Starting phenix.real_space_refine on Wed Mar 4 09:40:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y82_33678/03_2026/7y82_33678.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y82_33678/03_2026/7y82_33678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y82_33678/03_2026/7y82_33678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y82_33678/03_2026/7y82_33678.map" model { file = "/net/cci-nas-00/data/ceres_data/7y82_33678/03_2026/7y82_33678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y82_33678/03_2026/7y82_33678.cif" } resolution = 2.83 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= 0.057 sd= 0.202 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 66 5.49 5 Mg 1 5.21 5 S 33 5.16 5 C 7549 2.51 5 N 2147 2.21 5 O 2478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12278 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10869 Classifications: {'peptide': 1341} Link IDs: {'PTRANS': 60, 'TRANS': 1280} Chain breaks: 11 Chain: "B" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 859 Classifications: {'RNA': 41} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 12, 'rna3p_pur': 6, 'rna3p_pyr': 13} Link IDs: {'rna2p': 22, 'rna3p': 18} Chain: "C" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 16, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 21} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 1, ' ZN': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5559 SG CYS A 750 17.233 87.403 77.675 1.00 50.13 S ATOM 5572 SG CYS A 752 20.486 88.307 79.395 1.00 49.51 S ATOM 5594 SG CYS A 755 20.281 85.074 77.449 1.00 47.65 S ATOM 3484 SG CYS A 491 24.772 83.200 49.469 1.00 51.27 S ATOM 3566 SG CYS A 503 27.798 84.005 47.660 1.00 55.13 S ATOM 3588 SG CYS A 506 27.428 81.206 47.799 1.00 45.08 S ATOM 7485 SG CYS A1018 20.713 71.392 110.954 1.00 16.20 S ATOM 8652 SG CYS A1406 18.439 72.617 108.245 1.00 14.54 S ATOM 8703 SG CYS A1414 20.462 75.050 110.441 1.00 27.52 S ATOM 8720 SG CYS A1417 22.268 73.059 107.858 1.00 31.73 S ATOM 668 SG CYS A 88 30.731 71.787 18.806 1.00 53.90 S ATOM 939 SG CYS A 121 31.101 69.654 15.642 1.00 66.45 S ATOM 985 SG CYS A 127 33.362 69.126 18.711 1.00 55.44 S ATOM 1009 SG CYS A 130 29.754 68.099 18.835 1.00 56.81 S Time building chain proxies: 2.83, per 1000 atoms: 0.23 Number of scatterers: 12278 At special positions: 0 Unit cell: (72.6, 110, 157.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 33 16.00 P 66 15.00 Mg 1 11.99 O 2478 8.00 N 2147 7.00 C 7549 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: 1.11 Conformation dependent library (CDL) restraints added in 578.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" ND1 HIS A 747 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 752 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 755 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 750 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 506 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 491 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 503 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1018 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1414 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1417 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1406 " pdb=" ZN A1805 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 127 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 88 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 121 " Number of angles added : 15 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2460 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 21 sheets defined 35.4% alpha, 23.9% beta 22 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 removed outlier: 4.122A pdb=" N LYS A 30 " --> pdb=" O TRP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 39 through 41 No H-bonds generated for 'chain 'A' and resid 39 through 41' Processing helix chain 'A' and resid 59 through 78 Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 145 through 149 removed outlier: 3.555A pdb=" N ASP A 148 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR A 149 " --> pdb=" O ASN A 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 145 through 149' Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 227 removed outlier: 3.746A pdb=" N ALA A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 287 Processing helix chain 'A' and resid 290 through 304 removed outlier: 3.992A pdb=" N ARG A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 354 through 374 Processing helix chain 'A' and resid 471 through 488 Processing helix chain 'A' and resid 503 through 511 removed outlier: 3.605A pdb=" N ARG A 511 " --> pdb=" O ILE A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 580 Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 617 through 625 removed outlier: 3.514A pdb=" N TYR A 621 " --> pdb=" O LYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 630 through 637 Processing helix chain 'A' and resid 654 through 657 Processing helix chain 'A' and resid 658 through 665 Processing helix chain 'A' and resid 686 through 692 removed outlier: 3.545A pdb=" N THR A 692 " --> pdb=" O ILE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 740 Processing helix chain 'A' and resid 741 through 744 Processing helix chain 'A' and resid 752 through 759 Processing helix chain 'A' and resid 831 through 847 Processing helix chain 'A' and resid 908 through 914 removed outlier: 3.652A pdb=" N LYS A 912 " --> pdb=" O HIS A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1015 Processing helix chain 'A' and resid 1177 through 1201 Processing helix chain 'A' and resid 1201 through 1211 Processing helix chain 'A' and resid 1327 through 1340 Processing helix chain 'A' and resid 1346 through 1354 removed outlier: 4.373A pdb=" N ARG A1352 " --> pdb=" O GLU A1348 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1399 Processing helix chain 'A' and resid 1400 through 1404 Processing helix chain 'A' and resid 1414 through 1421 Processing helix chain 'A' and resid 1463 through 1468 removed outlier: 3.799A pdb=" N SER A1467 " --> pdb=" O ARG A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1493 removed outlier: 3.529A pdb=" N ILE A1490 " --> pdb=" O GLY A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1493 through 1501 Processing helix chain 'A' and resid 1528 through 1540 Processing helix chain 'A' and resid 1552 through 1556 Processing helix chain 'A' and resid 1583 through 1603 Processing helix chain 'A' and resid 1615 through 1618 removed outlier: 3.847A pdb=" N VAL A1618 " --> pdb=" O GLN A1615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1615 through 1618' Processing helix chain 'A' and resid 1619 through 1629 Processing helix chain 'A' and resid 1662 through 1668 Processing helix chain 'A' and resid 1673 through 1683 Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 153 removed outlier: 6.671A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA A 53 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG A 19 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N TRP A 44 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A 21 " --> pdb=" O TRP A 44 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N TRP A 46 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TRP A 195 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N GLU A 22 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 12.941A pdb=" N ARG A 193 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP A 190 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.349A pdb=" N THR A 110 " --> pdb=" O VAL A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 333 through 334 Processing sheet with id=AA6, first strand: chain 'A' and resid 512 through 514 removed outlier: 4.976A pdb=" N ARG A 421 " --> pdb=" O ASP A 606 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ASP A 606 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS A 423 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LEU A 604 " --> pdb=" O LYS A 423 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 514 removed outlier: 4.976A pdb=" N ARG A 421 " --> pdb=" O ASP A 606 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ASP A 606 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS A 423 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LEU A 604 " --> pdb=" O LYS A 423 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 431 through 432 removed outlier: 4.282A pdb=" N ASN A 459 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AB1, first strand: chain 'A' and resid 526 through 534 removed outlier: 10.184A pdb=" N GLU A 526 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N ASP A 547 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 11.035A pdb=" N ARG A 528 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N LEU A 545 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 10.044A pdb=" N ARG A 530 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 9.437A pdb=" N GLY A 543 " --> pdb=" O ARG A 530 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ALA A 532 " --> pdb=" O GLU A 541 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 539 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.487A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.487A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 699 through 700 removed outlier: 7.197A pdb=" N ALA A 699 " --> pdb=" O TYR A 808 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA A 791 " --> pdb=" O LEU A 800 " (cutoff:3.500A) removed outlier: 10.028A pdb=" N LYS A 802 " --> pdb=" O HIS A 789 " (cutoff:3.500A) removed outlier: 10.476A pdb=" N HIS A 789 " --> pdb=" O LYS A 802 " (cutoff:3.500A) removed outlier: 10.413A pdb=" N LYS A 804 " --> pdb=" O ILE A 787 " (cutoff:3.500A) removed outlier: 11.633A pdb=" N ILE A 787 " --> pdb=" O LYS A 804 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 707 through 708 Processing sheet with id=AB6, first strand: chain 'A' and resid 920 through 921 Processing sheet with id=AB7, first strand: chain 'A' and resid 924 through 927 Processing sheet with id=AB8, first strand: chain 'A' and resid 991 through 992 removed outlier: 3.513A pdb=" N GLU A 995 " --> pdb=" O ILE A 992 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU A 996 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A1436 " --> pdb=" O LEU A 996 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ALA A1434 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ASP A1521 " --> pdb=" O ALA A1434 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N TYR A1436 " --> pdb=" O SER A1519 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N SER A1519 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN A1438 " --> pdb=" O VAL A1517 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A1517 " --> pdb=" O THR A 960 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR A 960 " --> pdb=" O VAL A1517 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER A1519 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU A 958 " --> pdb=" O SER A1519 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASP A1521 " --> pdb=" O CYS A 956 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N CYS A 956 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ARG A1523 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE A 954 " --> pdb=" O ARG A1523 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLU A1525 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLY A 952 " --> pdb=" O GLU A1525 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1429 through 1431 removed outlier: 6.647A pdb=" N VAL A1517 " --> pdb=" O THR A 960 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR A 960 " --> pdb=" O VAL A1517 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER A1519 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU A 958 " --> pdb=" O SER A1519 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASP A1521 " --> pdb=" O CYS A 956 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N CYS A 956 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ARG A1523 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE A 954 " --> pdb=" O ARG A1523 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLU A1525 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLY A 952 " --> pdb=" O GLU A1525 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 967 through 968 removed outlier: 4.464A pdb=" N LYS A 988 " --> pdb=" O ASP A 968 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS A 985 " --> pdb=" O THR A1508 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N GLU A1510 " --> pdb=" O LYS A 985 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N TYR A 987 " --> pdb=" O GLU A1510 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1029 through 1031 Processing sheet with id=AC3, first strand: chain 'A' and resid 1369 through 1371 removed outlier: 3.604A pdb=" N SER A1380 " --> pdb=" O HIS A1371 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 2.88 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2168 1.33 - 1.45: 3601 1.45 - 1.57: 6741 1.57 - 1.69: 130 1.69 - 1.81: 45 Bond restraints: 12685 Sorted by residual: bond pdb=" C ARG A 719 " pdb=" O ARG A 719 " ideal model delta sigma weight residual 1.236 1.205 0.031 1.24e-02 6.50e+03 6.24e+00 bond pdb=" C PRO A 718 " pdb=" O PRO A 718 " ideal model delta sigma weight residual 1.233 1.204 0.029 1.19e-02 7.06e+03 6.06e+00 bond pdb=" C PRO A 716 " pdb=" O PRO A 716 " ideal model delta sigma weight residual 1.237 1.207 0.030 1.26e-02 6.30e+03 5.75e+00 bond pdb=" N PRO A 716 " pdb=" CA PRO A 716 " ideal model delta sigma weight residual 1.472 1.449 0.023 1.32e-02 5.74e+03 2.93e+00 bond pdb=" N GLU A 717 " pdb=" CA GLU A 717 " ideal model delta sigma weight residual 1.455 1.482 -0.027 1.60e-02 3.91e+03 2.87e+00 ... (remaining 12680 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 17122 1.83 - 3.66: 250 3.66 - 5.48: 33 5.48 - 7.31: 6 7.31 - 9.14: 3 Bond angle restraints: 17414 Sorted by residual: angle pdb=" O4' G B 47 " pdb=" C1' G B 47 " pdb=" N9 G B 47 " ideal model delta sigma weight residual 108.20 115.99 -7.79 1.50e+00 4.44e-01 2.70e+01 angle pdb=" O4' A B 35 " pdb=" C1' A B 35 " pdb=" N9 A B 35 " ideal model delta sigma weight residual 108.20 115.66 -7.46 1.50e+00 4.44e-01 2.47e+01 angle pdb=" N PRO A 648 " pdb=" CD PRO A 648 " pdb=" CG PRO A 648 " ideal model delta sigma weight residual 103.20 96.82 6.38 1.50e+00 4.44e-01 1.81e+01 angle pdb=" CA PRO A 648 " pdb=" N PRO A 648 " pdb=" CD PRO A 648 " ideal model delta sigma weight residual 112.00 106.42 5.58 1.40e+00 5.10e-01 1.59e+01 angle pdb=" C GLU A 717 " pdb=" CA GLU A 717 " pdb=" CB GLU A 717 " ideal model delta sigma weight residual 109.85 113.47 -3.62 1.14e+00 7.69e-01 1.01e+01 ... (remaining 17409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.94: 7115 32.94 - 65.89: 521 65.89 - 98.83: 53 98.83 - 131.77: 3 131.77 - 164.72: 1 Dihedral angle restraints: 7693 sinusoidal: 3854 harmonic: 3839 Sorted by residual: dihedral pdb=" O4' U C 14 " pdb=" C1' U C 14 " pdb=" N1 U C 14 " pdb=" C2 U C 14 " ideal model delta sinusoidal sigma weight residual 232.00 67.28 164.72 1 1.70e+01 3.46e-03 6.53e+01 dihedral pdb=" CA ASN A1689 " pdb=" C ASN A1689 " pdb=" N PRO A1690 " pdb=" CA PRO A1690 " ideal model delta harmonic sigma weight residual 180.00 155.93 24.07 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA PRO A1440 " pdb=" C PRO A1440 " pdb=" N GLU A1441 " pdb=" CA GLU A1441 " ideal model delta harmonic sigma weight residual -180.00 -161.25 -18.75 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 7690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1759 0.079 - 0.158: 136 0.158 - 0.237: 3 0.237 - 0.316: 1 0.316 - 0.395: 2 Chirality restraints: 1901 Sorted by residual: chirality pdb=" C1' G B 47 " pdb=" O4' G B 47 " pdb=" C2' G B 47 " pdb=" N9 G B 47 " both_signs ideal model delta sigma weight residual False 2.44 2.04 0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" C1' A B 35 " pdb=" O4' A B 35 " pdb=" C2' A B 35 " pdb=" N9 A B 35 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CB ILE A1444 " pdb=" CA ILE A1444 " pdb=" CG1 ILE A1444 " pdb=" CG2 ILE A1444 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1898 not shown) Planarity restraints: 2003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 47 " 0.051 2.00e-02 2.50e+03 2.29e-02 1.58e+01 pdb=" N9 G B 47 " -0.059 2.00e-02 2.50e+03 pdb=" C8 G B 47 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G B 47 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G B 47 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G B 47 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G B 47 " 0.013 2.00e-02 2.50e+03 pdb=" N1 G B 47 " 0.005 2.00e-02 2.50e+03 pdb=" C2 G B 47 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G B 47 " -0.006 2.00e-02 2.50e+03 pdb=" N3 G B 47 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G B 47 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 35 " 0.045 2.00e-02 2.50e+03 2.13e-02 1.24e+01 pdb=" N9 A B 35 " -0.052 2.00e-02 2.50e+03 pdb=" C8 A B 35 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A B 35 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A B 35 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A B 35 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A B 35 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A B 35 " 0.006 2.00e-02 2.50e+03 pdb=" C2 A B 35 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A B 35 " -0.009 2.00e-02 2.50e+03 pdb=" C4 A B 35 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 45 " 0.035 2.00e-02 2.50e+03 1.80e-02 7.32e+00 pdb=" N1 C B 45 " -0.038 2.00e-02 2.50e+03 pdb=" C2 C B 45 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C B 45 " -0.006 2.00e-02 2.50e+03 pdb=" N3 C B 45 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C B 45 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C B 45 " 0.012 2.00e-02 2.50e+03 pdb=" C5 C B 45 " -0.002 2.00e-02 2.50e+03 pdb=" C6 C B 45 " -0.006 2.00e-02 2.50e+03 ... (remaining 2000 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 127 2.49 - 3.09: 8549 3.09 - 3.69: 20912 3.69 - 4.30: 31507 4.30 - 4.90: 50559 Nonbonded interactions: 111654 Sorted by model distance: nonbonded pdb=" OD1 ASP A 137 " pdb="MG MG A1804 " model vdw 1.887 2.170 nonbonded pdb=" OP2 U B 26 " pdb="MG MG A1804 " model vdw 1.893 2.170 nonbonded pdb=" O GLY A 134 " pdb="MG MG A1804 " model vdw 2.000 2.170 nonbonded pdb=" O2 C B 38 " pdb=" N2 G C 16 " model vdw 2.093 2.496 nonbonded pdb=" O LYS A 189 " pdb=" O2' U C 19 " model vdw 2.099 3.040 ... (remaining 111649 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: 1.130 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.610 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 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 0.059 12700 Z= 0.143 Angle : 0.569 9.140 17429 Z= 0.303 Chirality : 0.042 0.395 1901 Planarity : 0.004 0.104 2003 Dihedral : 20.346 164.716 5233 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.59 % Allowed : 26.70 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.23), residues: 1317 helix: 1.63 (0.27), residues: 400 sheet: -0.53 (0.36), residues: 182 loop : 0.27 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 846 TYR 0.017 0.001 TYR A 903 PHE 0.014 0.001 PHE A 546 TRP 0.023 0.001 TRP A 82 HIS 0.012 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00307 (12685) covalent geometry : angle 0.56564 (17414) hydrogen bonds : bond 0.15551 ( 453) hydrogen bonds : angle 6.97578 ( 1310) metal coordination : bond 0.00534 ( 15) metal coordination : angle 2.21271 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 137 time to evaluate : 0.300 Fit side-chains REVERT: A 624 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6712 (tp30) REVERT: A 1619 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7121 (mp) outliers start: 54 outliers final: 46 residues processed: 188 average time/residue: 0.4730 time to fit residues: 97.9452 Evaluate side-chains 179 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 131 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 719 ARG Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 951 SER Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1184 LEU Chi-restraints excluded: chain A residue 1340 SER Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1355 THR Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1453 SER Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1649 ASN Chi-restraints excluded: chain A residue 1662 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.0570 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 GLN ** A1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 ASN A1502 GLN A1635 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.149540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.108561 restraints weight = 15150.109| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.88 r_work: 0.3209 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12700 Z= 0.262 Angle : 0.623 8.545 17429 Z= 0.323 Chirality : 0.046 0.444 1901 Planarity : 0.005 0.045 2003 Dihedral : 18.720 155.371 2563 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 5.36 % Allowed : 23.55 % 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: 0.59 (0.23), residues: 1317 helix: 1.60 (0.26), residues: 406 sheet: -0.90 (0.34), residues: 211 loop : 0.21 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 846 TYR 0.019 0.002 TYR A 903 PHE 0.016 0.002 PHE A 805 TRP 0.022 0.002 TRP A 82 HIS 0.007 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00600 (12685) covalent geometry : angle 0.61978 (17414) hydrogen bonds : bond 0.05170 ( 453) hydrogen bonds : angle 5.32599 ( 1310) metal coordination : bond 0.01019 ( 15) metal coordination : angle 2.08181 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 145 time to evaluate : 0.418 Fit side-chains REVERT: A 215 HIS cc_start: 0.8082 (t70) cc_final: 0.7795 (t70) REVERT: A 238 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6607 (mm-30) REVERT: A 390 TYR cc_start: 0.7373 (m-80) cc_final: 0.7043 (m-80) REVERT: A 516 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7363 (t0) REVERT: A 625 ARG cc_start: 0.7155 (mmt180) cc_final: 0.6892 (mpt90) REVERT: A 628 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.4528 (mtp180) REVERT: A 662 LYS cc_start: 0.7401 (mtmm) cc_final: 0.6824 (mtmt) REVERT: A 717 GLU cc_start: 0.7796 (pm20) cc_final: 0.7448 (tp30) REVERT: A 928 ASP cc_start: 0.7772 (p0) cc_final: 0.7365 (t0) outliers start: 63 outliers final: 29 residues processed: 196 average time/residue: 0.5866 time to fit residues: 124.8717 Evaluate side-chains 166 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1367 LEU Chi-restraints excluded: chain A residue 1368 VAL Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1407 THR Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1593 LYS Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1662 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 129 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 11 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 ASN A1502 GLN A1584 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.152454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.112003 restraints weight = 15381.271| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.88 r_work: 0.3271 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12700 Z= 0.158 Angle : 0.551 8.261 17429 Z= 0.289 Chirality : 0.043 0.456 1901 Planarity : 0.004 0.044 2003 Dihedral : 18.449 158.242 2513 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.34 % Allowed : 24.49 % Favored : 71.17 % 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: 0.72 (0.23), residues: 1317 helix: 1.82 (0.26), residues: 400 sheet: -0.86 (0.33), residues: 213 loop : 0.25 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 846 TYR 0.015 0.001 TYR A 903 PHE 0.015 0.001 PHE A 805 TRP 0.016 0.001 TRP A 82 HIS 0.005 0.001 HIS A1010 Details of bonding type rmsd covalent geometry : bond 0.00353 (12685) covalent geometry : angle 0.54865 (17414) hydrogen bonds : bond 0.04524 ( 453) hydrogen bonds : angle 4.95507 ( 1310) metal coordination : bond 0.00706 ( 15) metal coordination : angle 1.86627 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 150 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8164 (mtpt) cc_final: 0.7874 (mtpt) REVERT: A 208 ARG cc_start: 0.7475 (mtm-85) cc_final: 0.7169 (mtm-85) REVERT: A 215 HIS cc_start: 0.8080 (t70) cc_final: 0.7815 (t70) REVERT: A 236 ARG cc_start: 0.7953 (ptp-110) cc_final: 0.7709 (ptp-110) REVERT: A 238 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6609 (mm-30) REVERT: A 390 TYR cc_start: 0.7322 (m-80) cc_final: 0.6954 (m-80) REVERT: A 623 LYS cc_start: 0.7776 (ttpp) cc_final: 0.7473 (ttpt) REVERT: A 662 LYS cc_start: 0.7303 (mtmm) cc_final: 0.6877 (mtmt) REVERT: A 717 GLU cc_start: 0.7901 (pm20) cc_final: 0.7684 (pm20) REVERT: A 833 ASP cc_start: 0.7618 (t0) cc_final: 0.7418 (t0) REVERT: A 1448 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.7011 (m-40) REVERT: A 1495 LEU cc_start: 0.7961 (mm) cc_final: 0.7755 (mp) outliers start: 51 outliers final: 20 residues processed: 190 average time/residue: 0.5618 time to fit residues: 116.3209 Evaluate side-chains 156 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1367 LEU Chi-restraints excluded: chain A residue 1368 VAL Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1448 ASN Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1662 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 0.0370 chunk 71 optimal weight: 0.0980 chunk 14 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 0 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 986 ASN ** A1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 ASN A1485 ASN A1502 GLN A1584 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.154113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.113973 restraints weight = 15271.010| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.88 r_work: 0.3312 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12700 Z= 0.128 Angle : 0.530 8.376 17429 Z= 0.278 Chirality : 0.042 0.462 1901 Planarity : 0.004 0.046 2003 Dihedral : 18.391 162.105 2501 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.25 % Allowed : 24.57 % Favored : 71.17 % 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: 0.91 (0.23), residues: 1317 helix: 1.98 (0.26), residues: 406 sheet: -0.69 (0.33), residues: 219 loop : 0.33 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 846 TYR 0.015 0.001 TYR A 903 PHE 0.013 0.001 PHE A 805 TRP 0.015 0.001 TRP A 82 HIS 0.005 0.001 HIS A 727 Details of bonding type rmsd covalent geometry : bond 0.00285 (12685) covalent geometry : angle 0.52740 (17414) hydrogen bonds : bond 0.04252 ( 453) hydrogen bonds : angle 4.69153 ( 1310) metal coordination : bond 0.00525 ( 15) metal coordination : angle 1.79998 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 146 time to evaluate : 0.500 Fit side-chains REVERT: A 55 LYS cc_start: 0.8138 (mtpt) cc_final: 0.7715 (mtpt) REVERT: A 214 GLU cc_start: 0.7490 (tt0) cc_final: 0.6481 (pp20) REVERT: A 215 HIS cc_start: 0.8046 (t70) cc_final: 0.7526 (t70) REVERT: A 238 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6626 (mm-30) REVERT: A 390 TYR cc_start: 0.7259 (m-80) cc_final: 0.6896 (m-80) REVERT: A 516 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7179 (t0) REVERT: A 623 LYS cc_start: 0.7742 (ttpp) cc_final: 0.7294 (ttpt) REVERT: A 628 ARG cc_start: 0.6220 (OUTLIER) cc_final: 0.4108 (mtp180) REVERT: A 686 ASP cc_start: 0.6968 (t0) cc_final: 0.6377 (t0) REVERT: A 833 ASP cc_start: 0.7656 (t0) cc_final: 0.7338 (t0) REVERT: A 1446 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7903 (mmp80) outliers start: 50 outliers final: 24 residues processed: 187 average time/residue: 0.5674 time to fit residues: 115.7665 Evaluate side-chains 161 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 516 ASP Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1367 LEU Chi-restraints excluded: chain A residue 1368 VAL Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1446 ARG Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1662 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 64 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 75 optimal weight: 0.0170 chunk 98 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 129 optimal weight: 0.5980 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 HIS ** A1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 ASN A1502 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.152998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112623 restraints weight = 15304.130| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.88 r_work: 0.3269 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12700 Z= 0.161 Angle : 0.540 8.174 17429 Z= 0.283 Chirality : 0.043 0.452 1901 Planarity : 0.004 0.046 2003 Dihedral : 18.337 161.733 2498 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.34 % Allowed : 24.91 % Favored : 70.75 % 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: 0.89 (0.23), residues: 1317 helix: 2.03 (0.26), residues: 401 sheet: -0.71 (0.33), residues: 219 loop : 0.28 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 846 TYR 0.015 0.001 TYR A 903 PHE 0.019 0.001 PHE A 659 TRP 0.016 0.001 TRP A 82 HIS 0.005 0.001 HIS A 727 Details of bonding type rmsd covalent geometry : bond 0.00365 (12685) covalent geometry : angle 0.53795 (17414) hydrogen bonds : bond 0.04285 ( 453) hydrogen bonds : angle 4.67636 ( 1310) metal coordination : bond 0.00605 ( 15) metal coordination : angle 1.70439 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 143 time to evaluate : 0.451 Fit side-chains REVERT: A 25 ASP cc_start: 0.7543 (t0) cc_final: 0.7228 (t0) REVERT: A 55 LYS cc_start: 0.8186 (mtpt) cc_final: 0.7937 (mtpt) REVERT: A 179 ASN cc_start: 0.7994 (t0) cc_final: 0.7758 (t0) REVERT: A 214 GLU cc_start: 0.7419 (tt0) cc_final: 0.6520 (pp20) REVERT: A 215 HIS cc_start: 0.8044 (t70) cc_final: 0.7566 (t70) REVERT: A 236 ARG cc_start: 0.7936 (ptp-110) cc_final: 0.7674 (ptp-110) REVERT: A 238 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6563 (mm-30) REVERT: A 272 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7081 (tm-30) REVERT: A 390 TYR cc_start: 0.7280 (m-80) cc_final: 0.6880 (m-80) REVERT: A 465 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: A 625 ARG cc_start: 0.6820 (mmt-90) cc_final: 0.6590 (mpt180) REVERT: A 628 ARG cc_start: 0.6464 (OUTLIER) cc_final: 0.4293 (mtp180) REVERT: A 662 LYS cc_start: 0.7339 (mtmm) cc_final: 0.6875 (mtmt) REVERT: A 833 ASP cc_start: 0.7641 (t0) cc_final: 0.7378 (t0) REVERT: A 1363 LYS cc_start: 0.8211 (pttt) cc_final: 0.7723 (mttt) REVERT: A 1448 ASN cc_start: 0.7723 (OUTLIER) cc_final: 0.7072 (m-40) outliers start: 51 outliers final: 27 residues processed: 181 average time/residue: 0.5791 time to fit residues: 114.1744 Evaluate side-chains 162 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1367 LEU Chi-restraints excluded: chain A residue 1368 VAL Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1448 ASN Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1662 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 92 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 118 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 HIS ** A1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 ASN A1502 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.153283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.112922 restraints weight = 15248.788| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.88 r_work: 0.3274 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12700 Z= 0.152 Angle : 0.539 8.248 17429 Z= 0.281 Chirality : 0.042 0.458 1901 Planarity : 0.004 0.047 2003 Dihedral : 18.319 161.981 2498 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.93 % Allowed : 24.49 % Favored : 70.58 % 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: 0.89 (0.23), residues: 1317 helix: 2.01 (0.26), residues: 408 sheet: -0.68 (0.34), residues: 219 loop : 0.27 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1446 TYR 0.013 0.001 TYR A 903 PHE 0.017 0.001 PHE A 659 TRP 0.016 0.001 TRP A 82 HIS 0.005 0.001 HIS A 727 Details of bonding type rmsd covalent geometry : bond 0.00343 (12685) covalent geometry : angle 0.53650 (17414) hydrogen bonds : bond 0.04238 ( 453) hydrogen bonds : angle 4.63725 ( 1310) metal coordination : bond 0.00596 ( 15) metal coordination : angle 1.68066 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 146 time to evaluate : 0.558 Fit side-chains REVERT: A 25 ASP cc_start: 0.7557 (t0) cc_final: 0.7229 (t0) REVERT: A 55 LYS cc_start: 0.8187 (mtpt) cc_final: 0.7944 (mtpt) REVERT: A 214 GLU cc_start: 0.7371 (tt0) cc_final: 0.6502 (pp20) REVERT: A 215 HIS cc_start: 0.8023 (t70) cc_final: 0.7539 (t70) REVERT: A 236 ARG cc_start: 0.7938 (ptp-110) cc_final: 0.7654 (ptp-110) REVERT: A 238 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6548 (mm-30) REVERT: A 272 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7023 (tm-30) REVERT: A 390 TYR cc_start: 0.7301 (m-80) cc_final: 0.6893 (m-80) REVERT: A 434 GLN cc_start: 0.5973 (mm-40) cc_final: 0.5773 (mm110) REVERT: A 465 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: A 617 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.6987 (tttm) REVERT: A 625 ARG cc_start: 0.6862 (mmt-90) cc_final: 0.6596 (mpt180) REVERT: A 628 ARG cc_start: 0.6491 (OUTLIER) cc_final: 0.4283 (mtp180) REVERT: A 662 LYS cc_start: 0.7336 (mtmm) cc_final: 0.6843 (mtmt) REVERT: A 833 ASP cc_start: 0.7641 (t0) cc_final: 0.7374 (t0) REVERT: A 1363 LYS cc_start: 0.8191 (pttt) cc_final: 0.7755 (mttt) outliers start: 58 outliers final: 28 residues processed: 191 average time/residue: 0.5465 time to fit residues: 113.9447 Evaluate side-chains 172 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 617 LYS Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1367 LEU Chi-restraints excluded: chain A residue 1368 VAL Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1593 LYS Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1662 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 30 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 0.0970 chunk 15 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 HIS ** A1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 ASN A1502 GLN A1584 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.150816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.110075 restraints weight = 15203.311| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.88 r_work: 0.3237 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12700 Z= 0.210 Angle : 0.578 10.959 17429 Z= 0.299 Chirality : 0.044 0.442 1901 Planarity : 0.004 0.046 2003 Dihedral : 18.261 158.912 2490 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.68 % Allowed : 24.91 % Favored : 70.41 % 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: 0.79 (0.23), residues: 1317 helix: 1.95 (0.26), residues: 401 sheet: -0.76 (0.34), residues: 219 loop : 0.23 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1588 TYR 0.014 0.002 TYR A 903 PHE 0.019 0.002 PHE A 659 TRP 0.018 0.001 TRP A 82 HIS 0.005 0.001 HIS A1010 Details of bonding type rmsd covalent geometry : bond 0.00480 (12685) covalent geometry : angle 0.57652 (17414) hydrogen bonds : bond 0.04461 ( 453) hydrogen bonds : angle 4.75732 ( 1310) metal coordination : bond 0.00804 ( 15) metal coordination : angle 1.59128 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 138 time to evaluate : 0.423 Fit side-chains REVERT: A 25 ASP cc_start: 0.7553 (t0) cc_final: 0.7261 (t0) REVERT: A 215 HIS cc_start: 0.8037 (t70) cc_final: 0.7785 (t70) REVERT: A 238 GLU cc_start: 0.7125 (mm-30) cc_final: 0.6697 (mm-30) REVERT: A 272 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7067 (tm-30) REVERT: A 465 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7723 (mt-10) REVERT: A 617 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7204 (tttm) REVERT: A 618 ILE cc_start: 0.7651 (tp) cc_final: 0.7262 (mt) REVERT: A 625 ARG cc_start: 0.6924 (mmt-90) cc_final: 0.6646 (mpt180) REVERT: A 628 ARG cc_start: 0.6590 (OUTLIER) cc_final: 0.4376 (mtp180) REVERT: A 662 LYS cc_start: 0.7399 (mtmm) cc_final: 0.6877 (mtmt) REVERT: A 749 ASP cc_start: 0.6862 (m-30) cc_final: 0.6631 (m-30) REVERT: A 833 ASP cc_start: 0.7678 (t0) cc_final: 0.7420 (t0) REVERT: A 1363 LYS cc_start: 0.8130 (pttt) cc_final: 0.7711 (mtpt) REVERT: A 1417 CYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7590 (m) REVERT: A 1436 TYR cc_start: 0.8784 (t80) cc_final: 0.8581 (t80) REVERT: A 1448 ASN cc_start: 0.7811 (OUTLIER) cc_final: 0.7252 (m-40) REVERT: A 1543 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8544 (mmtt) outliers start: 55 outliers final: 32 residues processed: 177 average time/residue: 0.5697 time to fit residues: 110.0386 Evaluate side-chains 173 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 414 LYS Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 617 LYS Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1367 LEU Chi-restraints excluded: chain A residue 1368 VAL Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1417 CYS Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1448 ASN Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1543 LYS Chi-restraints excluded: chain A residue 1593 LYS Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1662 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 82 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 99 optimal weight: 0.0980 chunk 44 optimal weight: 0.0020 chunk 104 optimal weight: 0.6980 chunk 11 optimal weight: 0.0070 chunk 95 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 overall best weight: 0.2806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 179 ASN ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 HIS A 986 ASN ** A1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 ASN A1502 GLN A1584 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.155650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.118240 restraints weight = 15251.433| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.79 r_work: 0.3317 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12700 Z= 0.108 Angle : 0.533 11.023 17429 Z= 0.277 Chirality : 0.042 0.485 1901 Planarity : 0.004 0.046 2003 Dihedral : 18.259 164.444 2490 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.49 % Allowed : 26.45 % Favored : 70.07 % 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: 0.96 (0.23), residues: 1317 helix: 2.08 (0.26), residues: 409 sheet: -0.63 (0.34), residues: 217 loop : 0.29 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 846 TYR 0.020 0.001 TYR A 903 PHE 0.015 0.001 PHE A 659 TRP 0.017 0.001 TRP A 82 HIS 0.005 0.001 HIS A 727 Details of bonding type rmsd covalent geometry : bond 0.00235 (12685) covalent geometry : angle 0.53044 (17414) hydrogen bonds : bond 0.04060 ( 453) hydrogen bonds : angle 4.50863 ( 1310) metal coordination : bond 0.00486 ( 15) metal coordination : angle 1.99575 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 148 time to evaluate : 0.403 Fit side-chains REVERT: A 25 ASP cc_start: 0.7421 (t0) cc_final: 0.7103 (t0) REVERT: A 26 TRP cc_start: 0.7340 (t60) cc_final: 0.7019 (t60) REVERT: A 55 LYS cc_start: 0.7965 (mtpt) cc_final: 0.7676 (mtpt) REVERT: A 174 SER cc_start: 0.8261 (t) cc_final: 0.7938 (t) REVERT: A 183 PHE cc_start: 0.7573 (t80) cc_final: 0.7351 (t80) REVERT: A 215 HIS cc_start: 0.7913 (t70) cc_final: 0.7628 (t70) REVERT: A 238 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6697 (mm-30) REVERT: A 272 GLU cc_start: 0.7427 (mm-30) cc_final: 0.6911 (tm-30) REVERT: A 390 TYR cc_start: 0.7194 (m-80) cc_final: 0.6181 (m-80) REVERT: A 414 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7666 (mtpp) REVERT: A 465 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7623 (mt-10) REVERT: A 617 LYS cc_start: 0.7219 (OUTLIER) cc_final: 0.6874 (tttt) REVERT: A 625 ARG cc_start: 0.6689 (mmt-90) cc_final: 0.6423 (mpt180) REVERT: A 662 LYS cc_start: 0.7191 (mtmm) cc_final: 0.6797 (mtmt) REVERT: A 749 ASP cc_start: 0.6890 (m-30) cc_final: 0.6634 (m-30) REVERT: A 833 ASP cc_start: 0.7665 (t0) cc_final: 0.7352 (t0) REVERT: A 1417 CYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7565 (m) REVERT: A 1448 ASN cc_start: 0.7583 (OUTLIER) cc_final: 0.7058 (m-40) REVERT: A 1635 ASN cc_start: 0.5668 (OUTLIER) cc_final: 0.5367 (p0) outliers start: 41 outliers final: 22 residues processed: 178 average time/residue: 0.5470 time to fit residues: 106.3232 Evaluate side-chains 166 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 414 LYS Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 617 LYS Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1367 LEU Chi-restraints excluded: chain A residue 1368 VAL Chi-restraints excluded: chain A residue 1381 LEU Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1417 CYS Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1448 ASN Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1593 LYS Chi-restraints excluded: chain A residue 1635 ASN Chi-restraints excluded: chain A residue 1662 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 105 optimal weight: 6.9990 chunk 12 optimal weight: 0.2980 chunk 36 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 HIS ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 ASN A1502 GLN A1584 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.149227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.107991 restraints weight = 15146.931| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.88 r_work: 0.3208 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 12700 Z= 0.293 Angle : 0.633 10.584 17429 Z= 0.326 Chirality : 0.047 0.443 1901 Planarity : 0.004 0.057 2003 Dihedral : 18.259 157.444 2489 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.00 % Allowed : 25.34 % Favored : 70.66 % 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: 0.62 (0.23), residues: 1317 helix: 1.81 (0.26), residues: 401 sheet: -0.95 (0.34), residues: 217 loop : 0.15 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 236 TYR 0.018 0.002 TYR A 903 PHE 0.018 0.002 PHE A 659 TRP 0.023 0.002 TRP A 82 HIS 0.005 0.001 HIS A 789 Details of bonding type rmsd covalent geometry : bond 0.00679 (12685) covalent geometry : angle 0.63215 (17414) hydrogen bonds : bond 0.04737 ( 453) hydrogen bonds : angle 4.88044 ( 1310) metal coordination : bond 0.01094 ( 15) metal coordination : angle 1.48365 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 137 time to evaluate : 0.465 Fit side-chains REVERT: A 25 ASP cc_start: 0.7420 (t0) cc_final: 0.7139 (t0) REVERT: A 171 ASP cc_start: 0.7828 (t0) cc_final: 0.7477 (t0) REVERT: A 174 SER cc_start: 0.8499 (t) cc_final: 0.8186 (t) REVERT: A 194 THR cc_start: 0.8460 (p) cc_final: 0.8080 (t) REVERT: A 215 HIS cc_start: 0.7985 (t70) cc_final: 0.7750 (t70) REVERT: A 238 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6683 (mm-30) REVERT: A 272 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7041 (tm-30) REVERT: A 390 TYR cc_start: 0.7265 (m-80) cc_final: 0.6890 (m-80) REVERT: A 465 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: A 617 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.7190 (tttm) REVERT: A 618 ILE cc_start: 0.7618 (tp) cc_final: 0.7226 (mt) REVERT: A 625 ARG cc_start: 0.6900 (mmt-90) cc_final: 0.6685 (mpt180) REVERT: A 711 ASN cc_start: 0.7345 (t0) cc_final: 0.7123 (t0) REVERT: A 749 ASP cc_start: 0.6857 (m-30) cc_final: 0.6595 (m-30) REVERT: A 833 ASP cc_start: 0.7693 (t0) cc_final: 0.7422 (t0) REVERT: A 1363 LYS cc_start: 0.8076 (pttt) cc_final: 0.7756 (mttt) REVERT: A 1417 CYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7649 (m) outliers start: 47 outliers final: 26 residues processed: 171 average time/residue: 0.5720 time to fit residues: 106.8893 Evaluate side-chains 163 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 414 LYS Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 533 LYS Chi-restraints excluded: chain A residue 617 LYS Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1355 THR Chi-restraints excluded: chain A residue 1367 LEU Chi-restraints excluded: chain A residue 1368 VAL Chi-restraints excluded: chain A residue 1386 ILE Chi-restraints excluded: chain A residue 1417 CYS Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1593 LYS Chi-restraints excluded: chain A residue 1656 ILE Chi-restraints excluded: chain A residue 1662 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 18 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 HIS ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 ASN A1502 GLN A1584 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.152528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.112090 restraints weight = 15288.000| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.87 r_work: 0.3281 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12700 Z= 0.152 Angle : 0.567 10.725 17429 Z= 0.294 Chirality : 0.043 0.459 1901 Planarity : 0.004 0.055 2003 Dihedral : 18.271 160.125 2489 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.64 % Allowed : 27.30 % Favored : 70.07 % 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: 0.74 (0.23), residues: 1317 helix: 1.98 (0.26), residues: 401 sheet: -0.90 (0.34), residues: 211 loop : 0.16 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1588 TYR 0.016 0.001 TYR A 903 PHE 0.016 0.001 PHE A 805 TRP 0.023 0.001 TRP A 82 HIS 0.004 0.001 HIS A 727 Details of bonding type rmsd covalent geometry : bond 0.00343 (12685) covalent geometry : angle 0.56543 (17414) hydrogen bonds : bond 0.04336 ( 453) hydrogen bonds : angle 4.69729 ( 1310) metal coordination : bond 0.00594 ( 15) metal coordination : angle 1.69803 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2634 Ramachandran restraints generated. 1317 Oldfield, 0 Emsley, 1317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.514 Fit side-chains REVERT: A 25 ASP cc_start: 0.7479 (t0) cc_final: 0.7182 (t0) REVERT: A 55 LYS cc_start: 0.8121 (mtpt) cc_final: 0.7685 (mtpt) REVERT: A 171 ASP cc_start: 0.7773 (t0) cc_final: 0.7415 (t0) REVERT: A 174 SER cc_start: 0.8434 (t) cc_final: 0.8068 (t) REVERT: A 194 THR cc_start: 0.8406 (p) cc_final: 0.8030 (t) REVERT: A 208 ARG cc_start: 0.7512 (mtm-85) cc_final: 0.7233 (mtm-85) REVERT: A 215 HIS cc_start: 0.8043 (t70) cc_final: 0.7764 (t70) REVERT: A 238 GLU cc_start: 0.7064 (mm-30) cc_final: 0.6611 (mm-30) REVERT: A 272 GLU cc_start: 0.7470 (mm-30) cc_final: 0.6953 (tm-30) REVERT: A 390 TYR cc_start: 0.7225 (m-80) cc_final: 0.6604 (m-80) REVERT: A 465 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: A 617 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.6998 (tttm) REVERT: A 618 ILE cc_start: 0.7537 (tp) cc_final: 0.7165 (mt) REVERT: A 662 LYS cc_start: 0.7277 (mtmm) cc_final: 0.6856 (mtmt) REVERT: A 749 ASP cc_start: 0.6841 (m-30) cc_final: 0.6584 (m-30) REVERT: A 833 ASP cc_start: 0.7599 (t0) cc_final: 0.7304 (t0) REVERT: A 1417 CYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7624 (m) outliers start: 31 outliers final: 21 residues processed: 163 average time/residue: 0.5766 time to fit residues: 102.5240 Evaluate side-chains 161 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 414 LYS Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 617 LYS Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1367 LEU Chi-restraints excluded: chain A residue 1368 VAL Chi-restraints excluded: chain A residue 1417 CYS Chi-restraints excluded: chain A residue 1429 VAL Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1593 LYS Chi-restraints excluded: chain A residue 1662 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 139 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 HIS A 986 ASN ** A1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 ASN A1502 GLN A1584 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.152902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112561 restraints weight = 15230.116| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.87 r_work: 0.3277 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12700 Z= 0.152 Angle : 0.572 10.415 17429 Z= 0.297 Chirality : 0.043 0.458 1901 Planarity : 0.004 0.056 2003 Dihedral : 18.257 162.162 2489 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.55 % Allowed : 27.55 % Favored : 69.90 % 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: 0.78 (0.23), residues: 1317 helix: 2.03 (0.26), residues: 400 sheet: -0.88 (0.34), residues: 217 loop : 0.21 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 846 TYR 0.026 0.001 TYR A 903 PHE 0.014 0.001 PHE A 805 TRP 0.026 0.001 TRP A 82 HIS 0.004 0.001 HIS A 727 Details of bonding type rmsd covalent geometry : bond 0.00346 (12685) covalent geometry : angle 0.57015 (17414) hydrogen bonds : bond 0.04255 ( 453) hydrogen bonds : angle 4.63712 ( 1310) metal coordination : bond 0.00582 ( 15) metal coordination : angle 1.64476 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4957.54 seconds wall clock time: 85 minutes 6.49 seconds (5106.49 seconds total)