Starting phenix.real_space_refine on Wed Mar 4 20:54:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x8a_33056/03_2026/7x8a_33056.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x8a_33056/03_2026/7x8a_33056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x8a_33056/03_2026/7x8a_33056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x8a_33056/03_2026/7x8a_33056.map" model { file = "/net/cci-nas-00/data/ceres_data/7x8a_33056/03_2026/7x8a_33056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x8a_33056/03_2026/7x8a_33056.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 33 5.49 5 S 57 5.16 5 C 10097 2.51 5 N 2777 2.21 5 O 3063 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16031 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 5383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5383 Classifications: {'peptide': 674} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 21, 'TRANS': 652} Chain breaks: 2 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 4, 'GLN:plan1': 3, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "A" Number of atoms: 9955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1266, 9955 Classifications: {'peptide': 1266} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 59, 'TRANS': 1206} Chain breaks: 5 Unresolved non-hydrogen bonds: 258 Unresolved non-hydrogen angles: 314 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'HIS:plan': 3, 'GLN:plan1': 2, 'GLU:plan': 15, 'ASN:plan1': 9, 'ASP:plan': 12, 'ARG:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 172 Chain: "C" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 689 Classifications: {'RNA': 33} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 10, 'rna3p_pur': 1, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 12} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9001 SG CYS A 491 52.924 49.410 50.088 1.00 54.25 S ATOM 9069 SG CYS A 501 53.132 48.423 46.625 1.00 45.05 S ATOM 9083 SG CYS A 503 56.226 47.890 48.697 1.00 47.02 S ATOM 9105 SG CYS A 506 53.216 45.695 49.411 1.00 43.57 S ATOM 6059 SG CYS A 88 47.366 26.287 26.370 1.00 57.57 S ATOM 6330 SG CYS A 121 45.755 23.307 24.620 1.00 73.51 S ATOM 6376 SG CYS A 127 47.125 22.928 28.159 1.00 58.23 S ATOM 6400 SG CYS A 130 44.045 25.067 27.546 1.00 54.37 S ATOM 11073 SG CYS A 750 51.876 68.818 73.320 1.00 63.04 S ATOM 11086 SG CYS A 752 55.166 67.698 74.823 1.00 55.30 S ATOM 11108 SG CYS A 755 52.627 65.047 73.859 1.00 51.37 S ATOM 13050 SG CYS A1018 45.696 69.639 109.917 1.00 86.14 S ATOM 13231 SG CYS A1406 44.656 70.310 106.196 1.00 80.54 S ATOM 13282 SG CYS A1414 46.420 72.804 108.261 1.00 74.48 S ATOM 13299 SG CYS A1417 48.199 69.432 107.109 1.00 66.41 S Time building chain proxies: 3.44, per 1000 atoms: 0.21 Number of scatterers: 16031 At special positions: 0 Unit cell: (98.7999, 99.7499, 156.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 57 16.00 P 33 15.00 O 3063 8.00 N 2777 7.00 C 10097 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: 1.47 Conformation dependent library (CDL) restraints added in 738.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 491 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 501 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 506 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 503 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 88 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 127 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 121 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" ND1 HIS A 747 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 752 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 750 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 755 " pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1018 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1406 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1414 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1417 " Number of angles added : 21 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3594 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 23 sheets defined 41.5% alpha, 17.4% beta 0 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'D' and resid 15 through 32 Processing helix chain 'D' and resid 37 through 59 removed outlier: 3.865A pdb=" N LYS D 43 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU D 58 " --> pdb=" O GLY D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 81 Processing helix chain 'D' and resid 90 through 110 removed outlier: 3.634A pdb=" N LYS D 94 " --> pdb=" O PRO D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 136 Processing helix chain 'D' and resid 141 through 156 Processing helix chain 'D' and resid 163 through 176 removed outlier: 3.706A pdb=" N ILE D 167 " --> pdb=" O TYR D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 190 Processing helix chain 'D' and resid 194 through 205 Processing helix chain 'D' and resid 208 through 223 removed outlier: 4.267A pdb=" N LYS D 218 " --> pdb=" O GLU D 214 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS D 219 " --> pdb=" O HIS D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 226 No H-bonds generated for 'chain 'D' and resid 224 through 226' Processing helix chain 'D' and resid 230 through 246 removed outlier: 3.962A pdb=" N ASP D 234 " --> pdb=" O HIS D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 269 removed outlier: 3.704A pdb=" N ILE D 256 " --> pdb=" O ARG D 252 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR D 269 " --> pdb=" O GLN D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 296 Processing helix chain 'D' and resid 302 through 321 removed outlier: 4.432A pdb=" N LYS D 306 " --> pdb=" O ASP D 302 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS D 321 " --> pdb=" O SER D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 333 removed outlier: 3.890A pdb=" N ASP D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 361 removed outlier: 4.102A pdb=" N TYR D 360 " --> pdb=" O TYR D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 451 removed outlier: 3.870A pdb=" N LEU D 449 " --> pdb=" O ALA D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 469 Processing helix chain 'D' and resid 470 through 474 Processing helix chain 'D' and resid 490 through 495 Processing helix chain 'D' and resid 496 through 500 removed outlier: 3.569A pdb=" N SER D 500 " --> pdb=" O LEU D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 513 Processing helix chain 'D' and resid 521 through 525 Processing helix chain 'D' and resid 547 through 553 Processing helix chain 'D' and resid 566 through 572 removed outlier: 3.501A pdb=" N LEU D 570 " --> pdb=" O SER D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 595 Processing helix chain 'D' and resid 607 through 614 removed outlier: 3.612A pdb=" N LEU D 611 " --> pdb=" O TYR D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 644 through 652 removed outlier: 4.054A pdb=" N ALA D 648 " --> pdb=" O SER D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 675 removed outlier: 4.004A pdb=" N THR D 669 " --> pdb=" O ARG D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 692 removed outlier: 3.675A pdb=" N GLU D 690 " --> pdb=" O GLU D 686 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY D 692 " --> pdb=" O GLN D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'A' and resid 28 through 31 Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 59 through 78 Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 168 through 172 removed outlier: 3.674A pdb=" N ILE A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 168 through 172' 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 Processing helix chain 'A' and resid 270 through 287 Processing helix chain 'A' and resid 291 through 303 removed outlier: 4.530A pdb=" N ILE A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 320 through 324 removed outlier: 3.940A pdb=" N ASP A 324 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 351 Processing helix chain 'A' and resid 354 through 374 Processing helix chain 'A' and resid 390 through 395 Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.721A pdb=" N ILE A 439 " --> pdb=" O PRO A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 488 Processing helix chain 'A' and resid 503 through 510 Processing helix chain 'A' and resid 569 through 580 Processing helix chain 'A' and resid 595 through 598 Processing helix chain 'A' and resid 617 through 624 Processing helix chain 'A' and resid 625 through 628 Processing helix chain 'A' and resid 630 through 636 Processing helix chain 'A' and resid 638 through 642 removed outlier: 3.528A pdb=" N LEU A 642 " --> pdb=" O GLU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 657 Processing helix chain 'A' and resid 658 through 664 Processing helix chain 'A' and resid 688 through 693 Processing helix chain 'A' and resid 723 through 740 Processing helix chain 'A' and resid 752 through 759 Processing helix chain 'A' and resid 831 through 848 Processing helix chain 'A' and resid 855 through 859 Processing helix chain 'A' and resid 874 through 879 Processing helix chain 'A' and resid 909 through 914 removed outlier: 4.465A pdb=" N GLN A 913 " --> pdb=" O GLN A 909 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 909 through 914' Processing helix chain 'A' and resid 999 through 1015 Processing helix chain 'A' and resid 1400 through 1404 Processing helix chain 'A' and resid 1414 through 1420 Processing helix chain 'A' and resid 1486 through 1493 removed outlier: 3.993A pdb=" N ILE A1490 " --> pdb=" O GLY A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1493 through 1498 removed outlier: 3.713A pdb=" N ARG A1498 " --> pdb=" O GLN A1494 " (cutoff:3.500A) Processing helix chain 'A' and resid 1528 through 1540 removed outlier: 3.811A pdb=" N GLY A1533 " --> pdb=" O GLU A1529 " (cutoff:3.500A) 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: 3.523A 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 removed outlier: 3.779A pdb=" N LYS A1624 " --> pdb=" O PRO A1620 " (cutoff:3.500A) Processing helix chain 'A' and resid 1662 through 1666 removed outlier: 3.803A pdb=" N LEU A1666 " --> pdb=" O TYR A1663 " (cutoff:3.500A) Processing helix chain 'A' and resid 1673 through 1683 removed outlier: 3.553A pdb=" N LYS A1679 " --> pdb=" O LYS A1675 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 425 through 431 removed outlier: 3.693A pdb=" N MET D 413 " --> pdb=" O ASN D 408 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASN D 408 " --> pdb=" O MET D 413 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N CYS D 516 " --> pdb=" O PHE D 709 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER D 711 " --> pdb=" O CYS D 516 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL D 622 " --> pdb=" O VAL D 658 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N THR D 660 " --> pdb=" O VAL D 622 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 597 through 598 Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 153 removed outlier: 6.819A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TRP A 195 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N GLU A 22 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 13.206A pdb=" N ARG A 193 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ARG A 180 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR A 191 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU A 178 " --> pdb=" O TYR A 191 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ARG A 193 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG A 176 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N TRP A 195 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N SER A 174 " --> pdb=" O TRP A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA6, first strand: chain 'A' and resid 109 through 111 removed outlier: 5.897A pdb=" N THR A 110 " --> pdb=" O VAL A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 333 through 334 Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 514 removed outlier: 5.150A pdb=" N ARG A 421 " --> pdb=" O ASP A 606 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ASP A 606 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LYS A 423 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU A 604 " --> pdb=" O LYS A 423 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY A 600 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 512 through 514 removed outlier: 5.150A pdb=" N ARG A 421 " --> pdb=" O ASP A 606 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ASP A 606 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LYS A 423 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU A 604 " --> pdb=" O LYS A 423 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 431 through 432 removed outlier: 4.197A pdb=" N ASN A 459 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AB3, first strand: chain 'A' and resid 526 through 530 Processing sheet with id=AB4, first strand: chain 'A' and resid 533 through 534 removed outlier: 3.558A pdb=" N THR A 539 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.813A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 773 " --> pdb=" O LYS A 821 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.813A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 773 " --> pdb=" O LYS A 821 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N GLN A 673 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ILE A 868 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR A 675 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE A 866 " --> pdb=" O THR A 675 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLU A 677 " --> pdb=" O ALA A 864 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 699 through 700 removed outlier: 3.532A pdb=" N ALA A 699 " --> pdb=" O ASP A 806 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 707 through 708 Processing sheet with id=AB9, first strand: chain 'A' and resid 920 through 921 Processing sheet with id=AC1, first strand: chain 'A' and resid 924 through 927 Processing sheet with id=AC2, first strand: chain 'A' and resid 991 through 992 removed outlier: 7.006A pdb=" N LEU A 996 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A1436 " --> pdb=" O LEU A 996 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A1517 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1429 through 1431 removed outlier: 6.791A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 985 through 987 removed outlier: 6.154A pdb=" N LYS A 985 " --> pdb=" O THR A1508 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N GLU A1510 " --> pdb=" O LYS A 985 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N TYR A 987 " --> pdb=" O GLU A1510 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A1507 " --> pdb=" O LEU A1456 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1421 through 1422 688 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 7 stacking parallelities Total time for adding SS restraints: 3.61 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4531 1.33 - 1.45: 2869 1.45 - 1.57: 8907 1.57 - 1.69: 65 1.69 - 1.81: 80 Bond restraints: 16452 Sorted by residual: bond pdb=" CB PRO A 982 " pdb=" CG PRO A 982 " ideal model delta sigma weight residual 1.492 1.548 -0.056 5.00e-02 4.00e+02 1.26e+00 bond pdb=" CA ASP A1424 " pdb=" CB ASP A1424 " ideal model delta sigma weight residual 1.530 1.549 -0.018 1.69e-02 3.50e+03 1.18e+00 bond pdb=" CA VAL D 638 " pdb=" CB VAL D 638 " ideal model delta sigma weight residual 1.540 1.554 -0.014 1.36e-02 5.41e+03 1.05e+00 bond pdb=" C PHE D 324 " pdb=" N SER D 325 " ideal model delta sigma weight residual 1.328 1.337 -0.009 8.50e-03 1.38e+04 1.05e+00 bond pdb=" N GLY A 710 " pdb=" CA GLY A 710 " ideal model delta sigma weight residual 1.449 1.464 -0.015 1.45e-02 4.76e+03 1.00e+00 ... (remaining 16447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 21931 1.61 - 3.22: 369 3.22 - 4.83: 51 4.83 - 6.44: 12 6.44 - 8.05: 7 Bond angle restraints: 22370 Sorted by residual: angle pdb=" C ASP D 637 " pdb=" N VAL D 638 " pdb=" CA VAL D 638 " ideal model delta sigma weight residual 121.97 128.91 -6.94 1.80e+00 3.09e-01 1.49e+01 angle pdb=" C SER D 325 " pdb=" N LEU D 326 " pdb=" CA LEU D 326 " ideal model delta sigma weight residual 120.95 127.66 -6.71 1.78e+00 3.16e-01 1.42e+01 angle pdb=" N SER D 325 " pdb=" CA SER D 325 " pdb=" C SER D 325 " ideal model delta sigma weight residual 108.65 115.52 -6.87 1.85e+00 2.92e-01 1.38e+01 angle pdb=" C THR A1423 " pdb=" N ASP A1424 " pdb=" CA ASP A1424 " ideal model delta sigma weight residual 121.54 128.07 -6.53 1.91e+00 2.74e-01 1.17e+01 angle pdb=" C LYS A1543 " pdb=" N ASN A1544 " pdb=" CA ASN A1544 " ideal model delta sigma weight residual 121.54 127.27 -5.73 1.91e+00 2.74e-01 9.01e+00 ... (remaining 22365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 9697 35.94 - 71.89: 174 71.89 - 107.83: 32 107.83 - 143.77: 1 143.77 - 179.71: 3 Dihedral angle restraints: 9907 sinusoidal: 4318 harmonic: 5589 Sorted by residual: dihedral pdb=" O4' U C -9 " pdb=" C1' U C -9 " pdb=" N1 U C -9 " pdb=" C2 U C -9 " ideal model delta sinusoidal sigma weight residual 232.00 52.29 179.71 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U C -15 " pdb=" C1' U C -15 " pdb=" N1 U C -15 " pdb=" C2 U C -15 " ideal model delta sinusoidal sigma weight residual -128.00 44.36 -172.36 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O4' U C 10 " pdb=" C1' U C 10 " pdb=" N1 U C 10 " pdb=" C2 U C 10 " ideal model delta sinusoidal sigma weight residual -128.00 44.22 -172.22 1 1.70e+01 3.46e-03 6.61e+01 ... (remaining 9904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1940 0.046 - 0.093: 391 0.093 - 0.139: 113 0.139 - 0.186: 4 0.186 - 0.232: 1 Chirality restraints: 2449 Sorted by residual: chirality pdb=" CB VAL D 638 " pdb=" CA VAL D 638 " pdb=" CG1 VAL D 638 " pdb=" CG2 VAL D 638 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C1' C C 2 " pdb=" O4' C C 2 " pdb=" C2' C C 2 " pdb=" N1 C C 2 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.17 2.00e-01 2.50e+01 7.35e-01 chirality pdb=" CA ASP A1424 " pdb=" N ASP A1424 " pdb=" C ASP A1424 " pdb=" CB ASP A1424 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.22e-01 ... (remaining 2446 not shown) Planarity restraints: 2759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 981 " 0.037 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO A 982 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 982 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 982 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR D 629 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.29e+00 pdb=" C THR D 629 " -0.036 2.00e-02 2.50e+03 pdb=" O THR D 629 " 0.013 2.00e-02 2.50e+03 pdb=" N ASP D 630 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 633 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.68e+00 pdb=" N PRO D 634 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO D 634 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 634 " 0.026 5.00e-02 4.00e+02 ... (remaining 2756 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 424 2.70 - 3.25: 15748 3.25 - 3.80: 26227 3.80 - 4.35: 35418 4.35 - 4.90: 58659 Nonbonded interactions: 136476 Sorted by model distance: nonbonded pdb=" O ILE A 531 " pdb=" O2' A C 3 " model vdw 2.145 3.040 nonbonded pdb=" OE2 GLU A 11 " pdb=" OG1 THR A 204 " model vdw 2.146 3.040 nonbonded pdb=" O PHE A 104 " pdb=" O2' G C -10 " model vdw 2.186 3.040 nonbonded pdb=" OG1 THR A 941 " pdb=" OE1 GLU A 943 " model vdw 2.201 3.040 nonbonded pdb=" O TRP D 687 " pdb=" OG1 THR D 691 " model vdw 2.209 3.040 ... (remaining 136471 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: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 19.840 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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 0.056 16468 Z= 0.137 Angle : 0.543 8.261 22391 Z= 0.280 Chirality : 0.040 0.232 2449 Planarity : 0.004 0.055 2759 Dihedral : 15.005 179.712 6313 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.52 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.22 (0.19), residues: 1922 helix: 1.41 (0.20), residues: 689 sheet: -0.34 (0.34), residues: 232 loop : -0.60 (0.20), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 697 TYR 0.023 0.001 TYR A1595 PHE 0.026 0.001 PHE A 731 TRP 0.018 0.001 TRP D 278 HIS 0.004 0.001 HIS D 215 Details of bonding type rmsd covalent geometry : bond 0.00312 (16452) covalent geometry : angle 0.53134 (22370) hydrogen bonds : bond 0.18885 ( 649) hydrogen bonds : angle 6.92633 ( 1890) metal coordination : bond 0.00564 ( 16) metal coordination : angle 3.66776 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: D 139 LYS cc_start: 0.8522 (mttp) cc_final: 0.8287 (mttm) REVERT: A 145 ARG cc_start: 0.6862 (tmt170) cc_final: 0.6629 (ttp-170) REVERT: A 463 ASP cc_start: 0.7605 (t70) cc_final: 0.7117 (t0) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.6392 time to fit residues: 129.8314 Evaluate side-chains 125 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 ASN A 7 ASN A 269 HIS A 286 GLN A 919 ASN ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1506 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.129857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.096357 restraints weight = 21660.968| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.33 r_work: 0.3135 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16468 Z= 0.130 Angle : 0.558 8.468 22391 Z= 0.289 Chirality : 0.041 0.187 2449 Planarity : 0.004 0.047 2759 Dihedral : 13.018 178.784 2602 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.88 % Favored : 94.02 % Rotamer: Outliers : 1.18 % Allowed : 8.56 % Favored : 90.26 % 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: 0.41 (0.20), residues: 1922 helix: 1.58 (0.20), residues: 703 sheet: -0.20 (0.33), residues: 244 loop : -0.55 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1452 TYR 0.011 0.001 TYR D 607 PHE 0.019 0.001 PHE A 731 TRP 0.016 0.001 TRP A 612 HIS 0.003 0.001 HIS A 727 Details of bonding type rmsd covalent geometry : bond 0.00287 (16452) covalent geometry : angle 0.54625 (22370) hydrogen bonds : bond 0.04190 ( 649) hydrogen bonds : angle 4.84543 ( 1890) metal coordination : bond 0.00493 ( 16) metal coordination : angle 3.79870 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: D 35 ARG cc_start: 0.8609 (mtp-110) cc_final: 0.8408 (mpt-90) REVERT: D 136 ASP cc_start: 0.8525 (t0) cc_final: 0.8318 (t0) REVERT: D 139 LYS cc_start: 0.8624 (mttp) cc_final: 0.8294 (mttm) REVERT: A 145 ARG cc_start: 0.7289 (tmt170) cc_final: 0.7078 (tmm160) REVERT: A 337 THR cc_start: 0.8698 (m) cc_final: 0.8352 (t) REVERT: A 539 THR cc_start: 0.8822 (m) cc_final: 0.8602 (p) REVERT: A 677 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8237 (mp0) REVERT: A 901 ASN cc_start: 0.7683 (t0) cc_final: 0.6933 (t0) REVERT: A 925 TYR cc_start: 0.7814 (m-80) cc_final: 0.7578 (m-80) REVERT: A 959 GLU cc_start: 0.8954 (tt0) cc_final: 0.8573 (tt0) REVERT: A 1504 GLU cc_start: 0.7963 (pp20) cc_final: 0.7739 (pp20) REVERT: A 1589 GLU cc_start: 0.8014 (tp30) cc_final: 0.7685 (tp30) outliers start: 19 outliers final: 3 residues processed: 161 average time/residue: 0.5669 time to fit residues: 101.5811 Evaluate side-chains 128 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 124 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 677 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 50 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 163 optimal weight: 0.0870 chunk 65 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 164 optimal weight: 0.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 215 HIS A 7 ASN ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1506 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.129411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.095764 restraints weight = 21955.643| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.34 r_work: 0.3128 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16468 Z= 0.128 Angle : 0.537 7.171 22391 Z= 0.276 Chirality : 0.041 0.197 2449 Planarity : 0.004 0.064 2759 Dihedral : 12.976 179.042 2602 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.31 % Favored : 94.54 % Rotamer: Outliers : 1.30 % Allowed : 11.04 % Favored : 87.66 % 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: 0.43 (0.19), residues: 1922 helix: 1.61 (0.20), residues: 704 sheet: -0.21 (0.31), residues: 252 loop : -0.55 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1452 TYR 0.020 0.001 TYR A1595 PHE 0.018 0.001 PHE A 731 TRP 0.015 0.001 TRP A 612 HIS 0.003 0.001 HIS A 924 Details of bonding type rmsd covalent geometry : bond 0.00287 (16452) covalent geometry : angle 0.52638 (22370) hydrogen bonds : bond 0.03701 ( 649) hydrogen bonds : angle 4.50954 ( 1890) metal coordination : bond 0.00464 ( 16) metal coordination : angle 3.46397 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: D 136 ASP cc_start: 0.8480 (t0) cc_final: 0.8225 (t0) REVERT: D 139 LYS cc_start: 0.8628 (mttp) cc_final: 0.8230 (mttm) REVERT: A 539 THR cc_start: 0.8764 (m) cc_final: 0.8542 (p) REVERT: A 901 ASN cc_start: 0.7714 (t0) cc_final: 0.6787 (t0) REVERT: A 925 TYR cc_start: 0.7799 (m-80) cc_final: 0.7493 (m-80) REVERT: A 1504 GLU cc_start: 0.7945 (pp20) cc_final: 0.7716 (pp20) REVERT: A 1589 GLU cc_start: 0.8014 (tp30) cc_final: 0.7651 (tp30) outliers start: 21 outliers final: 6 residues processed: 149 average time/residue: 0.5673 time to fit residues: 94.2291 Evaluate side-chains 121 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1509 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 43 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 160 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 177 optimal weight: 0.6980 chunk 52 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 179 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 147 ASN ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1506 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.127532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.093706 restraints weight = 21615.185| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.31 r_work: 0.3091 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16468 Z= 0.164 Angle : 0.562 10.764 22391 Z= 0.287 Chirality : 0.042 0.197 2449 Planarity : 0.004 0.054 2759 Dihedral : 13.021 179.953 2602 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.67 % Favored : 94.17 % Rotamer: Outliers : 1.92 % Allowed : 12.66 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.40 (0.19), residues: 1922 helix: 1.58 (0.20), residues: 706 sheet: -0.17 (0.31), residues: 252 loop : -0.58 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 35 TYR 0.012 0.001 TYR D 607 PHE 0.019 0.001 PHE A 129 TRP 0.016 0.001 TRP A 612 HIS 0.004 0.001 HIS D 404 Details of bonding type rmsd covalent geometry : bond 0.00375 (16452) covalent geometry : angle 0.55090 (22370) hydrogen bonds : bond 0.03709 ( 649) hydrogen bonds : angle 4.42545 ( 1890) metal coordination : bond 0.00677 ( 16) metal coordination : angle 3.65915 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 35 ARG cc_start: 0.8571 (mtp-110) cc_final: 0.8321 (mpt-90) REVERT: A 539 THR cc_start: 0.8783 (m) cc_final: 0.8533 (p) REVERT: A 901 ASN cc_start: 0.7687 (t0) cc_final: 0.6906 (t0) REVERT: A 925 TYR cc_start: 0.7900 (m-80) cc_final: 0.7513 (m-80) REVERT: A 1504 GLU cc_start: 0.7967 (pp20) cc_final: 0.7708 (pp20) REVERT: A 1589 GLU cc_start: 0.8086 (tp30) cc_final: 0.7725 (tp30) outliers start: 31 outliers final: 11 residues processed: 149 average time/residue: 0.5365 time to fit residues: 89.5012 Evaluate side-chains 132 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1565 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 905 HIS ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1506 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.127945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.094114 restraints weight = 21742.429| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.32 r_work: 0.3100 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16468 Z= 0.142 Angle : 0.543 10.497 22391 Z= 0.277 Chirality : 0.041 0.208 2449 Planarity : 0.004 0.049 2759 Dihedral : 13.000 179.114 2602 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.67 % Favored : 94.22 % Rotamer: Outliers : 1.99 % Allowed : 13.77 % Favored : 84.24 % 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: 0.43 (0.19), residues: 1922 helix: 1.64 (0.20), residues: 707 sheet: -0.18 (0.31), residues: 250 loop : -0.58 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 137 TYR 0.013 0.001 TYR A1595 PHE 0.016 0.001 PHE A 731 TRP 0.016 0.001 TRP A 612 HIS 0.003 0.001 HIS A 727 Details of bonding type rmsd covalent geometry : bond 0.00324 (16452) covalent geometry : angle 0.53284 (22370) hydrogen bonds : bond 0.03486 ( 649) hydrogen bonds : angle 4.28220 ( 1890) metal coordination : bond 0.00582 ( 16) metal coordination : angle 3.42718 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 139 LYS cc_start: 0.8544 (mmtp) cc_final: 0.8016 (mttm) REVERT: D 166 ASP cc_start: 0.8781 (m-30) cc_final: 0.8408 (t0) REVERT: A 539 THR cc_start: 0.8775 (m) cc_final: 0.8531 (p) REVERT: A 776 ASN cc_start: 0.8017 (t0) cc_final: 0.7449 (p0) REVERT: A 901 ASN cc_start: 0.7675 (t0) cc_final: 0.6887 (t0) REVERT: A 925 TYR cc_start: 0.7905 (m-80) cc_final: 0.7508 (m-80) REVERT: A 1504 GLU cc_start: 0.7977 (pp20) cc_final: 0.7654 (pp20) REVERT: A 1589 GLU cc_start: 0.8117 (tp30) cc_final: 0.7765 (tp30) outliers start: 32 outliers final: 13 residues processed: 155 average time/residue: 0.5429 time to fit residues: 94.1122 Evaluate side-chains 140 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1565 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 89 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 173 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 699 HIS ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1506 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.127461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.093551 restraints weight = 21700.033| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.33 r_work: 0.3090 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16468 Z= 0.150 Angle : 0.550 8.636 22391 Z= 0.282 Chirality : 0.042 0.280 2449 Planarity : 0.004 0.046 2759 Dihedral : 13.012 179.581 2602 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.52 % Favored : 94.38 % Rotamer: Outliers : 1.61 % Allowed : 15.32 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.45 (0.19), residues: 1922 helix: 1.64 (0.20), residues: 707 sheet: -0.10 (0.32), residues: 242 loop : -0.58 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 35 TYR 0.012 0.001 TYR D 607 PHE 0.015 0.001 PHE A 731 TRP 0.016 0.001 TRP A 612 HIS 0.003 0.001 HIS D 404 Details of bonding type rmsd covalent geometry : bond 0.00344 (16452) covalent geometry : angle 0.53964 (22370) hydrogen bonds : bond 0.03498 ( 649) hydrogen bonds : angle 4.25343 ( 1890) metal coordination : bond 0.00611 ( 16) metal coordination : angle 3.48273 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 35 ARG cc_start: 0.8503 (mtp-110) cc_final: 0.8271 (mpt-90) REVERT: D 139 LYS cc_start: 0.8543 (mmtp) cc_final: 0.7964 (mttm) REVERT: D 166 ASP cc_start: 0.8816 (m-30) cc_final: 0.8431 (t0) REVERT: A 539 THR cc_start: 0.8785 (m) cc_final: 0.8538 (p) REVERT: A 776 ASN cc_start: 0.8037 (t0) cc_final: 0.7517 (p0) REVERT: A 821 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8628 (tttm) REVERT: A 901 ASN cc_start: 0.7667 (t0) cc_final: 0.6890 (t0) REVERT: A 925 TYR cc_start: 0.7933 (m-80) cc_final: 0.7533 (m-80) REVERT: A 985 LYS cc_start: 0.7665 (mmtt) cc_final: 0.7450 (mttm) REVERT: A 1504 GLU cc_start: 0.7933 (pp20) cc_final: 0.7666 (pp20) REVERT: A 1581 ARG cc_start: 0.7813 (ptm160) cc_final: 0.7152 (ttt180) REVERT: A 1589 GLU cc_start: 0.8146 (tp30) cc_final: 0.7778 (tp30) REVERT: A 1619 ILE cc_start: 0.7209 (mm) cc_final: 0.6938 (mm) outliers start: 26 outliers final: 12 residues processed: 147 average time/residue: 0.5305 time to fit residues: 87.6353 Evaluate side-chains 140 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1565 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 124 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 86 optimal weight: 0.3980 chunk 104 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 144 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 699 HIS ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1506 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.128373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.094616 restraints weight = 21623.927| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.32 r_work: 0.3109 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16468 Z= 0.128 Angle : 0.537 12.432 22391 Z= 0.274 Chirality : 0.041 0.232 2449 Planarity : 0.004 0.045 2759 Dihedral : 12.979 178.868 2602 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.52 % Favored : 94.43 % Rotamer: Outliers : 1.61 % Allowed : 16.07 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.50 (0.19), residues: 1922 helix: 1.69 (0.20), residues: 707 sheet: -0.06 (0.32), residues: 242 loop : -0.57 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 137 TYR 0.011 0.001 TYR D 607 PHE 0.013 0.001 PHE D 491 TRP 0.015 0.001 TRP A 612 HIS 0.003 0.001 HIS A 727 Details of bonding type rmsd covalent geometry : bond 0.00289 (16452) covalent geometry : angle 0.52736 (22370) hydrogen bonds : bond 0.03340 ( 649) hydrogen bonds : angle 4.18284 ( 1890) metal coordination : bond 0.00508 ( 16) metal coordination : angle 3.30283 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 35 ARG cc_start: 0.8547 (mtp-110) cc_final: 0.8298 (mpt-90) REVERT: D 139 LYS cc_start: 0.8574 (mmtp) cc_final: 0.8068 (mttm) REVERT: D 166 ASP cc_start: 0.8813 (m-30) cc_final: 0.8403 (t0) REVERT: A 6 MET cc_start: 0.7120 (mmp) cc_final: 0.6905 (mmp) REVERT: A 214 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8233 (mp0) REVERT: A 539 THR cc_start: 0.8785 (m) cc_final: 0.8525 (p) REVERT: A 776 ASN cc_start: 0.7998 (t0) cc_final: 0.7529 (p0) REVERT: A 901 ASN cc_start: 0.7653 (t0) cc_final: 0.6884 (t0) REVERT: A 925 TYR cc_start: 0.7911 (m-80) cc_final: 0.7498 (m-80) REVERT: A 985 LYS cc_start: 0.7664 (mmtt) cc_final: 0.7349 (mmtt) REVERT: A 1581 ARG cc_start: 0.7786 (ptm160) cc_final: 0.7138 (ttt180) REVERT: A 1589 GLU cc_start: 0.8137 (tp30) cc_final: 0.7764 (tp30) REVERT: A 1619 ILE cc_start: 0.7154 (mm) cc_final: 0.6870 (mm) outliers start: 26 outliers final: 14 residues processed: 147 average time/residue: 0.5407 time to fit residues: 88.9019 Evaluate side-chains 141 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 400 ASP Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1024 GLU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1565 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 169 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 178 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 184 optimal weight: 0.2980 chunk 114 optimal weight: 0.4980 chunk 96 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 183 HIS ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 699 HIS ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1506 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.128532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.094981 restraints weight = 21718.342| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.32 r_work: 0.3115 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16468 Z= 0.123 Angle : 0.530 11.442 22391 Z= 0.271 Chirality : 0.040 0.201 2449 Planarity : 0.004 0.044 2759 Dihedral : 12.952 178.878 2602 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.41 % Favored : 94.54 % Rotamer: Outliers : 1.49 % Allowed : 16.63 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.53 (0.19), residues: 1922 helix: 1.72 (0.20), residues: 707 sheet: -0.01 (0.32), residues: 242 loop : -0.56 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 697 TYR 0.011 0.001 TYR D 704 PHE 0.013 0.001 PHE D 491 TRP 0.015 0.001 TRP A 612 HIS 0.003 0.001 HIS A 727 Details of bonding type rmsd covalent geometry : bond 0.00278 (16452) covalent geometry : angle 0.52133 (22370) hydrogen bonds : bond 0.03269 ( 649) hydrogen bonds : angle 4.14074 ( 1890) metal coordination : bond 0.00473 ( 16) metal coordination : angle 3.20564 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 139 LYS cc_start: 0.8563 (mmtp) cc_final: 0.8095 (mttm) REVERT: D 166 ASP cc_start: 0.8817 (m-30) cc_final: 0.8399 (t0) REVERT: A 214 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8176 (mp0) REVERT: A 481 ARG cc_start: 0.8853 (ttp80) cc_final: 0.8631 (tmm160) REVERT: A 529 TYR cc_start: 0.8052 (m-10) cc_final: 0.7849 (m-10) REVERT: A 776 ASN cc_start: 0.8043 (t0) cc_final: 0.7597 (p0) REVERT: A 821 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8562 (tttm) REVERT: A 901 ASN cc_start: 0.7672 (t0) cc_final: 0.6933 (t0) REVERT: A 925 TYR cc_start: 0.7911 (m-80) cc_final: 0.7480 (m-80) REVERT: A 985 LYS cc_start: 0.7704 (mmtt) cc_final: 0.7295 (mttm) REVERT: A 1581 ARG cc_start: 0.7793 (ptm160) cc_final: 0.7271 (ttt180) REVERT: A 1589 GLU cc_start: 0.8166 (tp30) cc_final: 0.7822 (tp30) REVERT: A 1619 ILE cc_start: 0.7158 (mm) cc_final: 0.6870 (mm) outliers start: 24 outliers final: 12 residues processed: 145 average time/residue: 0.5248 time to fit residues: 85.4333 Evaluate side-chains 139 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 669 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1021 ILE Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1565 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 134 optimal weight: 4.9990 chunk 188 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 186 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 342 ASN ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 699 HIS ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1506 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.126378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.092479 restraints weight = 21706.755| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.32 r_work: 0.3071 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16468 Z= 0.176 Angle : 0.574 10.226 22391 Z= 0.291 Chirality : 0.042 0.199 2449 Planarity : 0.004 0.055 2759 Dihedral : 13.026 179.780 2602 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.83 % Favored : 94.12 % Rotamer: Outliers : 1.30 % Allowed : 17.00 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.45 (0.19), residues: 1922 helix: 1.66 (0.20), residues: 701 sheet: -0.09 (0.32), residues: 249 loop : -0.59 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 35 TYR 0.013 0.001 TYR D 607 PHE 0.014 0.001 PHE A 129 TRP 0.016 0.001 TRP A 612 HIS 0.004 0.001 HIS D 404 Details of bonding type rmsd covalent geometry : bond 0.00409 (16452) covalent geometry : angle 0.56313 (22370) hydrogen bonds : bond 0.03572 ( 649) hydrogen bonds : angle 4.26447 ( 1890) metal coordination : bond 0.00732 ( 16) metal coordination : angle 3.61344 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: D 35 ARG cc_start: 0.8578 (mtp-110) cc_final: 0.8342 (mpt-90) REVERT: D 139 LYS cc_start: 0.8559 (mmtp) cc_final: 0.8083 (mttm) REVERT: D 166 ASP cc_start: 0.8784 (m-30) cc_final: 0.8583 (m-30) REVERT: A 214 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8161 (mp0) REVERT: A 529 TYR cc_start: 0.8187 (m-10) cc_final: 0.7975 (m-10) REVERT: A 762 HIS cc_start: 0.8526 (m90) cc_final: 0.8196 (m90) REVERT: A 776 ASN cc_start: 0.8102 (t0) cc_final: 0.7648 (p0) REVERT: A 821 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8609 (tttm) REVERT: A 901 ASN cc_start: 0.7705 (t0) cc_final: 0.6757 (t0) REVERT: A 925 TYR cc_start: 0.8065 (m-80) cc_final: 0.7713 (m-80) REVERT: A 985 LYS cc_start: 0.7783 (mmtt) cc_final: 0.7566 (mmtt) REVERT: A 1581 ARG cc_start: 0.7804 (ptm160) cc_final: 0.7148 (ttt180) REVERT: A 1589 GLU cc_start: 0.8162 (tp30) cc_final: 0.7829 (tp30) REVERT: A 1619 ILE cc_start: 0.7264 (mm) cc_final: 0.6992 (mm) outliers start: 21 outliers final: 13 residues processed: 146 average time/residue: 0.5349 time to fit residues: 87.7272 Evaluate side-chains 140 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 669 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 1021 ILE Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1565 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 1 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 104 optimal weight: 0.1980 chunk 46 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 162 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.128382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.094817 restraints weight = 21694.916| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.32 r_work: 0.3113 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16468 Z= 0.123 Angle : 0.543 10.547 22391 Z= 0.278 Chirality : 0.041 0.210 2449 Planarity : 0.004 0.054 2759 Dihedral : 12.982 178.484 2602 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.52 % Favored : 94.43 % Rotamer: Outliers : 0.87 % Allowed : 17.93 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.54 (0.19), residues: 1922 helix: 1.77 (0.20), residues: 701 sheet: -0.07 (0.32), residues: 244 loop : -0.57 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 35 TYR 0.011 0.001 TYR D 704 PHE 0.013 0.001 PHE D 491 TRP 0.016 0.001 TRP A1487 HIS 0.003 0.001 HIS A 727 Details of bonding type rmsd covalent geometry : bond 0.00276 (16452) covalent geometry : angle 0.53393 (22370) hydrogen bonds : bond 0.03242 ( 649) hydrogen bonds : angle 4.15396 ( 1890) metal coordination : bond 0.00481 ( 16) metal coordination : angle 3.29878 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3844 Ramachandran restraints generated. 1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: D 35 ARG cc_start: 0.8585 (mtp-110) cc_final: 0.8352 (mpt-90) REVERT: D 139 LYS cc_start: 0.8510 (mmtp) cc_final: 0.8051 (mttm) REVERT: D 166 ASP cc_start: 0.8809 (m-30) cc_final: 0.8327 (t0) REVERT: A 6 MET cc_start: 0.7185 (mmm) cc_final: 0.6953 (mmp) REVERT: A 214 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8155 (mp0) REVERT: A 481 ARG cc_start: 0.8860 (ttp80) cc_final: 0.8618 (tmm160) REVERT: A 762 HIS cc_start: 0.8419 (m90) cc_final: 0.8188 (m90) REVERT: A 776 ASN cc_start: 0.8071 (t0) cc_final: 0.7591 (p0) REVERT: A 821 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8563 (tttm) REVERT: A 901 ASN cc_start: 0.7659 (t0) cc_final: 0.6923 (t0) REVERT: A 925 TYR cc_start: 0.7927 (m-80) cc_final: 0.7506 (m-80) REVERT: A 1581 ARG cc_start: 0.7775 (ptm160) cc_final: 0.7291 (ttt180) REVERT: A 1589 GLU cc_start: 0.8189 (tp30) cc_final: 0.7885 (tp30) REVERT: A 1619 ILE cc_start: 0.7166 (mm) cc_final: 0.6869 (mm) outliers start: 14 outliers final: 11 residues processed: 138 average time/residue: 0.5464 time to fit residues: 84.6478 Evaluate side-chains 134 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 669 THR Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1565 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 71 optimal weight: 0.3980 chunk 191 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 HIS ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1506 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.127420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.093764 restraints weight = 21743.986| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.31 r_work: 0.3092 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16468 Z= 0.148 Angle : 0.560 10.313 22391 Z= 0.284 Chirality : 0.041 0.224 2449 Planarity : 0.004 0.053 2759 Dihedral : 12.992 179.553 2602 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.67 % Favored : 94.28 % Rotamer: Outliers : 1.18 % Allowed : 17.74 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.19), residues: 1922 helix: 1.72 (0.20), residues: 701 sheet: -0.08 (0.32), residues: 244 loop : -0.59 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 35 TYR 0.014 0.001 TYR A 529 PHE 0.013 0.001 PHE A 659 TRP 0.017 0.001 TRP A1487 HIS 0.011 0.001 HIS D 210 Details of bonding type rmsd covalent geometry : bond 0.00342 (16452) covalent geometry : angle 0.55022 (22370) hydrogen bonds : bond 0.03375 ( 649) hydrogen bonds : angle 4.19266 ( 1890) metal coordination : bond 0.00565 ( 16) metal coordination : angle 3.36531 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5035.22 seconds wall clock time: 86 minutes 39.93 seconds (5199.93 seconds total)