2945 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 4.22 % Allowed : 22.76 % Favored : 73.02 % 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: -0.21 (0.19), residues: 1924 helix: 1.47 (0.21), residues: 634 sheet: 0.65 (0.32), residues: 267 loop : -1.48 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 273 TYR 0.019 0.002 TYR B 860 PHE 0.016 0.002 PHE B1570 TRP 0.016 0.001 TRP B 612 HIS 0.007 0.001 HIS B1621 Details of bonding type rmsd covalent geometry : bond 0.00402 (17332) covalent geometry : angle 0.58171 (23627) hydrogen bonds : bond 0.04226 ( 606) hydrogen bonds : angle 4.20556 ( 1780) metal coordination : bond 0.00826 ( 16) metal coordination : angle 3.00742 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 384 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 102 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7399 (tm-30) REVERT: C 120 ARG cc_start: 0.7806 (ttp80) cc_final: 0.7557 (mtp85) REVERT: C 216 MET cc_start: 0.6917 (OUTLIER) cc_final: 0.6557 (ptt) REVERT: C 218 LYS cc_start: 0.7910 (tptt) cc_final: 0.7615 (mtmm) REVERT: C 249 THR cc_start: 0.8373 (p) cc_final: 0.8164 (t) REVERT: C 650 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8339 (mp) REVERT: C 663 LYS cc_start: 0.8704 (mmmm) cc_final: 0.8483 (mttp) REVERT: B 34 SER cc_start: 0.8507 (m) cc_final: 0.8203 (t) REVERT: B 85 VAL cc_start: 0.8739 (OUTLIER) cc_final: 0.8536 (m) REVERT: B 95 ASP cc_start: 0.7560 (t0) cc_final: 0.7338 (t0) REVERT: B 171 ASP cc_start: 0.7650 (p0) cc_final: 0.7382 (p0) REVERT: B 313 LYS cc_start: 0.7883 (ptpp) cc_final: 0.7504 (mtmt) REVERT: B 349 SER cc_start: 0.8516 (p) cc_final: 0.8130 (m) REVERT: B 448 ASP cc_start: 0.6460 (t70) cc_final: 0.6190 (t70) REVERT: B 605 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.8090 (mtmt) REVERT: B 703 LYS cc_start: 0.8703 (mtmm) cc_final: 0.8447 (mtpt) REVERT: B 719 ARG cc_start: 0.7479 (ptp-170) cc_final: 0.7255 (ptp-170) REVERT: B 738 ARG cc_start: 0.8286 (tpp-160) cc_final: 0.7937 (mmt180) REVERT: B 973 ASN cc_start: 0.8361 (p0) cc_final: 0.8085 (p0) REVERT: B 995 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7305 (pm20) REVERT: B 997 MET cc_start: 0.8242 (ttp) cc_final: 0.8025 (ttm) outliers start: 72 outliers final: 41 residues processed: 422 average time/residue: 0.1658 time to fit residues: 100.6145 Evaluate side-chains 410 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 364 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 690 GLU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 854 SER Chi-restraints excluded: chain B residue 995 GLU Chi-restraints excluded: chain B residue 1436 TYR Chi-restraints excluded: chain B residue 1438 ASN Chi-restraints excluded: chain B residue 1563 LYS Chi-restraints excluded: chain B residue 1596 GLN Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1682 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 155 optimal weight: 3.9990 chunk 94 optimal weight: 0.4980 chunk 148 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 111 optimal weight: 0.0070 chunk 116 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 chunk 171 optimal weight: 5.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 514 HIS C 553 ASN B 112 GLN B 335 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.124628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.109659 restraints weight = 24978.506| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.94 r_work: 0.3210 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17348 Z= 0.182 Angle : 0.578 8.912 23648 Z= 0.299 Chirality : 0.043 0.215 2566 Planarity : 0.005 0.070 2844 Dihedral : 15.179 178.655 2933 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.46 % Allowed : 22.52 % Favored : 73.02 % 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: -0.24 (0.19), residues: 1924 helix: 1.46 (0.20), residues: 634 sheet: 0.58 (0.34), residues: 244 loop : -1.45 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 273 TYR 0.017 0.002 TYR B 860 PHE 0.014 0.001 PHE C 491 TRP 0.018 0.001 TRP B 612 HIS 0.008 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00422 (17332) covalent geometry : angle 0.56956 (23627) hydrogen bonds : bond 0.04339 ( 606) hydrogen bonds : angle 4.02556 ( 1780) metal coordination : bond 0.00967 ( 16) metal coordination : angle 3.31225 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 395 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 30 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7364 (pp20) REVERT: C 102 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7402 (tm-30) REVERT: C 120 ARG cc_start: 0.7833 (ttp80) cc_final: 0.7614 (mtp85) REVERT: C 164 GLU cc_start: 0.6912 (tm-30) cc_final: 0.6619 (tm-30) REVERT: C 216 MET cc_start: 0.6766 (OUTLIER) cc_final: 0.6462 (ptt) REVERT: C 218 LYS cc_start: 0.8000 (tptt) cc_final: 0.7632 (mtmm) REVERT: C 249 THR cc_start: 0.8453 (p) cc_final: 0.8230 (t) REVERT: C 266 GLU cc_start: 0.7715 (tp30) cc_final: 0.7490 (tp30) REVERT: C 267 LYS cc_start: 0.8147 (mttp) cc_final: 0.7862 (mmmm) REVERT: C 273 ARG cc_start: 0.8392 (mtt90) cc_final: 0.8005 (mtt90) REVERT: C 508 LYS cc_start: 0.8360 (tppt) cc_final: 0.7937 (mmtm) REVERT: C 560 SER cc_start: 0.8210 (m) cc_final: 0.7816 (p) REVERT: C 585 HIS cc_start: 0.8051 (OUTLIER) cc_final: 0.7614 (m90) REVERT: C 650 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8434 (mp) REVERT: C 663 LYS cc_start: 0.8786 (mmmm) cc_final: 0.8527 (mttp) REVERT: B 34 SER cc_start: 0.8518 (m) cc_final: 0.8194 (t) REVERT: B 85 VAL cc_start: 0.8749 (OUTLIER) cc_final: 0.8548 (m) REVERT: B 95 ASP cc_start: 0.7594 (t0) cc_final: 0.7321 (t0) REVERT: B 171 ASP cc_start: 0.7693 (p0) cc_final: 0.7372 (t0) REVERT: B 178 LEU cc_start: 0.8874 (mt) cc_final: 0.8576 (mp) REVERT: B 276 GLN cc_start: 0.7537 (mm-40) cc_final: 0.7334 (mm110) REVERT: B 313 LYS cc_start: 0.7932 (ptpp) cc_final: 0.7548 (mtmt) REVERT: B 349 SER cc_start: 0.8441 (p) cc_final: 0.8120 (m) REVERT: B 448 ASP cc_start: 0.6493 (t70) cc_final: 0.6223 (t70) REVERT: B 454 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7605 (mm-30) REVERT: B 591 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8325 (pp) REVERT: B 738 ARG cc_start: 0.8393 (tpp-160) cc_final: 0.8079 (mmt180) REVERT: B 849 LEU cc_start: 0.8550 (mt) cc_final: 0.8340 (mt) REVERT: B 928 ASP cc_start: 0.6984 (p0) cc_final: 0.6770 (p0) REVERT: B 933 VAL cc_start: 0.8452 (t) cc_final: 0.8169 (m) REVERT: B 973 ASN cc_start: 0.8332 (p0) cc_final: 0.8044 (p0) REVERT: B 997 MET cc_start: 0.8305 (ttp) cc_final: 0.8055 (ttm) REVERT: B 1496 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7598 (tm-30) REVERT: B 1557 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.7934 (t80) REVERT: B 1691 PHE cc_start: 0.8039 (t80) cc_final: 0.7667 (t80) outliers start: 76 outliers final: 48 residues processed: 435 average time/residue: 0.1638 time to fit residues: 102.8201 Evaluate side-chains 429 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 375 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 690 GLU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 854 SER Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1436 TYR Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1557 PHE Chi-restraints excluded: chain B residue 1563 LYS Chi-restraints excluded: chain B residue 1596 GLN Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1647 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 45 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 86 optimal weight: 0.0670 chunk 169 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 514 HIS C 553 ASN B 335 GLN B 498 GLN B1649 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.125167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.110271 restraints weight = 24894.779| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.94 r_work: 0.3217 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17348 Z= 0.132 Angle : 0.545 7.897 23648 Z= 0.282 Chirality : 0.041 0.202 2566 Planarity : 0.005 0.061 2844 Dihedral : 15.154 179.292 2933 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.05 % Allowed : 23.40 % Favored : 72.55 % 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: -0.12 (0.19), residues: 1924 helix: 1.63 (0.20), residues: 634 sheet: 0.53 (0.34), residues: 244 loop : -1.39 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 273 TYR 0.016 0.001 TYR B 578 PHE 0.017 0.001 PHE C 491 TRP 0.016 0.001 TRP B 612 HIS 0.008 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00305 (17332) covalent geometry : angle 0.53773 (23627) hydrogen bonds : bond 0.03654 ( 606) hydrogen bonds : angle 3.87827 ( 1780) metal coordination : bond 0.00445 ( 16) metal coordination : angle 3.08262 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 384 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 30 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7376 (pp20) REVERT: C 102 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7510 (tm-30) REVERT: C 164 GLU cc_start: 0.6800 (tm-30) cc_final: 0.6440 (tm-30) REVERT: C 216 MET cc_start: 0.6727 (OUTLIER) cc_final: 0.6397 (ptt) REVERT: C 218 LYS cc_start: 0.7977 (tptt) cc_final: 0.7663 (mtmm) REVERT: C 249 THR cc_start: 0.8461 (p) cc_final: 0.8241 (t) REVERT: C 266 GLU cc_start: 0.7739 (tp30) cc_final: 0.7177 (tp30) REVERT: C 267 LYS cc_start: 0.8154 (mttp) cc_final: 0.7880 (mmmm) REVERT: C 273 ARG cc_start: 0.8325 (mtt90) cc_final: 0.7936 (mtp85) REVERT: C 508 LYS cc_start: 0.8289 (tppt) cc_final: 0.7828 (mmtm) REVERT: C 560 SER cc_start: 0.8211 (m) cc_final: 0.7826 (p) REVERT: C 663 LYS cc_start: 0.8847 (mmmm) cc_final: 0.8608 (mttp) REVERT: C 697 LYS cc_start: 0.8343 (ttpp) cc_final: 0.8133 (ttpt) REVERT: B 34 SER cc_start: 0.8487 (m) cc_final: 0.8268 (p) REVERT: B 85 VAL cc_start: 0.8750 (OUTLIER) cc_final: 0.8537 (m) REVERT: B 95 ASP cc_start: 0.7615 (t0) cc_final: 0.7347 (t0) REVERT: B 171 ASP cc_start: 0.7657 (p0) cc_final: 0.7386 (p0) REVERT: B 178 LEU cc_start: 0.8876 (mt) cc_final: 0.8583 (mp) REVERT: B 276 GLN cc_start: 0.7544 (mm-40) cc_final: 0.7330 (mm110) REVERT: B 313 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7556 (mtmt) REVERT: B 349 SER cc_start: 0.8421 (p) cc_final: 0.8107 (m) REVERT: B 448 ASP cc_start: 0.6582 (t70) cc_final: 0.6230 (t70) REVERT: B 454 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7615 (mm-30) REVERT: B 591 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8277 (pp) REVERT: B 597 THR cc_start: 0.7943 (p) cc_final: 0.7080 (t) REVERT: B 617 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7639 (mmtt) REVERT: B 738 ARG cc_start: 0.8355 (tpp-160) cc_final: 0.8021 (mmt180) REVERT: B 754 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.8055 (ttm) REVERT: B 928 ASP cc_start: 0.7012 (p0) cc_final: 0.6780 (p0) REVERT: B 933 VAL cc_start: 0.8434 (t) cc_final: 0.8157 (m) REVERT: B 973 ASN cc_start: 0.8304 (p0) cc_final: 0.8019 (p0) REVERT: B 1496 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7415 (tm-30) REVERT: B 1557 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7857 (t80) REVERT: B 1691 PHE cc_start: 0.8032 (t80) cc_final: 0.7667 (t80) outliers start: 69 outliers final: 49 residues processed: 414 average time/residue: 0.1642 time to fit residues: 97.8258 Evaluate side-chains 436 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 380 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 428 TYR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 690 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 854 SER Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1436 TYR Chi-restraints excluded: chain B residue 1557 PHE Chi-restraints excluded: chain B residue 1563 LYS Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1666 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 110 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 34 optimal weight: 0.0060 chunk 116 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 514 HIS C 553 ASN B 335 GLN B1649 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.123940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.108701 restraints weight = 24205.966| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.97 r_work: 0.3210 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17348 Z= 0.166 Angle : 0.558 8.954 23648 Z= 0.289 Chirality : 0.042 0.223 2566 Planarity : 0.005 0.059 2844 Dihedral : 15.171 179.239 2933 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 5.10 % Allowed : 22.93 % Favored : 71.96 % 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: -0.15 (0.19), residues: 1924 helix: 1.58 (0.20), residues: 641 sheet: 0.53 (0.34), residues: 244 loop : -1.42 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 120 TYR 0.016 0.001 TYR B 578 PHE 0.017 0.001 PHE C 491 TRP 0.017 0.001 TRP B 612 HIS 0.008 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00387 (17332) covalent geometry : angle 0.55011 (23627) hydrogen bonds : bond 0.03851 ( 606) hydrogen bonds : angle 3.85337 ( 1780) metal coordination : bond 0.00659 ( 16) metal coordination : angle 3.25732 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 407 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 30 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7325 (pp20) REVERT: C 102 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7525 (tm-30) REVERT: C 161 ASP cc_start: 0.7236 (m-30) cc_final: 0.6580 (t0) REVERT: C 164 GLU cc_start: 0.6827 (tm-30) cc_final: 0.6527 (tm-30) REVERT: C 216 MET cc_start: 0.6751 (OUTLIER) cc_final: 0.6414 (ptt) REVERT: C 218 LYS cc_start: 0.8007 (tptt) cc_final: 0.7687 (mtmm) REVERT: C 249 THR cc_start: 0.8527 (p) cc_final: 0.8314 (t) REVERT: C 266 GLU cc_start: 0.7747 (tp30) cc_final: 0.7156 (tp30) REVERT: C 267 LYS cc_start: 0.8283 (mttp) cc_final: 0.7998 (mmmm) REVERT: C 273 ARG cc_start: 0.8301 (mtt90) cc_final: 0.7939 (mtp85) REVERT: C 275 ARG cc_start: 0.8113 (ttt90) cc_final: 0.7796 (tpt170) REVERT: C 483 ASP cc_start: 0.7770 (t70) cc_final: 0.7014 (t0) REVERT: C 508 LYS cc_start: 0.8156 (tppt) cc_final: 0.7743 (mmtm) REVERT: C 560 SER cc_start: 0.8246 (m) cc_final: 0.7857 (p) REVERT: C 576 ASN cc_start: 0.7816 (m-40) cc_final: 0.7525 (m110) REVERT: C 585 HIS cc_start: 0.8049 (OUTLIER) cc_final: 0.7571 (m90) REVERT: C 641 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6825 (tm-30) REVERT: C 650 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8481 (mp) REVERT: C 663 LYS cc_start: 0.8830 (mmmm) cc_final: 0.8583 (mttp) REVERT: C 697 LYS cc_start: 0.8349 (ttpp) cc_final: 0.8142 (ttpt) REVERT: B 34 SER cc_start: 0.8510 (m) cc_final: 0.8289 (p) REVERT: B 85 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8551 (m) REVERT: B 95 ASP cc_start: 0.7600 (t0) cc_final: 0.7348 (t0) REVERT: B 171 ASP cc_start: 0.7689 (p0) cc_final: 0.7440 (p0) REVERT: B 178 LEU cc_start: 0.8853 (mt) cc_final: 0.8642 (mp) REVERT: B 313 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7589 (mtmt) REVERT: B 349 SER cc_start: 0.8376 (p) cc_final: 0.8096 (m) REVERT: B 448 ASP cc_start: 0.6710 (t70) cc_final: 0.6411 (t70) REVERT: B 454 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7649 (mm-30) REVERT: B 591 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8291 (pp) REVERT: B 617 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7636 (mmtt) REVERT: B 836 LEU cc_start: 0.8075 (mt) cc_final: 0.7812 (mp) REVERT: B 933 VAL cc_start: 0.8483 (t) cc_final: 0.8205 (m) REVERT: B 973 ASN cc_start: 0.8247 (p0) cc_final: 0.7964 (p0) REVERT: B 1441 GLU cc_start: 0.6503 (mp0) cc_final: 0.6294 (mp0) REVERT: B 1496 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7331 (tm-30) REVERT: B 1557 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7795 (t80) REVERT: B 1691 PHE cc_start: 0.8058 (t80) cc_final: 0.7702 (t80) outliers start: 87 outliers final: 54 residues processed: 452 average time/residue: 0.1695 time to fit residues: 109.7298 Evaluate side-chains 456 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 394 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 428 TYR Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 588 MET Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 854 SER Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1436 TYR Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1557 PHE Chi-restraints excluded: chain B residue 1563 LYS Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1666 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 37 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 44 optimal weight: 0.0670 chunk 164 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 5 optimal weight: 0.0870 chunk 87 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 overall best weight: 0.6096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 GLN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 514 HIS C 553 ASN B1649 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.124372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.108196 restraints weight = 24127.905| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.09 r_work: 0.3215 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17348 Z= 0.124 Angle : 0.543 9.804 23648 Z= 0.279 Chirality : 0.041 0.203 2566 Planarity : 0.004 0.060 2844 Dihedral : 15.162 179.721 2933 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.16 % Allowed : 23.99 % Favored : 71.85 % 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: -0.06 (0.19), residues: 1924 helix: 1.73 (0.20), residues: 635 sheet: 0.52 (0.34), residues: 243 loop : -1.38 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 120 TYR 0.014 0.001 TYR B 578 PHE 0.018 0.001 PHE C 491 TRP 0.016 0.001 TRP C 400 HIS 0.008 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00284 (17332) covalent geometry : angle 0.53133 (23627) hydrogen bonds : bond 0.03466 ( 606) hydrogen bonds : angle 3.76398 ( 1780) metal coordination : bond 0.00859 ( 16) metal coordination : angle 3.85477 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 393 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 102 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7598 (tm-30) REVERT: C 161 ASP cc_start: 0.7200 (m-30) cc_final: 0.6558 (t0) REVERT: C 164 GLU cc_start: 0.6744 (tm-30) cc_final: 0.6491 (tm-30) REVERT: C 216 MET cc_start: 0.6698 (OUTLIER) cc_final: 0.6361 (ptt) REVERT: C 218 LYS cc_start: 0.8014 (tptt) cc_final: 0.7663 (mtmm) REVERT: C 249 THR cc_start: 0.8501 (p) cc_final: 0.8293 (t) REVERT: C 250 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8482 (tt) REVERT: C 266 GLU cc_start: 0.7806 (tp30) cc_final: 0.7176 (tp30) REVERT: C 267 LYS cc_start: 0.8282 (mttp) cc_final: 0.8011 (mmmm) REVERT: C 273 ARG cc_start: 0.8309 (mtt90) cc_final: 0.7975 (mtp85) REVERT: C 275 ARG cc_start: 0.8076 (ttt90) cc_final: 0.7777 (tpt170) REVERT: C 326 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8442 (mm) REVERT: C 483 ASP cc_start: 0.7825 (t70) cc_final: 0.7200 (t0) REVERT: C 508 LYS cc_start: 0.8177 (tppt) cc_final: 0.7640 (mmtm) REVERT: C 585 HIS cc_start: 0.7996 (OUTLIER) cc_final: 0.7543 (m90) REVERT: C 697 LYS cc_start: 0.8377 (ttpp) cc_final: 0.8175 (ttpt) REVERT: B 34 SER cc_start: 0.8458 (m) cc_final: 0.8230 (p) REVERT: B 85 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8547 (m) REVERT: B 95 ASP cc_start: 0.7569 (t0) cc_final: 0.7356 (t0) REVERT: B 171 ASP cc_start: 0.7649 (p0) cc_final: 0.7378 (p0) REVERT: B 178 LEU cc_start: 0.8858 (mt) cc_final: 0.8649 (mp) REVERT: B 313 LYS cc_start: 0.7945 (ptpp) cc_final: 0.7602 (mtmt) REVERT: B 349 SER cc_start: 0.8397 (p) cc_final: 0.8145 (m) REVERT: B 448 ASP cc_start: 0.6705 (t70) cc_final: 0.6406 (t70) REVERT: B 454 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7682 (mm-30) REVERT: B 591 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8213 (pp) REVERT: B 597 THR cc_start: 0.7977 (p) cc_final: 0.7138 (t) REVERT: B 617 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7611 (mmtt) REVERT: B 632 LYS cc_start: 0.8035 (mptt) cc_final: 0.7670 (mptt) REVERT: B 737 ARG cc_start: 0.8813 (mtm180) cc_final: 0.8572 (mtp180) REVERT: B 738 ARG cc_start: 0.8380 (tpp-160) cc_final: 0.8037 (mmt180) REVERT: B 752 CYS cc_start: 0.7095 (p) cc_final: 0.6534 (p) REVERT: B 836 LEU cc_start: 0.8101 (mt) cc_final: 0.7810 (mp) REVERT: B 933 VAL cc_start: 0.8516 (t) cc_final: 0.8236 (m) REVERT: B 973 ASN cc_start: 0.8261 (p0) cc_final: 0.8001 (p0) REVERT: B 1496 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7197 (tm-30) REVERT: B 1557 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.7813 (t80) REVERT: B 1691 PHE cc_start: 0.8019 (t80) cc_final: 0.7682 (t80) outliers start: 71 outliers final: 49 residues processed: 427 average time/residue: 0.1614 time to fit residues: 99.5621 Evaluate side-chains 436 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 379 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 428 TYR Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 854 SER Chi-restraints excluded: chain B residue 917 ASN Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 997 MET Chi-restraints excluded: chain B residue 1436 TYR Chi-restraints excluded: chain B residue 1438 ASN Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1475 ILE Chi-restraints excluded: chain B residue 1557 PHE Chi-restraints excluded: chain B residue 1563 LYS Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1666 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 37 optimal weight: 1.9990 chunk 187 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 120 optimal weight: 0.0000 chunk 3 optimal weight: 0.8980 chunk 170 optimal weight: 0.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 ASN C 685 ASN B1649 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.122777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.106780 restraints weight = 24145.080| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.07 r_work: 0.3181 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17348 Z= 0.189 Angle : 0.585 9.542 23648 Z= 0.301 Chirality : 0.043 0.235 2566 Planarity : 0.005 0.061 2844 Dihedral : 15.221 179.201 2933 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 4.87 % Allowed : 24.28 % Favored : 70.85 % 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: -0.14 (0.19), residues: 1924 helix: 1.60 (0.20), residues: 642 sheet: 0.50 (0.34), residues: 243 loop : -1.40 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 120 TYR 0.015 0.002 TYR B 578 PHE 0.017 0.001 PHE C 491 TRP 0.016 0.001 TRP B 612 HIS 0.008 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00442 (17332) covalent geometry : angle 0.57321 (23627) hydrogen bonds : bond 0.04011 ( 606) hydrogen bonds : angle 3.81155 ( 1780) metal coordination : bond 0.00999 ( 16) metal coordination : angle 3.92166 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 394 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 102 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7595 (tm-30) REVERT: C 161 ASP cc_start: 0.7174 (m-30) cc_final: 0.6534 (t0) REVERT: C 164 GLU cc_start: 0.6839 (tm-30) cc_final: 0.6567 (tm-30) REVERT: C 187 LEU cc_start: 0.7802 (tp) cc_final: 0.7293 (tp) REVERT: C 210 HIS cc_start: 0.6817 (t70) cc_final: 0.6553 (m-70) REVERT: C 216 MET cc_start: 0.6742 (OUTLIER) cc_final: 0.6394 (ptt) REVERT: C 217 ASP cc_start: 0.7782 (t0) cc_final: 0.7480 (t0) REVERT: C 218 LYS cc_start: 0.8020 (tptt) cc_final: 0.7757 (mtmm) REVERT: C 266 GLU cc_start: 0.7817 (tp30) cc_final: 0.7232 (tp30) REVERT: C 267 LYS cc_start: 0.8407 (mttp) cc_final: 0.8084 (mmmm) REVERT: C 273 ARG cc_start: 0.8284 (mtt90) cc_final: 0.7967 (mtp85) REVERT: C 275 ARG cc_start: 0.8125 (ttt90) cc_final: 0.7812 (tpt170) REVERT: C 326 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8469 (mt) REVERT: C 508 LYS cc_start: 0.8154 (tppt) cc_final: 0.7698 (mmtm) REVERT: C 585 HIS cc_start: 0.8097 (OUTLIER) cc_final: 0.7661 (m90) REVERT: C 663 LYS cc_start: 0.8877 (mmmm) cc_final: 0.8650 (mttp) REVERT: B 34 SER cc_start: 0.8490 (m) cc_final: 0.8147 (t) REVERT: B 85 VAL cc_start: 0.8763 (OUTLIER) cc_final: 0.8556 (m) REVERT: B 95 ASP cc_start: 0.7571 (t0) cc_final: 0.7297 (t0) REVERT: B 142 VAL cc_start: 0.7873 (t) cc_final: 0.7522 (m) REVERT: B 171 ASP cc_start: 0.7678 (p0) cc_final: 0.7404 (p0) REVERT: B 178 LEU cc_start: 0.8880 (mt) cc_final: 0.8590 (mp) REVERT: B 313 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7620 (mtmt) REVERT: B 349 SER cc_start: 0.8383 (p) cc_final: 0.8156 (m) REVERT: B 448 ASP cc_start: 0.6806 (t70) cc_final: 0.6506 (t70) REVERT: B 454 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7723 (mm-30) REVERT: B 617 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7693 (mmtt) REVERT: B 632 LYS cc_start: 0.8031 (mptt) cc_final: 0.7679 (mptt) REVERT: B 737 ARG cc_start: 0.8835 (mtm180) cc_final: 0.8583 (mtp180) REVERT: B 738 ARG cc_start: 0.8451 (tpp-160) cc_final: 0.8088 (mmt180) REVERT: B 752 CYS cc_start: 0.7096 (p) cc_final: 0.6581 (p) REVERT: B 836 LEU cc_start: 0.8122 (mt) cc_final: 0.7810 (mp) REVERT: B 933 VAL cc_start: 0.8521 (t) cc_final: 0.8253 (m) REVERT: B 973 ASN cc_start: 0.8260 (p0) cc_final: 0.7981 (p0) REVERT: B 1496 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7159 (tm-30) REVERT: B 1557 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.7800 (t80) REVERT: B 1593 LYS cc_start: 0.8447 (mtpp) cc_final: 0.8103 (mtpp) REVERT: B 1691 PHE cc_start: 0.8016 (t80) cc_final: 0.7366 (t80) outliers start: 83 outliers final: 62 residues processed: 439 average time/residue: 0.1570 time to fit residues: 99.0870 Evaluate side-chains 452 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 383 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 428 TYR Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 588 MET Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 854 SER Chi-restraints excluded: chain B residue 917 ASN Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 997 MET Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1436 TYR Chi-restraints excluded: chain B residue 1438 ASN Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1475 ILE Chi-restraints excluded: chain B residue 1557 PHE Chi-restraints excluded: chain B residue 1563 LYS Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1666 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 93 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 112 optimal weight: 0.0970 chunk 77 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 424 ASN ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 685 ASN ** B 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1649 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.123942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.108353 restraints weight = 24253.915| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.96 r_work: 0.3224 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17348 Z= 0.136 Angle : 0.562 8.969 23648 Z= 0.290 Chirality : 0.041 0.214 2566 Planarity : 0.004 0.064 2844 Dihedral : 15.215 179.543 2933 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.40 % Allowed : 24.63 % Favored : 70.97 % 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: -0.08 (0.19), residues: 1924 helix: 1.68 (0.20), residues: 637 sheet: 0.46 (0.34), residues: 245 loop : -1.36 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 120 TYR 0.014 0.001 TYR B 578 PHE 0.017 0.001 PHE C 491 TRP 0.020 0.001 TRP C 400 HIS 0.007 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00316 (17332) covalent geometry : angle 0.55214 (23627) hydrogen bonds : bond 0.03569 ( 606) hydrogen bonds : angle 3.76808 ( 1780) metal coordination : bond 0.00772 ( 16) metal coordination : angle 3.56188 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 387 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 102 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7528 (tm-30) REVERT: C 161 ASP cc_start: 0.7108 (m-30) cc_final: 0.6470 (t0) REVERT: C 164 GLU cc_start: 0.6700 (OUTLIER) cc_final: 0.6392 (tm-30) REVERT: C 187 LEU cc_start: 0.7732 (tp) cc_final: 0.7285 (tp) REVERT: C 210 HIS cc_start: 0.6744 (t70) cc_final: 0.6453 (m-70) REVERT: C 216 MET cc_start: 0.6672 (OUTLIER) cc_final: 0.6298 (ptt) REVERT: C 217 ASP cc_start: 0.7730 (t0) cc_final: 0.7523 (t0) REVERT: C 218 LYS cc_start: 0.7977 (tptt) cc_final: 0.7726 (mtmm) REVERT: C 250 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8433 (tt) REVERT: C 266 GLU cc_start: 0.7746 (tp30) cc_final: 0.7126 (tp30) REVERT: C 267 LYS cc_start: 0.8316 (mttp) cc_final: 0.7999 (mmmm) REVERT: C 273 ARG cc_start: 0.8252 (mtt90) cc_final: 0.7922 (mtp85) REVERT: C 275 ARG cc_start: 0.8076 (ttt90) cc_final: 0.7775 (tpt170) REVERT: C 326 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8419 (mt) REVERT: C 508 LYS cc_start: 0.8121 (tppt) cc_final: 0.7711 (mmtm) REVERT: C 585 HIS cc_start: 0.8018 (OUTLIER) cc_final: 0.7566 (m90) REVERT: C 663 LYS cc_start: 0.8835 (mmmm) cc_final: 0.8619 (mttm) REVERT: C 688 GLN cc_start: 0.8070 (mt0) cc_final: 0.7700 (mt0) REVERT: B 34 SER cc_start: 0.8454 (m) cc_final: 0.8095 (t) REVERT: B 72 GLU cc_start: 0.7892 (tt0) cc_final: 0.7574 (mt-10) REVERT: B 85 VAL cc_start: 0.8737 (OUTLIER) cc_final: 0.8531 (m) REVERT: B 95 ASP cc_start: 0.7546 (t0) cc_final: 0.7285 (t0) REVERT: B 142 VAL cc_start: 0.7842 (t) cc_final: 0.7491 (m) REVERT: B 171 ASP cc_start: 0.7667 (p0) cc_final: 0.7384 (p0) REVERT: B 178 LEU cc_start: 0.8818 (mt) cc_final: 0.8564 (mp) REVERT: B 313 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7612 (mtmt) REVERT: B 448 ASP cc_start: 0.6826 (t70) cc_final: 0.6424 (t0) REVERT: B 454 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7677 (mm-30) REVERT: B 580 GLU cc_start: 0.7934 (tt0) cc_final: 0.7682 (tt0) REVERT: B 617 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7640 (mmtt) REVERT: B 632 LYS cc_start: 0.8005 (mptt) cc_final: 0.7651 (mptt) REVERT: B 737 ARG cc_start: 0.8746 (mtm180) cc_final: 0.8532 (mtp180) REVERT: B 738 ARG cc_start: 0.8373 (tpp-160) cc_final: 0.8014 (mmt180) REVERT: B 752 CYS cc_start: 0.6995 (p) cc_final: 0.6478 (p) REVERT: B 836 LEU cc_start: 0.8046 (mt) cc_final: 0.7811 (mp) REVERT: B 933 VAL cc_start: 0.8481 (t) cc_final: 0.8208 (m) REVERT: B 973 ASN cc_start: 0.8216 (p0) cc_final: 0.7913 (p0) REVERT: B 1496 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7126 (tm-30) REVERT: B 1557 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.7733 (t80) REVERT: B 1593 LYS cc_start: 0.8382 (mtpp) cc_final: 0.8027 (mtpp) outliers start: 75 outliers final: 52 residues processed: 425 average time/residue: 0.1673 time to fit residues: 101.8259 Evaluate side-chains 438 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 377 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 428 TYR Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 854 SER Chi-restraints excluded: chain B residue 917 ASN Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1436 TYR Chi-restraints excluded: chain B residue 1438 ASN Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1475 ILE Chi-restraints excluded: chain B residue 1557 PHE Chi-restraints excluded: chain B residue 1563 LYS Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1666 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 46 optimal weight: 0.8980 chunk 166 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 80 optimal weight: 0.4980 chunk 73 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 514 HIS C 685 ASN ** B 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1649 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.124185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.108681 restraints weight = 24180.454| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.96 r_work: 0.3228 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17348 Z= 0.132 Angle : 0.559 8.729 23648 Z= 0.289 Chirality : 0.041 0.221 2566 Planarity : 0.005 0.066 2844 Dihedral : 15.211 179.862 2933 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.22 % Allowed : 25.16 % Favored : 70.62 % 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: -0.02 (0.19), residues: 1924 helix: 1.75 (0.20), residues: 636 sheet: 0.45 (0.34), residues: 245 loop : -1.32 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 212 TYR 0.014 0.001 TYR B 578 PHE 0.018 0.001 PHE C 491 TRP 0.023 0.001 TRP C 400 HIS 0.006 0.001 HIS B1621 Details of bonding type rmsd covalent geometry : bond 0.00308 (17332) covalent geometry : angle 0.55006 (23627) hydrogen bonds : bond 0.03469 ( 606) hydrogen bonds : angle 3.74964 ( 1780) metal coordination : bond 0.00608 ( 16) metal coordination : angle 3.42388 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 380 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 102 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7560 (tm-30) REVERT: C 161 ASP cc_start: 0.7084 (m-30) cc_final: 0.6471 (t0) REVERT: C 164 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.6456 (tm-30) REVERT: C 187 LEU cc_start: 0.7744 (tp) cc_final: 0.7343 (tp) REVERT: C 210 HIS cc_start: 0.6706 (t70) cc_final: 0.6436 (m-70) REVERT: C 216 MET cc_start: 0.6685 (OUTLIER) cc_final: 0.6326 (ptt) REVERT: C 218 LYS cc_start: 0.8001 (tptt) cc_final: 0.7758 (mtmm) REVERT: C 250 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8429 (tt) REVERT: C 266 GLU cc_start: 0.7756 (tp30) cc_final: 0.7118 (tp30) REVERT: C 267 LYS cc_start: 0.8329 (mttp) cc_final: 0.8016 (mmmm) REVERT: C 273 ARG cc_start: 0.8253 (mtt90) cc_final: 0.7942 (mtp85) REVERT: C 275 ARG cc_start: 0.8069 (ttt90) cc_final: 0.7771 (tpt170) REVERT: C 326 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8404 (mt) REVERT: C 508 LYS cc_start: 0.8168 (tppt) cc_final: 0.7744 (mmtm) REVERT: C 585 HIS cc_start: 0.8008 (OUTLIER) cc_final: 0.7566 (m90) REVERT: C 688 GLN cc_start: 0.8072 (mt0) cc_final: 0.7702 (mt0) REVERT: B 72 GLU cc_start: 0.7890 (tt0) cc_final: 0.7581 (mt-10) REVERT: B 85 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8537 (m) REVERT: B 95 ASP cc_start: 0.7590 (t0) cc_final: 0.7364 (t0) REVERT: B 142 VAL cc_start: 0.7837 (t) cc_final: 0.7481 (m) REVERT: B 171 ASP cc_start: 0.7664 (p0) cc_final: 0.7360 (p0) REVERT: B 178 LEU cc_start: 0.8826 (mt) cc_final: 0.8562 (mp) REVERT: B 218 LYS cc_start: 0.8515 (tppt) cc_final: 0.8280 (mmtm) REVERT: B 313 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7597 (mtmt) REVERT: B 448 ASP cc_start: 0.6862 (t70) cc_final: 0.6515 (t0) REVERT: B 580 GLU cc_start: 0.7917 (tt0) cc_final: 0.7678 (tt0) REVERT: B 617 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7645 (mmtt) REVERT: B 717 GLU cc_start: 0.7381 (pm20) cc_final: 0.6874 (pm20) REVERT: B 737 ARG cc_start: 0.8775 (mtm180) cc_final: 0.8541 (mtp180) REVERT: B 744 LYS cc_start: 0.7897 (mtmt) cc_final: 0.7519 (mtmt) REVERT: B 752 CYS cc_start: 0.6936 (p) cc_final: 0.6254 (p) REVERT: B 836 LEU cc_start: 0.8052 (mt) cc_final: 0.7823 (mp) REVERT: B 847 ASP cc_start: 0.7644 (p0) cc_final: 0.7426 (t0) REVERT: B 933 VAL cc_start: 0.8491 (t) cc_final: 0.8209 (m) REVERT: B 973 ASN cc_start: 0.8176 (p0) cc_final: 0.7937 (p0) REVERT: B 1496 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7132 (tm-30) REVERT: B 1557 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.7799 (t80) REVERT: B 1593 LYS cc_start: 0.8395 (mtpp) cc_final: 0.8045 (mtpp) outliers start: 72 outliers final: 53 residues processed: 413 average time/residue: 0.1697 time to fit residues: 100.2256 Evaluate side-chains 437 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 375 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 428 TYR Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 854 SER Chi-restraints excluded: chain B residue 917 ASN Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1436 TYR Chi-restraints excluded: chain B residue 1438 ASN Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1475 ILE Chi-restraints excluded: chain B residue 1557 PHE Chi-restraints excluded: chain B residue 1563 LYS Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1666 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 74 optimal weight: 0.0770 chunk 168 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 107 optimal weight: 0.2980 chunk 158 optimal weight: 0.2980 chunk 145 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 514 HIS C 576 ASN ** B 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1649 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.124045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108520 restraints weight = 24157.056| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.96 r_work: 0.3191 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17348 Z= 0.138 Angle : 0.566 8.536 23648 Z= 0.292 Chirality : 0.041 0.224 2566 Planarity : 0.005 0.068 2844 Dihedral : 15.218 179.969 2933 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.87 % Allowed : 25.57 % Favored : 70.56 % 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: 0.01 (0.19), residues: 1924 helix: 1.78 (0.20), residues: 636 sheet: 0.46 (0.34), residues: 246 loop : -1.31 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 212 TYR 0.014 0.001 TYR B 578 PHE 0.018 0.001 PHE C 491 TRP 0.043 0.001 TRP C 400 HIS 0.006 0.001 HIS B1621 Details of bonding type rmsd covalent geometry : bond 0.00322 (17332) covalent geometry : angle 0.55741 (23627) hydrogen bonds : bond 0.03485 ( 606) hydrogen bonds : angle 3.75117 ( 1780) metal coordination : bond 0.00641 ( 16) metal coordination : angle 3.35813 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 377 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 102 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7492 (tm-30) REVERT: C 161 ASP cc_start: 0.7115 (m-30) cc_final: 0.6457 (t0) REVERT: C 164 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6335 (tm-30) REVERT: C 187 LEU cc_start: 0.7612 (tp) cc_final: 0.7241 (tp) REVERT: C 210 HIS cc_start: 0.6693 (t70) cc_final: 0.6361 (m-70) REVERT: C 216 MET cc_start: 0.6626 (OUTLIER) cc_final: 0.6284 (ptt) REVERT: C 218 LYS cc_start: 0.7963 (tptt) cc_final: 0.7643 (mtmm) REVERT: C 250 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8405 (tt) REVERT: C 266 GLU cc_start: 0.7719 (tp30) cc_final: 0.7097 (tp30) REVERT: C 267 LYS cc_start: 0.8332 (mttp) cc_final: 0.7991 (mmmm) REVERT: C 273 ARG cc_start: 0.8242 (mtt90) cc_final: 0.7889 (mtp85) REVERT: C 275 ARG cc_start: 0.8057 (ttt90) cc_final: 0.7745 (tpt170) REVERT: C 326 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8407 (mt) REVERT: C 508 LYS cc_start: 0.8186 (tppt) cc_final: 0.7739 (mmtm) REVERT: C 585 HIS cc_start: 0.7937 (OUTLIER) cc_final: 0.7491 (m90) REVERT: C 688 GLN cc_start: 0.8018 (mt0) cc_final: 0.7661 (mt0) REVERT: B 72 GLU cc_start: 0.7872 (tt0) cc_final: 0.7565 (mt-10) REVERT: B 85 VAL cc_start: 0.8705 (OUTLIER) cc_final: 0.8494 (m) REVERT: B 95 ASP cc_start: 0.7588 (t0) cc_final: 0.7310 (t0) REVERT: B 142 VAL cc_start: 0.7817 (t) cc_final: 0.7450 (m) REVERT: B 171 ASP cc_start: 0.7643 (p0) cc_final: 0.7360 (p0) REVERT: B 178 LEU cc_start: 0.8763 (mt) cc_final: 0.8522 (mp) REVERT: B 218 LYS cc_start: 0.8517 (tppt) cc_final: 0.8292 (mmtm) REVERT: B 313 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7543 (mtmt) REVERT: B 448 ASP cc_start: 0.6878 (t70) cc_final: 0.6527 (t0) REVERT: B 580 GLU cc_start: 0.7942 (tt0) cc_final: 0.7717 (tt0) REVERT: B 617 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7602 (mmtt) REVERT: B 717 GLU cc_start: 0.7432 (pm20) cc_final: 0.6923 (pm20) REVERT: B 737 ARG cc_start: 0.8754 (mtm180) cc_final: 0.8512 (mtp180) REVERT: B 744 LYS cc_start: 0.7852 (mtmt) cc_final: 0.7445 (mtmt) REVERT: B 752 CYS cc_start: 0.6864 (p) cc_final: 0.6152 (p) REVERT: B 836 LEU cc_start: 0.7965 (mt) cc_final: 0.7710 (mp) REVERT: B 933 VAL cc_start: 0.8476 (t) cc_final: 0.8197 (m) REVERT: B 973 ASN cc_start: 0.8134 (p0) cc_final: 0.7882 (p0) REVERT: B 1496 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7087 (tm-30) REVERT: B 1557 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7751 (t80) REVERT: B 1593 LYS cc_start: 0.8318 (mtpp) cc_final: 0.7954 (mtpp) outliers start: 66 outliers final: 50 residues processed: 408 average time/residue: 0.1675 time to fit residues: 97.8025 Evaluate side-chains 435 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 376 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain C residue 428 TYR Chi-restraints excluded: chain C residue 474 CYS Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 854 SER Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1438 ASN Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1475 ILE Chi-restraints excluded: chain B residue 1557 PHE Chi-restraints excluded: chain B residue 1628 LEU Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1666 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 146 optimal weight: 0.0370 chunk 156 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 188 optimal weight: 0.3980 chunk 89 optimal weight: 0.3980 chunk 54 optimal weight: 4.9990 chunk 142 optimal weight: 0.0870 chunk 125 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 514 HIS ** B 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1649 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.125448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.109531 restraints weight = 24194.301| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.07 r_work: 0.3226 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17348 Z= 0.105 Angle : 0.544 7.524 23648 Z= 0.281 Chirality : 0.040 0.226 2566 Planarity : 0.004 0.067 2844 Dihedral : 15.194 179.346 2933 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.28 % Allowed : 26.22 % Favored : 70.50 % 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: 0.12 (0.19), residues: 1924 helix: 1.92 (0.20), residues: 635 sheet: 0.52 (0.34), residues: 240 loop : -1.27 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 212 TYR 0.014 0.001 TYR C 518 PHE 0.032 0.001 PHE C 419 TRP 0.026 0.001 TRP C 400 HIS 0.007 0.001 HIS B1621 Details of bonding type rmsd covalent geometry : bond 0.00239 (17332) covalent geometry : angle 0.53673 (23627) hydrogen bonds : bond 0.03082 ( 606) hydrogen bonds : angle 3.67451 ( 1780) metal coordination : bond 0.00389 ( 16) metal coordination : angle 3.07218 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4484.59 seconds wall clock time: 77 minutes 35.78 seconds (4655.78 seconds total)