Starting phenix.real_space_refine on Sat Jul 4 00:11:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xss_33433/07_2026/7xss_33433.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xss_33433/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xss_33433/07_2026/7xss_33433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xss_33433/07_2026/7xss_33433.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7xss_33433/07_2026/7xss_33433.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xss_33433/07_2026/7xss_33433.cif" model { file = "/net/cci-nas-00/data/ceres_data/7xss_33433/07_2026/7xss_33433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xss_33433/07_2026/7xss_33433.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 2.93, per 1000 atoms: 0.17 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: 1.31 Conformation dependent library (CDL) restraints added in 513.4 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: 1.78 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: 3.36 Time building geometry restraints manager: 1.64 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: 9877 35.92 - 71.83: 391 71.83 - 107.74: 21 107.74 - 143.66: 0 143.66 - 179.57: 4 Dihedral angle restraints: 10293 sinusoidal: 4700 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 10290 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: 1.570 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.250 Find NCS groups from input model: 0.050 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 : 17.989 179.575 6699 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/Z covalent geometry : bond 0.00271 / 0.13 (17332) covalent geometry : angle 0.61267 / 0.35 (23627) hydrogen bonds : bond 0.17429 / 12.01 ( 606) hydrogen bonds : angle 5.78758 / 4.27 ( 1780) metal coordination : bond 0.00428 / 0.29 ( 16) metal coordination : angle 2.96188 / 1.88 ( 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 : 0.433 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: 0.1549 time to fit residues: 82.1070 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 : 0.543 ------------------------------------------------------------------------------- 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... ** 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 = 0.3602 r_free = 0.3602 target = 0.127110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.111820 restraints weight = 24782.290| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.97 r_work: 0.3262 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17348 Z= 0.171 Angle : 0.583 6.397 23648 Z= 0.303 Chirality : 0.042 0.198 2566 Planarity : 0.005 0.086 2844 Dihedral : 11.748 179.891 2757 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.28 % Allowed : 22.87 % Favored : 72.84 % 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: 1.48 (0.21), residues: 634 sheet: 0.66 (0.32), residues: 267 loop : -1.49 (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 0.017 0.002 PHE B1570 TRP 0.016 0.001 TRP B 612 HIS 0.006 0.001 HIS B1621 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (17332) covalent geometry : angle 0.57660 / 0.30 (23627) hydrogen bonds : bond 0.04389 / 2.97 ( 606) hydrogen bonds : angle 4.23271 / 3.14 ( 1780) metal coordination : bond 0.00783 / 0.51 ( 16) metal coordination : angle 2.98793 / 1.88 ( 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 455 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 382 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 102 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7393 (tm-30) REVERT: C 120 ARG cc_start: 0.7801 (ttp80) cc_final: 0.7549 (mtp85) REVERT: C 216 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.6552 (ptt) REVERT: C 218 LYS cc_start: 0.7916 (tptt) cc_final: 0.7625 (mtmm) REVERT: C 249 THR cc_start: 0.8365 (p) cc_final: 0.8157 (t) REVERT: C 641 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6729 (tm-30) REVERT: C 650 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8335 (mp) REVERT: C 663 LYS cc_start: 0.8703 (mmmm) cc_final: 0.8484 (mttp) REVERT: B 34 SER cc_start: 0.8527 (m) cc_final: 0.8208 (t) REVERT: B 85 VAL cc_start: 0.8748 (OUTLIER) cc_final: 0.8546 (m) REVERT: B 95 ASP cc_start: 0.7542 (t0) cc_final: 0.7339 (t0) REVERT: B 171 ASP cc_start: 0.7668 (p0) cc_final: 0.7397 (p0) REVERT: B 313 LYS cc_start: 0.7872 (ptpp) cc_final: 0.7477 (mtmt) REVERT: B 349 SER cc_start: 0.8518 (p) cc_final: 0.8127 (m) REVERT: B 448 ASP cc_start: 0.6462 (t70) cc_final: 0.6199 (t70) REVERT: B 703 LYS cc_start: 0.8706 (mtmm) cc_final: 0.8456 (mtpt) REVERT: B 738 ARG cc_start: 0.8278 (tpp-160) cc_final: 0.7931 (mmt180) REVERT: B 788 ASP cc_start: 0.7724 (m-30) cc_final: 0.7512 (m-30) REVERT: B 973 ASN cc_start: 0.8354 (p0) cc_final: 0.8087 (p0) REVERT: B 995 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7300 (pm20) REVERT: B 997 MET cc_start: 0.8258 (ttp) cc_final: 0.8038 (ttm) REVERT: B 1571 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7850 (tptm) outliers start: 73 outliers final: 41 residues processed: 422 average time/residue: 0.1482 time to fit residues: 90.5098 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 : 0.470 ------------------------------------------------------------------------------- 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 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 573 SER 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 773 GLU Chi-restraints excluded: chain B residue 796 THR Chi-restraints excluded: chain B residue 830 PHE 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 1571 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: 0.8980 chunk 148 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 111 optimal weight: 0.0970 chunk 116 optimal weight: 0.9990 chunk 187 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 171 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 514 HIS C 553 ASN B 335 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.126540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.111439 restraints weight = 24993.711| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.96 r_work: 0.3240 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1538 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= 0.139 Angle : 0.548 7.619 23648 Z= 0.284 Chirality : 0.041 0.195 2566 Planarity : 0.005 0.067 2844 Dihedral : 11.635 179.422 2745 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.70 % Allowed : 23.58 % Favored : 72.73 % 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: -0.16 (0.19), residues: 1924 helix: 1.57 (0.20), residues: 634 sheet: 0.52 (0.33), residues: 246 loop : -1.41 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 273 TYR 0.016 0.001 TYR B 621 PHE 0.015 0.001 PHE C 491 TRP 0.016 0.001 TRP B 612 HIS 0.007 0.001 HIS C 514 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (17332) covalent geometry : angle 0.54062 / 0.28 (23627) hydrogen bonds : bond 0.03878 / 2.62 ( 606) hydrogen bonds : angle 3.99292 / 2.96 ( 1780) metal coordination : bond 0.00562 / 0.33 ( 16) metal coordination : angle 3.00243 / 1.91 ( 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 448 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 385 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 102 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7417 (tm-30) REVERT: C 120 ARG cc_start: 0.7794 (ttp80) cc_final: 0.7567 (mtp85) REVERT: C 164 GLU cc_start: 0.6852 (tm-30) cc_final: 0.6564 (tm-30) REVERT: C 216 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.6423 (ptt) REVERT: C 218 LYS cc_start: 0.7929 (tptt) cc_final: 0.7559 (mtmm) REVERT: C 249 THR cc_start: 0.8397 (p) cc_final: 0.8176 (t) REVERT: C 318 ASP cc_start: 0.8330 (t0) cc_final: 0.8053 (t70) REVERT: C 560 SER cc_start: 0.8199 (m) cc_final: 0.7785 (p) REVERT: C 641 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6776 (tm-30) REVERT: C 663 LYS cc_start: 0.8799 (mmmm) cc_final: 0.8556 (mttp) REVERT: B 34 SER cc_start: 0.8504 (m) cc_final: 0.8186 (t) REVERT: B 85 VAL cc_start: 0.8746 (OUTLIER) cc_final: 0.8536 (m) REVERT: B 95 ASP cc_start: 0.7565 (t0) cc_final: 0.7285 (t0) REVERT: B 171 ASP cc_start: 0.7673 (p0) cc_final: 0.7262 (t0) REVERT: B 185 THR cc_start: 0.8657 (p) cc_final: 0.8422 (t) REVERT: B 313 LYS cc_start: 0.7945 (ptpp) cc_final: 0.7543 (mtmt) REVERT: B 349 SER cc_start: 0.8433 (p) cc_final: 0.8082 (m) REVERT: B 409 GLU cc_start: 0.7443 (mp0) cc_final: 0.7161 (pm20) REVERT: B 591 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8288 (pp) REVERT: B 597 THR cc_start: 0.7907 (p) cc_final: 0.7004 (t) REVERT: B 632 LYS cc_start: 0.8051 (mptt) cc_final: 0.7735 (mptt) REVERT: B 703 LYS cc_start: 0.8689 (mtmm) cc_final: 0.8479 (mtpt) REVERT: B 928 ASP cc_start: 0.7015 (p0) cc_final: 0.6805 (p0) REVERT: B 968 ASP cc_start: 0.7795 (t0) cc_final: 0.7575 (t70) REVERT: B 973 ASN cc_start: 0.8336 (p0) cc_final: 0.8025 (p0) REVERT: B 1496 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7556 (tm-30) outliers start: 63 outliers final: 43 residues processed: 414 average time/residue: 0.1581 time to fit residues: 94.9623 Evaluate side-chains 420 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 374 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 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 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 614 VAL 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 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 348 GLN Chi-restraints excluded: chain B residue 377 VAL 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 754 MET Chi-restraints excluded: chain B residue 763 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 986 ASN Chi-restraints excluded: chain B residue 995 GLU Chi-restraints excluded: chain B residue 1007 LEU Chi-restraints excluded: chain B residue 1436 TYR Chi-restraints excluded: chain B residue 1563 LYS Chi-restraints excluded: chain B residue 1596 GLN Chi-restraints excluded: chain B residue 1628 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 45 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 514 HIS C 553 ASN C 612 ASN B 335 GLN B 498 GLN B1649 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.125379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.110447 restraints weight = 24867.665| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.94 r_work: 0.3220 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17348 Z= 0.151 Angle : 0.548 8.228 23648 Z= 0.283 Chirality : 0.041 0.204 2566 Planarity : 0.004 0.061 2844 Dihedral : 11.686 179.559 2745 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.81 % Allowed : 22.70 % Favored : 72.49 % 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: 1.60 (0.20), residues: 634 sheet: 0.53 (0.34), residues: 246 loop : -1.37 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 273 TYR 0.018 0.001 TYR B 578 PHE 0.016 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/Z covalent geometry : bond 0.00351 / 0.15 (17332) covalent geometry : angle 0.53955 / 0.28 (23627) hydrogen bonds : bond 0.03778 / 2.53 ( 606) hydrogen bonds : angle 3.88654 / 2.88 ( 1780) metal coordination : bond 0.00601 / 0.41 ( 16) metal coordination : angle 3.18826 / 2.00 ( 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 472 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 390 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 102 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7547 (tm-30) REVERT: C 164 GLU cc_start: 0.6819 (tm-30) cc_final: 0.6449 (tm-30) REVERT: C 216 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.6417 (ptt) REVERT: C 218 LYS cc_start: 0.7982 (tptt) cc_final: 0.7636 (mtmm) REVERT: C 249 THR cc_start: 0.8426 (p) cc_final: 0.8205 (t) REVERT: C 266 GLU cc_start: 0.7731 (tp30) cc_final: 0.7481 (tp30) REVERT: C 267 LYS cc_start: 0.8140 (mttp) cc_final: 0.7847 (mmmm) REVERT: C 508 LYS cc_start: 0.8296 (tppt) cc_final: 0.7842 (mmtm) REVERT: C 560 SER cc_start: 0.8200 (m) cc_final: 0.7804 (p) REVERT: C 585 HIS cc_start: 0.8007 (OUTLIER) cc_final: 0.7521 (m90) REVERT: C 650 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8472 (mp) REVERT: C 663 LYS cc_start: 0.8836 (mmmm) cc_final: 0.8587 (mttp) REVERT: B 34 SER cc_start: 0.8495 (m) cc_final: 0.8270 (p) REVERT: B 85 VAL cc_start: 0.8759 (OUTLIER) cc_final: 0.8546 (m) REVERT: B 95 ASP cc_start: 0.7613 (t0) cc_final: 0.7340 (t0) REVERT: B 171 ASP cc_start: 0.7657 (p0) cc_final: 0.7390 (p0) REVERT: B 178 LEU cc_start: 0.8872 (mt) cc_final: 0.8579 (mp) REVERT: B 185 THR cc_start: 0.8661 (p) cc_final: 0.8428 (t) REVERT: B 313 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7552 (mtmt) REVERT: B 349 SER cc_start: 0.8423 (p) cc_final: 0.8111 (m) REVERT: B 357 LYS cc_start: 0.8212 (mtpp) cc_final: 0.8006 (mtpp) REVERT: B 409 GLU cc_start: 0.7451 (mp0) cc_final: 0.7175 (pm20) REVERT: B 454 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7613 (mm-30) REVERT: B 591 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8314 (pp) REVERT: B 597 THR cc_start: 0.7945 (p) cc_final: 0.7059 (t) REVERT: B 617 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7719 (mmtt) REVERT: B 632 LYS cc_start: 0.8050 (mptt) cc_final: 0.7717 (mptt) REVERT: B 719 ARG cc_start: 0.7537 (ptp-170) cc_final: 0.7259 (ptp-170) REVERT: B 738 ARG cc_start: 0.8391 (tpt170) cc_final: 0.8130 (mmt180) REVERT: B 928 ASP cc_start: 0.7013 (p0) cc_final: 0.6787 (p0) REVERT: B 933 VAL cc_start: 0.8479 (t) cc_final: 0.8200 (m) REVERT: B 973 ASN cc_start: 0.8329 (p0) cc_final: 0.8025 (p0) REVERT: B 1496 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7432 (tm-30) REVERT: B 1691 PHE cc_start: 0.8009 (t80) cc_final: 0.7630 (t80) outliers start: 82 outliers final: 55 residues processed: 430 average time/residue: 0.1599 time to fit residues: 99.6203 Evaluate side-chains 441 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 379 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 30 GLU 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 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 550 LEU Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 622 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 313 LYS Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 384 LEU 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 591 LEU Chi-restraints excluded: chain B residue 604 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 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 977 LEU Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 1436 TYR Chi-restraints excluded: chain B residue 1468 ILE 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 1666 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 110 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 155 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 424 ASN C 514 HIS C 553 ASN B 112 GLN B 335 GLN B1649 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.122059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.106697 restraints weight = 24229.469| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.02 r_work: 0.3160 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17348 Z= 0.261 Angle : 0.638 10.883 23648 Z= 0.328 Chirality : 0.046 0.261 2566 Planarity : 0.005 0.064 2844 Dihedral : 11.899 178.701 2745 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 5.69 % Allowed : 22.35 % 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: -0.34 (0.19), residues: 1924 helix: 1.36 (0.20), residues: 641 sheet: 0.44 (0.34), residues: 249 loop : -1.49 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 273 TYR 0.018 0.002 TYR B 578 PHE 0.017 0.002 PHE B 610 TRP 0.021 0.002 TRP B 612 HIS 0.011 0.002 HIS C 514 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.26 (17332) covalent geometry : angle 0.62453 / 0.33 (23627) hydrogen bonds : bond 0.04795 / 3.23 ( 606) hydrogen bonds : angle 4.00959 / 2.98 ( 1780) metal coordination : bond 0.01045 / 0.71 ( 16) metal coordination : angle 4.40839 / 2.69 ( 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 507 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 410 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 ASP cc_start: 0.7566 (t0) cc_final: 0.6894 (m-30) REVERT: C 102 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7558 (tm-30) REVERT: C 134 ARG cc_start: 0.8224 (tmm-80) cc_final: 0.7716 (ttp80) REVERT: C 161 ASP cc_start: 0.7268 (m-30) cc_final: 0.6622 (t0) REVERT: C 164 GLU cc_start: 0.6943 (tm-30) cc_final: 0.6684 (tm-30) REVERT: C 218 LYS cc_start: 0.8018 (tptt) cc_final: 0.7735 (mtmm) REVERT: C 249 THR cc_start: 0.8560 (p) cc_final: 0.8319 (t) REVERT: C 257 LYS cc_start: 0.8397 (mtpt) cc_final: 0.8176 (mtpt) REVERT: C 266 GLU cc_start: 0.7813 (tp30) cc_final: 0.7272 (tp30) REVERT: C 267 LYS cc_start: 0.8448 (mttp) cc_final: 0.8099 (mmmm) REVERT: C 273 ARG cc_start: 0.8344 (mtt90) cc_final: 0.7999 (mtp85) REVERT: C 483 ASP cc_start: 0.7804 (t70) cc_final: 0.7189 (t0) REVERT: C 502 GLU cc_start: 0.7713 (pm20) cc_final: 0.7397 (pm20) REVERT: C 508 LYS cc_start: 0.8277 (tppt) cc_final: 0.7486 (mmtm) REVERT: C 576 ASN cc_start: 0.7896 (m-40) cc_final: 0.7603 (m110) REVERT: C 585 HIS cc_start: 0.8169 (OUTLIER) cc_final: 0.7704 (m90) REVERT: C 641 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6847 (tm-30) REVERT: C 650 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8602 (mp) REVERT: C 663 LYS cc_start: 0.8877 (mmmm) cc_final: 0.8642 (mttp) REVERT: B 34 SER cc_start: 0.8535 (m) cc_final: 0.8199 (t) REVERT: B 85 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8562 (m) REVERT: B 95 ASP cc_start: 0.7561 (t0) cc_final: 0.7332 (t0) REVERT: B 142 VAL cc_start: 0.7954 (t) cc_final: 0.7599 (m) REVERT: B 168 ARG cc_start: 0.7937 (ttt180) cc_final: 0.7542 (ttt180) REVERT: B 171 ASP cc_start: 0.7708 (p0) cc_final: 0.7458 (p0) REVERT: B 178 LEU cc_start: 0.8867 (mt) cc_final: 0.8581 (mp) REVERT: B 313 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7462 (mtmm) REVERT: B 349 SER cc_start: 0.8345 (p) cc_final: 0.8117 (m) REVERT: B 448 ASP cc_start: 0.6777 (t70) cc_final: 0.6390 (t70) REVERT: B 454 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7682 (mm-30) REVERT: B 561 LEU cc_start: 0.8332 (tt) cc_final: 0.8097 (tp) REVERT: B 617 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7748 (mmtt) REVERT: B 619 ASN cc_start: 0.8011 (m110) cc_final: 0.7778 (m110) REVERT: B 623 LYS cc_start: 0.8525 (tttp) cc_final: 0.8302 (tttp) REVERT: B 738 ARG cc_start: 0.8461 (tpt170) cc_final: 0.8171 (mmt180) REVERT: B 752 CYS cc_start: 0.7150 (p) cc_final: 0.6615 (p) REVERT: B 836 LEU cc_start: 0.8152 (mt) cc_final: 0.7865 (mp) REVERT: B 933 VAL cc_start: 0.8489 (t) cc_final: 0.8230 (m) REVERT: B 973 ASN cc_start: 0.8289 (p0) cc_final: 0.7962 (p0) REVERT: B 997 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8228 (ttm) REVERT: B 1496 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7322 (tm-30) REVERT: B 1557 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.7834 (t80) REVERT: B 1593 LYS cc_start: 0.8427 (mtpp) cc_final: 0.8084 (mtpp) REVERT: B 1691 PHE cc_start: 0.8054 (t80) cc_final: 0.7719 (t80) outliers start: 97 outliers final: 64 residues processed: 459 average time/residue: 0.1550 time to fit residues: 103.1482 Evaluate side-chains 468 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 397 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 44 ILE 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 108 ILE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 186 ASN 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 85 VAL Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 151 ILE 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 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 604 LEU Chi-restraints excluded: chain B residue 617 LYS Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 636 GLU 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 847 ASP 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 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 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: 4.9990 chunk 161 optimal weight: 0.3980 chunk 44 optimal weight: 0.8980 chunk 164 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 5 optimal weight: 0.0370 chunk 87 optimal weight: 0.5980 chunk 4 optimal weight: 0.0170 chunk 27 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 119 GLN ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 514 HIS C 612 ASN B1649 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.124866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.108893 restraints weight = 24100.379| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.08 r_work: 0.3201 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17348 Z= 0.108 Angle : 0.545 8.590 23648 Z= 0.281 Chirality : 0.040 0.197 2566 Planarity : 0.004 0.063 2844 Dihedral : 11.788 179.609 2745 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 4.16 % Allowed : 24.11 % Favored : 71.73 % 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: -0.11 (0.19), residues: 1924 helix: 1.72 (0.20), residues: 635 sheet: 0.33 (0.34), residues: 251 loop : -1.40 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 273 TYR 0.014 0.001 TYR B 578 PHE 0.017 0.001 PHE C 491 TRP 0.017 0.001 TRP B 612 HIS 0.007 0.001 HIS B1621 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (17332) covalent geometry : angle 0.53542 / 0.28 (23627) hydrogen bonds : bond 0.03336 / 2.23 ( 606) hydrogen bonds : angle 3.79976 / 2.82 ( 1780) metal coordination : bond 0.00541 / 0.32 ( 16) metal coordination : angle 3.52664 / 2.17 ( 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 462 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 391 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 ASP cc_start: 0.7507 (t0) cc_final: 0.6806 (m-30) REVERT: C 76 TYR cc_start: 0.8323 (t80) cc_final: 0.8045 (t80) REVERT: C 102 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7593 (tm-30) REVERT: C 161 ASP cc_start: 0.7187 (m-30) cc_final: 0.6571 (t0) REVERT: C 164 GLU cc_start: 0.6736 (tm-30) cc_final: 0.6490 (tm-30) REVERT: C 187 LEU cc_start: 0.7764 (tp) cc_final: 0.7264 (tp) REVERT: C 216 MET cc_start: 0.6631 (OUTLIER) cc_final: 0.6287 (ptt) REVERT: C 218 LYS cc_start: 0.8031 (tptt) cc_final: 0.7690 (mtmm) REVERT: C 249 THR cc_start: 0.8494 (p) cc_final: 0.8274 (t) REVERT: C 266 GLU cc_start: 0.7792 (tp30) cc_final: 0.7161 (tp30) REVERT: C 267 LYS cc_start: 0.8286 (mttp) cc_final: 0.8021 (mmmm) REVERT: C 273 ARG cc_start: 0.8306 (mtt90) cc_final: 0.7951 (mtp85) REVERT: C 502 GLU cc_start: 0.7681 (pm20) cc_final: 0.7396 (pm20) REVERT: C 508 LYS cc_start: 0.8179 (tppt) cc_final: 0.7342 (mmtm) REVERT: C 628 GLU cc_start: 0.6829 (tt0) cc_final: 0.6581 (tt0) REVERT: B 34 SER cc_start: 0.8442 (m) cc_final: 0.8212 (p) REVERT: B 72 GLU cc_start: 0.7891 (tt0) cc_final: 0.7587 (mt-10) REVERT: B 85 VAL cc_start: 0.8749 (OUTLIER) cc_final: 0.8538 (m) REVERT: B 95 ASP cc_start: 0.7589 (t0) cc_final: 0.7359 (t0) REVERT: B 142 VAL cc_start: 0.7835 (t) cc_final: 0.7486 (m) REVERT: B 171 ASP cc_start: 0.7687 (p0) cc_final: 0.7386 (p0) REVERT: B 178 LEU cc_start: 0.8860 (mt) cc_final: 0.8568 (mp) REVERT: B 238 GLU cc_start: 0.7969 (pm20) cc_final: 0.7706 (pm20) REVERT: B 313 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7597 (mtmt) REVERT: B 349 SER cc_start: 0.8372 (p) cc_final: 0.8157 (m) REVERT: B 384 LEU cc_start: 0.8279 (mm) cc_final: 0.7901 (mt) REVERT: B 448 ASP cc_start: 0.6698 (t70) cc_final: 0.6333 (t70) REVERT: B 454 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7704 (mm-30) REVERT: B 597 THR cc_start: 0.7982 (p) cc_final: 0.7138 (t) REVERT: B 617 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7610 (mmtt) REVERT: B 738 ARG cc_start: 0.8420 (tpt170) cc_final: 0.8137 (mmt180) REVERT: B 752 CYS cc_start: 0.7048 (p) cc_final: 0.6501 (p) REVERT: B 836 LEU cc_start: 0.8094 (mt) cc_final: 0.7792 (mp) REVERT: B 933 VAL cc_start: 0.8498 (t) cc_final: 0.8234 (m) REVERT: B 973 ASN cc_start: 0.8222 (p0) cc_final: 0.7933 (p0) REVERT: B 1496 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7187 (tm-30) REVERT: B 1557 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.7808 (t80) REVERT: B 1593 LYS cc_start: 0.8417 (mtpp) cc_final: 0.8075 (mtpp) REVERT: B 1691 PHE cc_start: 0.7973 (t80) cc_final: 0.7663 (t80) outliers start: 71 outliers final: 47 residues processed: 423 average time/residue: 0.1483 time to fit residues: 90.9782 Evaluate side-chains 435 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 383 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 42 LYS 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 216 MET 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 516 CYS Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain B residue 6 MET 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 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 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 714 ILE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 847 ASP 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 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 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: 0.5980 chunk 187 optimal weight: 6.9990 chunk 141 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 23 optimal weight: 0.0370 chunk 24 optimal weight: 0.6980 chunk 120 optimal weight: 0.0470 chunk 3 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 514 HIS C 576 ASN C 685 ASN B1649 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.125187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.109232 restraints weight = 24150.717| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.08 r_work: 0.3228 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17348 Z= 0.109 Angle : 0.536 7.863 23648 Z= 0.276 Chirality : 0.040 0.212 2566 Planarity : 0.004 0.062 2844 Dihedral : 11.730 179.705 2745 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.87 % Allowed : 24.63 % Favored : 71.50 % 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: -0.00 (0.19), residues: 1924 helix: 1.84 (0.20), residues: 634 sheet: 0.40 (0.33), residues: 249 loop : -1.35 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 212 TYR 0.011 0.001 TYR C 450 PHE 0.019 0.001 PHE C 491 TRP 0.015 0.001 TRP B 612 HIS 0.008 0.001 HIS C 514 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (17332) covalent geometry : angle 0.52750 / 0.28 (23627) hydrogen bonds : bond 0.03218 / 2.15 ( 606) hydrogen bonds : angle 3.72930 / 2.77 ( 1780) metal coordination : bond 0.00476 / 0.27 ( 16) metal coordination : angle 3.19689 / 1.99 ( 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 456 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 390 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 29 ASP cc_start: 0.7503 (t0) cc_final: 0.6806 (m-30) REVERT: C 102 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7607 (tm-30) REVERT: C 161 ASP cc_start: 0.7124 (m-30) cc_final: 0.6519 (t0) REVERT: C 164 GLU cc_start: 0.6706 (tm-30) cc_final: 0.6449 (tm-30) REVERT: C 187 LEU cc_start: 0.7752 (tp) cc_final: 0.7308 (tp) REVERT: C 210 HIS cc_start: 0.6681 (t70) cc_final: 0.6415 (m-70) REVERT: C 216 MET cc_start: 0.6624 (OUTLIER) cc_final: 0.6283 (ptt) REVERT: C 218 LYS cc_start: 0.8027 (tptt) cc_final: 0.7698 (mtmm) REVERT: C 249 THR cc_start: 0.8480 (p) cc_final: 0.8255 (t) REVERT: C 266 GLU cc_start: 0.7783 (tp30) cc_final: 0.7172 (tp30) REVERT: C 267 LYS cc_start: 0.8292 (mttp) cc_final: 0.8011 (mmmm) REVERT: C 273 ARG cc_start: 0.8296 (mtt90) cc_final: 0.7937 (mtp85) REVERT: C 326 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8378 (mt) REVERT: C 502 GLU cc_start: 0.7706 (pm20) cc_final: 0.7430 (pm20) REVERT: C 508 LYS cc_start: 0.8225 (tppt) cc_final: 0.7339 (mmtm) REVERT: C 663 LYS cc_start: 0.8864 (mmmm) cc_final: 0.8638 (mttm) REVERT: C 688 GLN cc_start: 0.8050 (mt0) cc_final: 0.7661 (mt0) REVERT: B 34 SER cc_start: 0.8445 (m) cc_final: 0.8215 (p) REVERT: B 72 GLU cc_start: 0.7906 (tt0) cc_final: 0.7590 (mt-10) REVERT: B 85 VAL cc_start: 0.8770 (OUTLIER) cc_final: 0.8556 (m) REVERT: B 95 ASP cc_start: 0.7590 (t0) cc_final: 0.7362 (t0) REVERT: B 171 ASP cc_start: 0.7687 (p0) cc_final: 0.7398 (p0) REVERT: B 178 LEU cc_start: 0.8833 (mt) cc_final: 0.8570 (mp) REVERT: B 218 LYS cc_start: 0.8533 (tppt) cc_final: 0.8307 (mmtm) REVERT: B 313 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7593 (mtmt) REVERT: B 448 ASP cc_start: 0.6753 (t70) cc_final: 0.6319 (t0) REVERT: B 454 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7683 (mm-30) REVERT: B 597 THR cc_start: 0.7941 (p) cc_final: 0.7088 (t) REVERT: B 617 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7603 (mmtt) REVERT: B 717 GLU cc_start: 0.7322 (pm20) cc_final: 0.7067 (pm20) REVERT: B 738 ARG cc_start: 0.8386 (tpt170) cc_final: 0.8098 (mmt180) REVERT: B 752 CYS cc_start: 0.7070 (p) cc_final: 0.6523 (p) REVERT: B 836 LEU cc_start: 0.8109 (mt) cc_final: 0.7790 (mp) REVERT: B 933 VAL cc_start: 0.8494 (t) cc_final: 0.8219 (m) REVERT: B 973 ASN cc_start: 0.8214 (p0) cc_final: 0.7905 (p0) REVERT: B 1496 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7168 (tm-30) REVERT: B 1557 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.7757 (t80) REVERT: B 1570 PHE cc_start: 0.8405 (p90) cc_final: 0.7631 (p90) REVERT: B 1593 LYS cc_start: 0.8411 (mtpp) cc_final: 0.8068 (mtpp) REVERT: B 1691 PHE cc_start: 0.7918 (t80) cc_final: 0.7268 (t80) outliers start: 66 outliers final: 47 residues processed: 417 average time/residue: 0.1543 time to fit residues: 93.3890 Evaluate side-chains 438 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 385 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 GLU 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 216 MET Chi-restraints excluded: chain C residue 224 LYS 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 516 CYS Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain B residue 6 MET 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 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 457 SER Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 617 LYS 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 847 ASP 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 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: 0.0970 chunk 147 optimal weight: 0.7980 chunk 153 optimal weight: 0.3980 chunk 99 optimal weight: 0.5980 chunk 112 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN ** C 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 685 ASN B1649 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.125021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.109039 restraints weight = 24350.112| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.09 r_work: 0.3224 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2559 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= 0.117 Angle : 0.540 7.839 23648 Z= 0.279 Chirality : 0.040 0.212 2566 Planarity : 0.004 0.064 2844 Dihedral : 11.724 179.494 2745 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.99 % Allowed : 24.81 % Favored : 71.20 % 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: 1.85 (0.20), residues: 635 sheet: 0.43 (0.33), residues: 249 loop : -1.34 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 212 TYR 0.012 0.001 TYR B 578 PHE 0.018 0.001 PHE C 491 TRP 0.015 0.001 TRP B 612 HIS 0.007 0.001 HIS C 514 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (17332) covalent geometry : angle 0.53283 / 0.28 (23627) hydrogen bonds : bond 0.03249 / 2.17 ( 606) hydrogen bonds : angle 3.68709 / 2.74 ( 1780) metal coordination : bond 0.00543 / 0.34 ( 16) metal coordination : angle 3.07851 / 1.92 ( 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 461 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 393 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 26 ARG cc_start: 0.7936 (ttp80) cc_final: 0.7451 (ttp80) REVERT: C 29 ASP cc_start: 0.7490 (t0) cc_final: 0.6799 (m-30) REVERT: C 102 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7606 (tm-30) REVERT: C 161 ASP cc_start: 0.7130 (m-30) cc_final: 0.6521 (t0) REVERT: C 164 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6401 (tm-30) REVERT: C 187 LEU cc_start: 0.7720 (tp) cc_final: 0.7349 (tp) REVERT: C 210 HIS cc_start: 0.6719 (t70) cc_final: 0.6447 (m-70) REVERT: C 216 MET cc_start: 0.6626 (OUTLIER) cc_final: 0.6294 (ptt) REVERT: C 218 LYS cc_start: 0.8025 (tptt) cc_final: 0.7687 (mtmm) REVERT: C 249 THR cc_start: 0.8468 (p) cc_final: 0.8228 (t) REVERT: C 266 GLU cc_start: 0.7768 (tp30) cc_final: 0.7133 (tp30) REVERT: C 267 LYS cc_start: 0.8302 (mttp) cc_final: 0.8003 (mmmm) REVERT: C 282 ARG cc_start: 0.7499 (ttm170) cc_final: 0.7213 (ttm170) REVERT: C 326 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8376 (mt) REVERT: C 502 GLU cc_start: 0.7716 (pm20) cc_final: 0.7455 (pm20) REVERT: C 508 LYS cc_start: 0.8262 (tppt) cc_final: 0.7380 (mmtm) REVERT: C 585 HIS cc_start: 0.7907 (OUTLIER) cc_final: 0.7454 (m90) REVERT: C 688 GLN cc_start: 0.8042 (mt0) cc_final: 0.7654 (mt0) REVERT: B 72 GLU cc_start: 0.7905 (tt0) cc_final: 0.7588 (mt-10) REVERT: B 85 VAL cc_start: 0.8764 (OUTLIER) cc_final: 0.8549 (m) REVERT: B 95 ASP cc_start: 0.7594 (t0) cc_final: 0.7355 (t0) REVERT: B 171 ASP cc_start: 0.7685 (p0) cc_final: 0.7365 (p0) REVERT: B 178 LEU cc_start: 0.8833 (mt) cc_final: 0.8573 (mp) REVERT: B 182 ASP cc_start: 0.7705 (t0) cc_final: 0.7505 (t0) REVERT: B 218 LYS cc_start: 0.8531 (tppt) cc_final: 0.8304 (mmtm) REVERT: B 313 LYS cc_start: 0.7936 (ptpp) cc_final: 0.7601 (mtmt) REVERT: B 448 ASP cc_start: 0.6818 (t70) cc_final: 0.6469 (t0) REVERT: B 454 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7686 (mm-30) REVERT: B 580 GLU cc_start: 0.7916 (tt0) cc_final: 0.7654 (tt0) REVERT: B 617 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7619 (mmtt) REVERT: B 633 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7354 (tp30) REVERT: B 717 GLU cc_start: 0.7327 (pm20) cc_final: 0.7020 (pm20) REVERT: B 737 ARG cc_start: 0.8785 (mtm180) cc_final: 0.8454 (mtm180) REVERT: B 738 ARG cc_start: 0.8382 (tpt170) cc_final: 0.8105 (mmt180) REVERT: B 752 CYS cc_start: 0.7111 (p) cc_final: 0.6573 (p) REVERT: B 836 LEU cc_start: 0.8102 (mt) cc_final: 0.7875 (mp) REVERT: B 933 VAL cc_start: 0.8480 (t) cc_final: 0.8205 (m) REVERT: B 973 ASN cc_start: 0.8191 (p0) cc_final: 0.7916 (p0) REVERT: B 997 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.8133 (ttm) REVERT: B 1496 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7164 (tm-30) REVERT: B 1557 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.7758 (t80) REVERT: B 1593 LYS cc_start: 0.8403 (mtpp) cc_final: 0.8054 (mtpp) outliers start: 68 outliers final: 47 residues processed: 421 average time/residue: 0.1537 time to fit residues: 93.1640 Evaluate side-chains 443 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 387 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 GLU 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 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 516 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 6 MET 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 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 604 LEU 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 703 LYS Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 847 ASP 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 997 MET 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 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 1666 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 46 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 chunk 102 optimal weight: 0.0980 chunk 7 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 80 optimal weight: 0.0070 chunk 73 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3585 r_free = 0.3585 target = 0.125607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.109636 restraints weight = 24205.251| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.08 r_work: 0.3237 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2607 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= 0.107 Angle : 0.530 7.462 23648 Z= 0.275 Chirality : 0.040 0.213 2566 Planarity : 0.004 0.066 2844 Dihedral : 11.708 179.245 2745 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.70 % Allowed : 25.22 % Favored : 71.09 % 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: 0.07 (0.19), residues: 1924 helix: 1.91 (0.21), residues: 636 sheet: 0.45 (0.34), residues: 243 loop : -1.31 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 212 TYR 0.012 0.001 TYR B1645 PHE 0.018 0.001 PHE C 491 TRP 0.015 0.001 TRP B 612 HIS 0.006 0.001 HIS B1621 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (17332) covalent geometry : angle 0.52335 / 0.27 (23627) hydrogen bonds : bond 0.03091 / 2.06 ( 606) hydrogen bonds : angle 3.65801 / 2.72 ( 1780) metal coordination : bond 0.00390 / 0.22 ( 16) metal coordination : angle 2.92828 / 1.87 ( 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 455 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 392 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 26 ARG cc_start: 0.7939 (ttp80) cc_final: 0.7486 (ttp80) REVERT: C 29 ASP cc_start: 0.7504 (t0) cc_final: 0.6828 (m-30) REVERT: C 102 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7612 (tm-30) REVERT: C 161 ASP cc_start: 0.7122 (m-30) cc_final: 0.6522 (t0) REVERT: C 164 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.6436 (tm-30) REVERT: C 187 LEU cc_start: 0.7681 (tp) cc_final: 0.7334 (tp) REVERT: C 210 HIS cc_start: 0.6675 (t70) cc_final: 0.6414 (m-70) REVERT: C 216 MET cc_start: 0.6659 (OUTLIER) cc_final: 0.6340 (ptt) REVERT: C 218 LYS cc_start: 0.8029 (tptt) cc_final: 0.7678 (mtmm) REVERT: C 249 THR cc_start: 0.8472 (p) cc_final: 0.8240 (t) REVERT: C 266 GLU cc_start: 0.7775 (tp30) cc_final: 0.7127 (tp30) REVERT: C 267 LYS cc_start: 0.8270 (mttp) cc_final: 0.8007 (mmmm) REVERT: C 273 ARG cc_start: 0.8278 (mtt90) cc_final: 0.7921 (mtp85) REVERT: C 282 ARG cc_start: 0.7495 (ttm170) cc_final: 0.7207 (ttm170) REVERT: C 326 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8368 (mt) REVERT: C 502 GLU cc_start: 0.7716 (pm20) cc_final: 0.7456 (pm20) REVERT: C 508 LYS cc_start: 0.8272 (tppt) cc_final: 0.7382 (mmtm) REVERT: C 585 HIS cc_start: 0.7879 (OUTLIER) cc_final: 0.7429 (m90) REVERT: B 72 GLU cc_start: 0.7897 (tt0) cc_final: 0.7577 (mt-10) REVERT: B 85 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8525 (m) REVERT: B 95 ASP cc_start: 0.7572 (t0) cc_final: 0.7337 (t0) REVERT: B 171 ASP cc_start: 0.7668 (p0) cc_final: 0.7397 (p0) REVERT: B 178 LEU cc_start: 0.8833 (mt) cc_final: 0.8568 (mp) REVERT: B 182 ASP cc_start: 0.7708 (t0) cc_final: 0.7500 (t0) REVERT: B 185 THR cc_start: 0.8628 (p) cc_final: 0.8394 (t) REVERT: B 218 LYS cc_start: 0.8518 (tppt) cc_final: 0.8299 (mmtm) REVERT: B 313 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7603 (mtmt) REVERT: B 448 ASP cc_start: 0.6849 (t70) cc_final: 0.6479 (t0) REVERT: B 454 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7679 (mm-30) REVERT: B 580 GLU cc_start: 0.7932 (tt0) cc_final: 0.7694 (tt0) REVERT: B 617 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7595 (mmtt) REVERT: B 633 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7358 (tp30) REVERT: B 737 ARG cc_start: 0.8773 (mtm180) cc_final: 0.8451 (mtm180) REVERT: B 738 ARG cc_start: 0.8348 (tpt170) cc_final: 0.8072 (mmt180) REVERT: B 752 CYS cc_start: 0.7067 (p) cc_final: 0.6487 (p) REVERT: B 836 LEU cc_start: 0.8090 (mt) cc_final: 0.7861 (mp) REVERT: B 933 VAL cc_start: 0.8484 (t) cc_final: 0.8211 (m) REVERT: B 973 ASN cc_start: 0.8182 (p0) cc_final: 0.7906 (p0) REVERT: B 997 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.8097 (ttm) REVERT: B 1433 PHE cc_start: 0.8074 (m-80) cc_final: 0.7410 (m-80) REVERT: B 1496 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7149 (tm-30) REVERT: B 1557 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.7815 (t80) REVERT: B 1593 LYS cc_start: 0.8396 (mtpp) cc_final: 0.8058 (mtpp) REVERT: B 1689 ASN cc_start: 0.7300 (t0) cc_final: 0.7046 (t0) REVERT: B 1691 PHE cc_start: 0.8064 (t80) cc_final: 0.7323 (t80) outliers start: 63 outliers final: 45 residues processed: 416 average time/residue: 0.1389 time to fit residues: 83.6459 Evaluate side-chains 443 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 388 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 GLU 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 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 516 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 36 MET Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 189 LYS Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 313 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 617 LYS Chi-restraints excluded: chain B residue 627 MET Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 703 LYS Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 847 ASP 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 997 MET 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 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 1666 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 74 optimal weight: 0.6980 chunk 168 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 189 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3566 r_free = 0.3566 target = 0.124264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.108313 restraints weight = 24146.453| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.07 r_work: 0.3206 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2697 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= 0.145 Angle : 0.555 8.182 23648 Z= 0.287 Chirality : 0.041 0.225 2566 Planarity : 0.005 0.067 2844 Dihedral : 11.756 179.569 2745 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.52 % Allowed : 25.40 % Favored : 71.09 % 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: 1.89 (0.20), residues: 636 sheet: 0.43 (0.34), residues: 244 loop : -1.31 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 212 TYR 0.013 0.001 TYR B 578 PHE 0.017 0.001 PHE C 491 TRP 0.015 0.001 TRP B 612 HIS 0.006 0.001 HIS B1621 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (17332) covalent geometry : angle 0.54755 / 0.29 (23627) hydrogen bonds : bond 0.03440 / 2.29 ( 606) hydrogen bonds : angle 3.69644 / 2.75 ( 1780) metal coordination : bond 0.00630 / 0.41 ( 16) metal coordination : angle 3.09164 / 1.93 ( 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 447 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 387 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 29 ASP cc_start: 0.7500 (t0) cc_final: 0.6845 (m-30) REVERT: C 102 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7698 (tm-30) REVERT: C 161 ASP cc_start: 0.7151 (m-30) cc_final: 0.6540 (t0) REVERT: C 164 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6529 (tm-30) REVERT: C 187 LEU cc_start: 0.7676 (tp) cc_final: 0.7324 (tp) REVERT: C 210 HIS cc_start: 0.6776 (t70) cc_final: 0.6487 (m-70) REVERT: C 216 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.6325 (ptt) REVERT: C 218 LYS cc_start: 0.8064 (tptt) cc_final: 0.7708 (mtmm) REVERT: C 266 GLU cc_start: 0.7816 (tp30) cc_final: 0.7161 (tp30) REVERT: C 267 LYS cc_start: 0.8335 (mttp) cc_final: 0.8024 (mmmm) REVERT: C 273 ARG cc_start: 0.8309 (mtt90) cc_final: 0.7958 (mtp85) REVERT: C 282 ARG cc_start: 0.7523 (ttm170) cc_final: 0.7247 (ttm170) REVERT: C 326 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8397 (mt) REVERT: C 502 GLU cc_start: 0.7721 (pm20) cc_final: 0.7490 (pm20) REVERT: C 508 LYS cc_start: 0.8335 (tppt) cc_final: 0.7436 (mmtm) REVERT: C 585 HIS cc_start: 0.7918 (OUTLIER) cc_final: 0.7462 (m90) REVERT: B 72 GLU cc_start: 0.7875 (tt0) cc_final: 0.7566 (mt-10) REVERT: B 85 VAL cc_start: 0.8773 (OUTLIER) cc_final: 0.8559 (m) REVERT: B 95 ASP cc_start: 0.7571 (t0) cc_final: 0.7327 (t0) REVERT: B 171 ASP cc_start: 0.7672 (p0) cc_final: 0.7372 (p0) REVERT: B 178 LEU cc_start: 0.8845 (mt) cc_final: 0.8583 (mp) REVERT: B 218 LYS cc_start: 0.8531 (tppt) cc_final: 0.8303 (mmtm) REVERT: B 313 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7606 (mtmt) REVERT: B 454 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7721 (mm-30) REVERT: B 580 GLU cc_start: 0.7973 (tt0) cc_final: 0.7735 (tt0) REVERT: B 617 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7654 (mmtt) REVERT: B 633 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7372 (tp30) REVERT: B 737 ARG cc_start: 0.8807 (mtm180) cc_final: 0.8453 (mtm180) REVERT: B 752 CYS cc_start: 0.7054 (p) cc_final: 0.6492 (p) REVERT: B 836 LEU cc_start: 0.8098 (mt) cc_final: 0.7849 (mp) REVERT: B 933 VAL cc_start: 0.8491 (t) cc_final: 0.8219 (m) REVERT: B 973 ASN cc_start: 0.8181 (p0) cc_final: 0.7890 (p0) REVERT: B 997 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8192 (ttm) REVERT: B 1496 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7158 (tm-30) REVERT: B 1523 ARG cc_start: 0.8190 (mtp-110) cc_final: 0.7990 (mtp-110) REVERT: B 1557 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.7791 (t80) REVERT: B 1593 LYS cc_start: 0.8432 (mtpp) cc_final: 0.8092 (mtpp) REVERT: B 1689 ASN cc_start: 0.7282 (t0) cc_final: 0.6975 (t0) outliers start: 60 outliers final: 43 residues processed: 412 average time/residue: 0.1358 time to fit residues: 80.5366 Evaluate side-chains 436 residues out of total 1707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 383 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 GLU 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 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 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 36 MET 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 240 ILE Chi-restraints excluded: chain B residue 313 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 604 LEU 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 703 LYS Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 754 MET Chi-restraints excluded: chain B residue 847 ASP 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 997 MET 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 1475 ILE Chi-restraints excluded: chain B residue 1557 PHE Chi-restraints excluded: chain B residue 1628 LEU 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: 1.9990 chunk 156 optimal weight: 0.9980 chunk 172 optimal weight: 0.6980 chunk 188 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 142 optimal weight: 20.0000 chunk 125 optimal weight: 2.9990 chunk 2 optimal weight: 0.2980 chunk 109 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3563 r_free = 0.3563 target = 0.123981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.108040 restraints weight = 24194.334| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.08 r_work: 0.3200 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2747 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= 0.142 Angle : 0.558 8.268 23648 Z= 0.289 Chirality : 0.041 0.224 2566 Planarity : 0.005 0.067 2844 Dihedral : 11.796 179.799 2745 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.46 % Allowed : 25.57 % 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: 0.06 (0.19), residues: 1924 helix: 1.90 (0.20), residues: 636 sheet: 0.43 (0.34), residues: 244 loop : -1.31 (0.19), residues: 1044 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 0.028 0.001 PHE B 136 TRP 0.015 0.001 TRP B 612 HIS 0.006 0.001 HIS B1621 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (17332) covalent geometry : angle 0.55081 / 0.29 (23627) hydrogen bonds : bond 0.03449 / 2.30 ( 606) hydrogen bonds : angle 3.70174 / 2.76 ( 1780) metal coordination : bond 0.00611 / 0.41 ( 16) metal coordination : angle 3.09884 / 1.94 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4324.48 seconds wall clock time: 74 minutes 51.22 seconds (4491.22 seconds total)