Starting phenix.real_space_refine on Sat Sep 12 00:38:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y82_33678/09_2026/7y82_33678.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y82_33678/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7y82_33678/09_2026/7y82_33678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y82_33678/09_2026/7y82_33678.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y82_33678/09_2026/7y82_33678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y82_33678/09_2026/7y82_33678.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7y82_33678/09_2026/7y82_33678.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y82_33678/09_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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: {'RNAv2': 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: 2.54, per 1000 atoms: 0.21 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: 1.04 Conformation dependent library (CDL) restraints added in 556.4 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: 1.81 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: 3.06 Time building geometry restraints manager: 1.40 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: 16863 1.83 - 3.66: 443 3.66 - 5.48: 96 5.48 - 7.31: 10 7.31 - 9.14: 2 Bond angle restraints: 17414 Sorted by residual: 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=" O4' G B 47 " pdb=" C1' G B 47 " pdb=" N9 G B 47 " ideal model delta sigma weight residual 108.50 115.99 -7.49 2.00e+00 2.50e-01 1.40e+01 angle pdb=" O4' A B 35 " pdb=" C1' A B 35 " pdb=" N9 A B 35 " ideal model delta sigma weight residual 108.50 115.66 -7.16 2.00e+00 2.50e-01 1.28e+01 angle pdb=" O3' A B 35 " pdb=" C3' A B 35 " pdb=" C2' A B 35 " ideal model delta sigma weight residual 113.80 106.90 6.90 2.00e+00 2.50e-01 1.19e+01 ... (remaining 17409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 5990 17.13 - 34.27: 935 34.27 - 51.40: 325 51.40 - 68.54: 158 68.54 - 85.67: 45 Dihedral angle restraints: 7453 sinusoidal: 3614 harmonic: 3839 Sorted by residual: dihedral pdb=" C4' G B 47 " pdb=" C3' G B 47 " pdb=" C2' G B 47 " pdb=" C1' G B 47 " ideal model delta sinusoidal sigma weight residual 36.34 -39.02 75.36 1 3.10e+00 1.04e-01 7.47e+02 dihedral pdb=" C4' A B 35 " pdb=" C3' A B 35 " pdb=" C2' A B 35 " pdb=" C1' A B 35 " ideal model delta sinusoidal sigma weight residual 36.34 -37.88 74.22 1 3.10e+00 1.04e-01 7.27e+02 dihedral pdb=" C4' A C -2 " pdb=" C3' A C -2 " pdb=" C2' A C -2 " pdb=" C1' A C -2 " ideal model delta sinusoidal sigma weight residual 36.34 -37.63 73.97 1 3.10e+00 1.04e-01 7.23e+02 ... (remaining 7450 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1656 0.083 - 0.165: 124 0.165 - 0.248: 73 0.248 - 0.330: 44 0.330 - 0.413: 4 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 2.46 2.04 0.41 2.00e-01 2.50e+01 4.27e+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 2.46 2.05 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" C3' A B 35 " pdb=" C4' A B 35 " pdb=" O3' A B 35 " pdb=" C2' A B 35 " both_signs ideal model delta sigma weight residual False -2.50 -2.85 0.35 2.00e-01 2.50e+01 3.07e+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: 1.440 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.760 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 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= 0.151 Angle : 0.707 9.140 17429 Z= 0.331 Chirality : 0.074 0.413 1901 Planarity : 0.004 0.104 2003 Dihedral : 20.465 85.672 4993 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/Z covalent geometry : bond 0.00326 / 0.15 (12685) covalent geometry : angle 0.70423 / 0.33 (17414) hydrogen bonds : bond 0.15551 / 10.58 ( 453) hydrogen bonds : angle 6.97578 / 4.95 ( 1310) metal coordination : bond 0.00534 / 0.35 ( 15) metal coordination : angle 2.21271 / 1.26 ( 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 : 0.445 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: 0.4578 time to fit residues: 95.5473 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 : 0.393 ------------------------------------------------------------------------------- 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: 1.9990 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: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3913 r_free = 0.3913 target = 0.153255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.113076 restraints weight = 15155.663| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.85 r_work: 0.3277 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12700 Z= 0.245 Angle : 1.103 27.762 17429 Z= 0.455 Chirality : 0.107 1.704 1901 Planarity : 0.005 0.045 2003 Dihedral : 16.147 161.253 2323 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 5.19 % Allowed : 23.55 % Favored : 71.26 % 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: 0.71 (0.23), residues: 1317 helix: 1.72 (0.26), residues: 400 sheet: -0.82 (0.34), residues: 211 loop : 0.28 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 476 TYR 0.016 0.002 TYR A 903 PHE 0.014 0.002 PHE A 805 TRP 0.019 0.002 TRP A 82 HIS 0.008 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.25 (12685) covalent geometry : angle 1.10240 / 0.46 (17414) hydrogen bonds : bond 0.05615 / 3.75 ( 453) hydrogen bonds : angle 5.34733 / 3.80 ( 1310) metal coordination : bond 0.00842 / 0.53 ( 15) metal coordination : angle 1.89536 / 1.25 ( 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 207 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 146 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8335 (mtpt) cc_final: 0.7989 (mtpt) REVERT: A 215 HIS cc_start: 0.8091 (t70) cc_final: 0.7809 (t70) REVERT: A 238 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6807 (mm-30) REVERT: A 390 TYR cc_start: 0.7345 (m-80) cc_final: 0.7010 (m-80) REVERT: A 662 LYS cc_start: 0.7399 (mtmm) cc_final: 0.6882 (mtmt) REVERT: A 717 GLU cc_start: 0.7764 (pm20) cc_final: 0.7457 (tp30) REVERT: A 928 ASP cc_start: 0.7804 (p0) cc_final: 0.7433 (t0) outliers start: 61 outliers final: 30 residues processed: 196 average time/residue: 0.5293 time to fit residues: 113.4011 Evaluate side-chains 163 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 513 THR Chi-restraints excluded: chain A residue 733 THR 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 1355 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 1386 ILE Chi-restraints excluded: chain A residue 1410 SER Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1463 ARG Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1507 VAL 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: 0.8980 chunk 124 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 43 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN 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 = 0.3944 r_free = 0.3944 target = 0.155662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.115941 restraints weight = 15368.635| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.86 r_work: 0.3325 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12700 Z= 0.186 Angle : 0.901 22.345 17429 Z= 0.384 Chirality : 0.090 1.693 1901 Planarity : 0.004 0.044 2003 Dihedral : 16.030 162.180 2275 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 4.93 % Allowed : 23.64 % Favored : 71.43 % 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: 0.73 (0.23), residues: 1317 helix: 1.81 (0.26), residues: 400 sheet: -0.77 (0.34), residues: 207 loop : 0.22 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 476 TYR 0.018 0.001 TYR A1663 PHE 0.012 0.001 PHE A 805 TRP 0.017 0.001 TRP A 82 HIS 0.005 0.001 HIS A 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (12685) covalent geometry : angle 0.89962 / 0.38 (17414) hydrogen bonds : bond 0.04781 / 3.20 ( 453) hydrogen bonds : angle 4.97070 / 3.56 ( 1310) metal coordination : bond 0.00801 / 0.51 ( 15) metal coordination : angle 1.80809 / 1.14 ( 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 208 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 150 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7486 (t0) cc_final: 0.7186 (t0) REVERT: A 55 LYS cc_start: 0.8297 (mtpt) cc_final: 0.8013 (mtpt) REVERT: A 208 ARG cc_start: 0.7479 (mtm-85) cc_final: 0.7180 (mtm-85) REVERT: A 215 HIS cc_start: 0.8074 (t70) cc_final: 0.7806 (t70) REVERT: A 236 ARG cc_start: 0.7790 (ptp-110) cc_final: 0.7590 (ptp-110) REVERT: A 238 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6681 (mm-30) REVERT: A 390 TYR cc_start: 0.7204 (m-80) cc_final: 0.6824 (m-80) REVERT: A 516 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.7286 (t0) REVERT: A 623 LYS cc_start: 0.7868 (ttpp) cc_final: 0.7586 (ttpt) REVERT: A 625 ARG cc_start: 0.7042 (mmt-90) cc_final: 0.6829 (mpt180) REVERT: A 628 ARG cc_start: 0.6439 (OUTLIER) cc_final: 0.4272 (mtp180) REVERT: A 662 LYS cc_start: 0.7369 (mtmm) cc_final: 0.6871 (mtmt) REVERT: A 833 ASP cc_start: 0.7661 (t0) cc_final: 0.7437 (t0) REVERT: A 1448 ASN cc_start: 0.7730 (OUTLIER) cc_final: 0.7102 (m-40) outliers start: 58 outliers final: 24 residues processed: 192 average time/residue: 0.5463 time to fit residues: 114.6755 Evaluate side-chains 162 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 174 SER 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 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 1007 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1344 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 1429 VAL Chi-restraints excluded: chain A residue 1448 ASN Chi-restraints excluded: chain A residue 1463 ARG 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 0.0170 chunk 71 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN 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 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 = 0.3924 r_free = 0.3924 target = 0.154165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.114135 restraints weight = 15237.589| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.86 r_work: 0.3304 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12700 Z= 0.208 Angle : 0.878 18.771 17429 Z= 0.379 Chirality : 0.087 1.694 1901 Planarity : 0.004 0.045 2003 Dihedral : 16.122 163.942 2261 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 5.10 % Allowed : 23.89 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.23), residues: 1317 helix: 1.82 (0.26), residues: 401 sheet: -0.76 (0.34), residues: 213 loop : 0.14 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 476 TYR 0.015 0.002 TYR A 903 PHE 0.013 0.002 PHE A 805 TRP 0.013 0.001 TRP A 612 HIS 0.005 0.001 HIS A1010 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 (12685) covalent geometry : angle 0.87660 / 0.38 (17414) hydrogen bonds : bond 0.04723 / 3.15 ( 453) hydrogen bonds : angle 4.92108 / 3.52 ( 1310) metal coordination : bond 0.00770 / 0.49 ( 15) metal coordination : angle 1.64584 / 1.05 ( 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 201 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 141 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7473 (t0) cc_final: 0.7178 (t0) REVERT: A 55 LYS cc_start: 0.8287 (mtpt) cc_final: 0.7986 (mtpt) REVERT: A 208 ARG cc_start: 0.7688 (mtm-85) cc_final: 0.7434 (mtm-85) REVERT: A 215 HIS cc_start: 0.8079 (t70) cc_final: 0.7769 (t70) REVERT: A 236 ARG cc_start: 0.7825 (ptp-110) cc_final: 0.7540 (ptp-110) REVERT: A 238 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6557 (mm-30) REVERT: A 272 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7072 (tm-30) REVERT: A 390 TYR cc_start: 0.7196 (m-80) cc_final: 0.6867 (m-80) REVERT: A 516 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7337 (t0) REVERT: A 623 LYS cc_start: 0.7915 (ttpp) cc_final: 0.7632 (ttpt) REVERT: A 628 ARG cc_start: 0.6389 (OUTLIER) cc_final: 0.4189 (mtp180) REVERT: A 833 ASP cc_start: 0.7666 (t0) cc_final: 0.7356 (t0) REVERT: A 1363 LYS cc_start: 0.8257 (pttt) cc_final: 0.7729 (mttt) REVERT: A 1448 ASN cc_start: 0.7764 (OUTLIER) cc_final: 0.7080 (m-40) outliers start: 60 outliers final: 28 residues processed: 186 average time/residue: 0.5595 time to fit residues: 113.0062 Evaluate side-chains 168 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 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 174 SER 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 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 868 ILE 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 1027 THR Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1344 ILE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 64 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 29 optimal weight: 0.0870 chunk 39 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN ** 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 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 = 0.3955 r_free = 0.3955 target = 0.156770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.117619 restraints weight = 15346.389| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.86 r_work: 0.3363 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12700 Z= 0.155 Angle : 0.817 17.053 17429 Z= 0.355 Chirality : 0.081 1.724 1901 Planarity : 0.004 0.048 2003 Dihedral : 16.146 165.751 2261 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.68 % Allowed : 24.66 % 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: 0.81 (0.23), residues: 1317 helix: 1.97 (0.26), residues: 401 sheet: -0.60 (0.34), residues: 217 loop : 0.17 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 476 TYR 0.014 0.001 TYR A 903 PHE 0.012 0.001 PHE A 805 TRP 0.012 0.001 TRP A 612 HIS 0.005 0.001 HIS A 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (12685) covalent geometry : angle 0.81553 / 0.35 (17414) hydrogen bonds : bond 0.04573 / 3.02 ( 453) hydrogen bonds : angle 4.73896 / 3.40 ( 1310) metal coordination : bond 0.00560 / 0.38 ( 15) metal coordination : angle 1.85754 / 1.08 ( 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 204 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 149 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7437 (t0) cc_final: 0.7103 (t0) REVERT: A 26 TRP cc_start: 0.7569 (t60) cc_final: 0.7311 (t60) REVERT: A 55 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7880 (mtpt) REVERT: A 208 ARG cc_start: 0.7633 (mtm-85) cc_final: 0.7303 (mtm-85) REVERT: A 214 GLU cc_start: 0.7399 (tt0) cc_final: 0.6493 (pp20) REVERT: A 215 HIS cc_start: 0.8011 (t70) cc_final: 0.7511 (t70) REVERT: A 236 ARG cc_start: 0.7762 (ptp-110) cc_final: 0.7501 (ptp-110) REVERT: A 238 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6600 (mm-30) REVERT: A 272 GLU cc_start: 0.7440 (mm-30) cc_final: 0.6962 (tm-30) REVERT: A 390 TYR cc_start: 0.7169 (m-80) cc_final: 0.6788 (m-80) REVERT: A 465 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7695 (mt-10) REVERT: A 516 ASP cc_start: 0.7489 (OUTLIER) cc_final: 0.7239 (t0) REVERT: A 607 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7651 (tt) REVERT: A 623 LYS cc_start: 0.7807 (ttpp) cc_final: 0.7500 (ttpt) REVERT: A 625 ARG cc_start: 0.7020 (mpt180) cc_final: 0.6795 (mpt180) REVERT: A 628 ARG cc_start: 0.6289 (OUTLIER) cc_final: 0.4065 (mtp180) REVERT: A 686 ASP cc_start: 0.6928 (t0) cc_final: 0.6376 (t0) REVERT: A 717 GLU cc_start: 0.7753 (pm20) cc_final: 0.7412 (pm20) REVERT: A 719 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7863 (mtt90) REVERT: A 749 ASP cc_start: 0.6881 (m-30) cc_final: 0.6646 (m-30) REVERT: A 833 ASP cc_start: 0.7563 (t0) cc_final: 0.7299 (t0) REVERT: A 1448 ASN cc_start: 0.7710 (OUTLIER) cc_final: 0.7049 (m-40) REVERT: A 1495 LEU cc_start: 0.7945 (mm) cc_final: 0.7733 (mp) outliers start: 55 outliers final: 25 residues processed: 191 average time/residue: 0.5266 time to fit residues: 109.6192 Evaluate side-chains 170 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 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 516 ASP Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain A residue 719 ARG Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 858 VAL 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 1007 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1215 ILE Chi-restraints excluded: chain A residue 1344 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 1448 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 92 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 118 optimal weight: 0.5980 chunk 111 optimal weight: 0.0870 chunk 67 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN ** 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 ** 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 = 0.3970 r_free = 0.3970 target = 0.158024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.119011 restraints weight = 15352.065| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.87 r_work: 0.3394 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12700 Z= 0.143 Angle : 0.793 16.559 17429 Z= 0.344 Chirality : 0.079 1.674 1901 Planarity : 0.004 0.045 2003 Dihedral : 16.017 166.780 2260 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.42 % Allowed : 24.74 % Favored : 70.83 % 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: 2.09 (0.26), residues: 401 sheet: -0.58 (0.34), residues: 217 loop : 0.19 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 476 TYR 0.018 0.001 TYR A 903 PHE 0.011 0.001 PHE A 805 TRP 0.013 0.001 TRP A 612 HIS 0.005 0.001 HIS A 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (12685) covalent geometry : angle 0.79141 / 0.34 (17414) hydrogen bonds : bond 0.04460 / 2.92 ( 453) hydrogen bonds : angle 4.62000 / 3.32 ( 1310) metal coordination : bond 0.00506 / 0.34 ( 15) metal coordination : angle 1.78524 / 1.01 ( 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 203 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 151 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 25 ASP cc_start: 0.7438 (t0) cc_final: 0.7117 (t0) REVERT: A 26 TRP cc_start: 0.7531 (t60) cc_final: 0.7251 (t60) REVERT: A 55 LYS cc_start: 0.8190 (mtpt) cc_final: 0.7873 (mtpt) REVERT: A 208 ARG cc_start: 0.7759 (mtm-85) cc_final: 0.7368 (mtm-85) REVERT: A 214 GLU cc_start: 0.7351 (tt0) cc_final: 0.6496 (pp20) REVERT: A 215 HIS cc_start: 0.7982 (t70) cc_final: 0.7507 (t70) REVERT: A 236 ARG cc_start: 0.7715 (ptp-110) cc_final: 0.7410 (ptp-110) REVERT: A 238 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6723 (mm-30) REVERT: A 272 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6903 (tm-30) REVERT: A 390 TYR cc_start: 0.7143 (m-80) cc_final: 0.6708 (m-80) REVERT: A 465 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7674 (mt-10) REVERT: A 618 ILE cc_start: 0.7580 (tp) cc_final: 0.7182 (mt) REVERT: A 623 LYS cc_start: 0.7791 (ttpp) cc_final: 0.7557 (ttpt) REVERT: A 662 LYS cc_start: 0.7351 (mtmm) cc_final: 0.6845 (mtmt) REVERT: A 686 ASP cc_start: 0.6887 (t0) cc_final: 0.6484 (t0) REVERT: A 689 SER cc_start: 0.8417 (p) cc_final: 0.7968 (p) REVERT: A 717 GLU cc_start: 0.7825 (pm20) cc_final: 0.7444 (pm20) REVERT: A 719 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7856 (mtt90) REVERT: A 833 ASP cc_start: 0.7642 (t0) cc_final: 0.7363 (t0) REVERT: A 1363 LYS cc_start: 0.8209 (pttt) cc_final: 0.7749 (mttt) outliers start: 52 outliers final: 23 residues processed: 188 average time/residue: 0.5457 time to fit residues: 111.7802 Evaluate side-chains 167 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL 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 607 ILE Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain A residue 719 ARG Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 868 ILE 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 1344 ILE 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 1423 THR Chi-restraints excluded: chain A residue 1429 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 30 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 113 optimal weight: 0.0970 chunk 105 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 80 optimal weight: 0.5980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN ** 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** ** 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 = 0.3925 r_free = 0.3925 target = 0.154165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.114526 restraints weight = 15256.610| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.85 r_work: 0.3316 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12700 Z= 0.227 Angle : 0.855 18.211 17429 Z= 0.372 Chirality : 0.082 1.647 1901 Planarity : 0.004 0.046 2003 Dihedral : 15.997 165.366 2251 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.59 % Allowed : 25.34 % 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: 0.72 (0.23), residues: 1317 helix: 1.87 (0.26), residues: 407 sheet: -0.71 (0.34), residues: 219 loop : 0.14 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 476 TYR 0.018 0.002 TYR A 903 PHE 0.014 0.002 PHE A1520 TRP 0.013 0.001 TRP A 612 HIS 0.005 0.001 HIS A 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.23 (12685) covalent geometry : angle 0.85464 / 0.37 (17414) hydrogen bonds : bond 0.04656 / 3.05 ( 453) hydrogen bonds : angle 4.78834 / 3.42 ( 1310) metal coordination : bond 0.00791 / 0.49 ( 15) metal coordination : angle 1.50737 / 0.97 ( 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 195 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 141 time to evaluate : 0.344 Fit side-chains REVERT: A 25 ASP cc_start: 0.7443 (t0) cc_final: 0.7143 (t0) REVERT: A 55 LYS cc_start: 0.8241 (mtpt) cc_final: 0.7807 (mtpt) REVERT: A 208 ARG cc_start: 0.7730 (mtm-85) cc_final: 0.7476 (mtm-85) REVERT: A 214 GLU cc_start: 0.7491 (tt0) cc_final: 0.6505 (pp20) REVERT: A 215 HIS cc_start: 0.8015 (t70) cc_final: 0.7529 (t70) REVERT: A 236 ARG cc_start: 0.7810 (ptp-110) cc_final: 0.7490 (ptp-110) REVERT: A 238 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6622 (mm-30) REVERT: A 465 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7714 (mt-10) REVERT: A 607 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7596 (tt) REVERT: A 618 ILE cc_start: 0.7613 (tp) cc_final: 0.7225 (mt) REVERT: A 623 LYS cc_start: 0.7821 (ttpp) cc_final: 0.7557 (ttpt) REVERT: A 628 ARG cc_start: 0.6354 (OUTLIER) cc_final: 0.4099 (mtp180) REVERT: A 659 PHE cc_start: 0.7062 (t80) cc_final: 0.6800 (t80) REVERT: A 686 ASP cc_start: 0.7090 (t0) cc_final: 0.6678 (t0) REVERT: A 717 GLU cc_start: 0.7850 (pm20) cc_final: 0.7442 (pm20) REVERT: A 719 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7891 (mtt90) REVERT: A 833 ASP cc_start: 0.7691 (t0) cc_final: 0.7421 (t0) REVERT: A 1363 LYS cc_start: 0.8121 (pttt) cc_final: 0.7730 (mttt) REVERT: A 1417 CYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7649 (m) outliers start: 54 outliers final: 25 residues processed: 182 average time/residue: 0.5297 time to fit residues: 105.2700 Evaluate side-chains 168 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 85 VAL Chi-restraints excluded: chain A residue 201 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 597 THR Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain A residue 719 ARG Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1344 ILE 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 82 optimal weight: 6.9990 chunk 109 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 44 optimal weight: 0.0870 chunk 104 optimal weight: 0.8980 chunk 11 optimal weight: 0.0770 chunk 95 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN A 179 ASN ** 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** ** 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 = 0.3973 r_free = 0.3973 target = 0.158187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.119281 restraints weight = 15307.595| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.87 r_work: 0.3398 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12700 Z= 0.139 Angle : 0.794 16.237 17429 Z= 0.345 Chirality : 0.078 1.699 1901 Planarity : 0.004 0.045 2003 Dihedral : 15.891 166.795 2251 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.32 % Allowed : 26.36 % Favored : 70.32 % 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: 2.10 (0.26), residues: 401 sheet: -0.59 (0.35), residues: 217 loop : 0.19 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1446 TYR 0.018 0.001 TYR A 903 PHE 0.012 0.001 PHE A 805 TRP 0.012 0.001 TRP A 612 HIS 0.005 0.001 HIS A 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (12685) covalent geometry : angle 0.79256 / 0.34 (17414) hydrogen bonds : bond 0.04445 / 2.93 ( 453) hydrogen bonds : angle 4.61080 / 3.30 ( 1310) metal coordination : bond 0.00509 / 0.35 ( 15) metal coordination : angle 1.86827 / 1.03 ( 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 188 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 0.446 Fit side-chains REVERT: A 25 ASP cc_start: 0.7422 (t0) cc_final: 0.7084 (t0) REVERT: A 26 TRP cc_start: 0.7513 (t60) cc_final: 0.7263 (t60) REVERT: A 55 LYS cc_start: 0.8176 (mtpt) cc_final: 0.7847 (mtpt) REVERT: A 174 SER cc_start: 0.8458 (t) cc_final: 0.8090 (t) REVERT: A 206 THR cc_start: 0.8419 (m) cc_final: 0.8187 (m) REVERT: A 208 ARG cc_start: 0.7672 (mtm-85) cc_final: 0.7418 (mtm-85) REVERT: A 210 THR cc_start: 0.7737 (p) cc_final: 0.7534 (t) REVERT: A 214 GLU cc_start: 0.7385 (tt0) cc_final: 0.6555 (pp20) REVERT: A 215 HIS cc_start: 0.7947 (t70) cc_final: 0.7449 (t70) REVERT: A 238 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6806 (mm-30) REVERT: A 465 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7676 (mt-10) REVERT: A 607 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7609 (tt) REVERT: A 618 ILE cc_start: 0.7589 (tp) cc_final: 0.7228 (mt) REVERT: A 625 ARG cc_start: 0.6439 (mpp-170) cc_final: 0.5962 (mpt180) REVERT: A 628 ARG cc_start: 0.6366 (OUTLIER) cc_final: 0.4233 (mtp180) REVERT: A 662 LYS cc_start: 0.7302 (mtmm) cc_final: 0.7038 (mtmt) REVERT: A 717 GLU cc_start: 0.7881 (pm20) cc_final: 0.7477 (pm20) REVERT: A 719 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7880 (mtt90) REVERT: A 833 ASP cc_start: 0.7682 (t0) cc_final: 0.7390 (t0) outliers start: 39 outliers final: 21 residues processed: 177 average time/residue: 0.5187 time to fit residues: 100.6134 Evaluate side-chains 162 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 201 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 607 ILE Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain A residue 719 ARG Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 868 ILE 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 1344 ILE 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 1410 SER Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1593 LYS Chi-restraints excluded: chain A residue 1649 ASN Chi-restraints excluded: chain A residue 1656 ILE 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: 4.9990 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 123 optimal weight: 0.0870 chunk 82 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN ** 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 ** 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 = 0.3932 r_free = 0.3932 target = 0.154739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.114862 restraints weight = 15240.867| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.86 r_work: 0.3314 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12700 Z= 0.215 Angle : 0.845 18.058 17429 Z= 0.368 Chirality : 0.081 1.639 1901 Planarity : 0.004 0.049 2003 Dihedral : 15.912 165.299 2250 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.06 % Allowed : 26.45 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.23), residues: 1317 helix: 1.88 (0.26), residues: 407 sheet: -0.62 (0.35), residues: 217 loop : 0.13 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 476 TYR 0.014 0.002 TYR A 903 PHE 0.012 0.002 PHE A1520 TRP 0.013 0.001 TRP A 612 HIS 0.005 0.001 HIS A 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (12685) covalent geometry : angle 0.84432 / 0.37 (17414) hydrogen bonds : bond 0.04589 / 3.01 ( 453) hydrogen bonds : angle 4.75506 / 3.40 ( 1310) metal coordination : bond 0.00777 / 0.49 ( 15) metal coordination : angle 1.51510 / 0.97 ( 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 171 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.447 Fit side-chains REVERT: A 25 ASP cc_start: 0.7434 (t0) cc_final: 0.7147 (t0) REVERT: A 26 TRP cc_start: 0.7567 (t60) cc_final: 0.7320 (t60) REVERT: A 55 LYS cc_start: 0.8241 (mtpt) cc_final: 0.7807 (mtpt) REVERT: A 208 ARG cc_start: 0.7752 (mtm-85) cc_final: 0.7497 (mtm-85) REVERT: A 210 THR cc_start: 0.7864 (p) cc_final: 0.7573 (t) REVERT: A 214 GLU cc_start: 0.7446 (tt0) cc_final: 0.6550 (pp20) REVERT: A 215 HIS cc_start: 0.7999 (t70) cc_final: 0.7532 (t70) REVERT: A 238 GLU cc_start: 0.7068 (mm-30) cc_final: 0.6772 (mm-30) REVERT: A 465 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7730 (mt-10) REVERT: A 607 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7595 (tt) REVERT: A 618 ILE cc_start: 0.7664 (tp) cc_final: 0.7283 (mt) REVERT: A 625 ARG cc_start: 0.6603 (mpp-170) cc_final: 0.6397 (mmt90) REVERT: A 628 ARG cc_start: 0.6570 (OUTLIER) cc_final: 0.4588 (mtp180) REVERT: A 662 LYS cc_start: 0.7431 (mtmm) cc_final: 0.7131 (mtmt) REVERT: A 689 SER cc_start: 0.8514 (p) cc_final: 0.8274 (p) REVERT: A 717 GLU cc_start: 0.7912 (pm20) cc_final: 0.7528 (pm20) REVERT: A 719 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7907 (mtt90) REVERT: A 833 ASP cc_start: 0.7703 (t0) cc_final: 0.7417 (t0) REVERT: A 1363 LYS cc_start: 0.8150 (pttt) cc_final: 0.7732 (mtpt) REVERT: A 1417 CYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7691 (m) outliers start: 36 outliers final: 24 residues processed: 161 average time/residue: 0.5139 time to fit residues: 91.0850 Evaluate side-chains 160 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 310 VAL 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 465 GLU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain A residue 719 ARG Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1344 ILE 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 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 1649 ASN 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: 2.9990 chunk 123 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 133 optimal weight: 0.2980 chunk 84 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3989 r_free = 0.3989 target = 0.159423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.120391 restraints weight = 15350.120| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.90 r_work: 0.3413 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2343 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= 0.134 Angle : 0.785 15.994 17429 Z= 0.342 Chirality : 0.077 1.712 1901 Planarity : 0.004 0.046 2003 Dihedral : 15.706 166.800 2250 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.47 % Allowed : 27.13 % 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: 0.89 (0.23), residues: 1317 helix: 2.09 (0.26), residues: 402 sheet: -0.54 (0.35), residues: 217 loop : 0.17 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1446 TYR 0.018 0.001 TYR A 903 PHE 0.011 0.001 PHE A 805 TRP 0.011 0.001 TRP A 612 HIS 0.005 0.001 HIS A 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (12685) covalent geometry : angle 0.78376 / 0.34 (17414) hydrogen bonds : bond 0.04427 / 2.92 ( 453) hydrogen bonds : angle 4.58615 / 3.29 ( 1310) metal coordination : bond 0.00492 / 0.33 ( 15) metal coordination : angle 1.87482 / 1.01 ( 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 169 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.345 Fit side-chains REVERT: A 25 ASP cc_start: 0.7373 (t0) cc_final: 0.7137 (t0) REVERT: A 26 TRP cc_start: 0.7408 (t60) cc_final: 0.7156 (t60) REVERT: A 55 LYS cc_start: 0.8098 (mtpt) cc_final: 0.7753 (mtpt) REVERT: A 174 SER cc_start: 0.8380 (t) cc_final: 0.8023 (t) REVERT: A 194 THR cc_start: 0.8357 (p) cc_final: 0.7997 (t) REVERT: A 206 THR cc_start: 0.8284 (m) cc_final: 0.8065 (m) REVERT: A 208 ARG cc_start: 0.7682 (mtm-85) cc_final: 0.7375 (mtm-85) REVERT: A 210 THR cc_start: 0.7764 (p) cc_final: 0.7457 (t) REVERT: A 214 GLU cc_start: 0.7276 (tt0) cc_final: 0.6489 (pp20) REVERT: A 215 HIS cc_start: 0.7920 (t70) cc_final: 0.7420 (t70) REVERT: A 238 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6689 (mm-30) REVERT: A 465 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7647 (mt-10) REVERT: A 607 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7510 (tt) REVERT: A 618 ILE cc_start: 0.7503 (tp) cc_final: 0.7149 (mt) REVERT: A 624 GLU cc_start: 0.7130 (tp30) cc_final: 0.6145 (tp30) REVERT: A 628 ARG cc_start: 0.6466 (OUTLIER) cc_final: 0.4279 (mtp180) REVERT: A 662 LYS cc_start: 0.7268 (mtmm) cc_final: 0.7022 (mtmt) REVERT: A 689 SER cc_start: 0.8351 (p) cc_final: 0.8146 (p) REVERT: A 717 GLU cc_start: 0.7882 (pm20) cc_final: 0.7459 (pm20) REVERT: A 719 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7841 (mtt90) REVERT: A 833 ASP cc_start: 0.7616 (t0) cc_final: 0.7301 (t0) REVERT: A 1352 ARG cc_start: 0.5610 (mtt180) cc_final: 0.5160 (mmm160) REVERT: A 1417 CYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7416 (m) outliers start: 29 outliers final: 21 residues processed: 160 average time/residue: 0.4665 time to fit residues: 82.3453 Evaluate side-chains 163 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 211 LEU 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 465 GLU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 628 ARG Chi-restraints excluded: chain A residue 719 ARG Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1344 ILE 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 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 139 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN A 286 GLN ** 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.155092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.115271 restraints weight = 15198.645| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.86 r_work: 0.3313 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12700 Z= 0.215 Angle : 0.841 17.883 17429 Z= 0.367 Chirality : 0.081 1.623 1901 Planarity : 0.004 0.056 2003 Dihedral : 15.771 165.680 2250 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.81 % Allowed : 27.21 % Favored : 69.98 % 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: 1.87 (0.26), residues: 407 sheet: -0.62 (0.35), residues: 217 loop : 0.13 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1588 TYR 0.020 0.002 TYR A 903 PHE 0.012 0.001 PHE A1520 TRP 0.012 0.001 TRP A 416 HIS 0.005 0.001 HIS A 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 (12685) covalent geometry : angle 0.84001 / 0.37 (17414) hydrogen bonds : bond 0.04557 / 2.98 ( 453) hydrogen bonds : angle 4.73471 / 3.38 ( 1310) metal coordination : bond 0.00782 / 0.48 ( 15) metal coordination : angle 1.41473 / 0.90 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4746.32 seconds wall clock time: 81 minutes 44.61 seconds (4904.61 seconds total)