Starting phenix.real_space_refine on Sat Sep 12 14:20:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7x8a_33056/09_2026/7x8a_33056.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x8a_33056/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7x8a_33056/09_2026/7x8a_33056.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7x8a_33056/09_2026/7x8a_33056.cif" model { file = "/net/cci-nas-00/data/ceres_data/7x8a_33056/09_2026/7x8a_33056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x8a_33056/09_2026/7x8a_33056.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x8a_33056/09_2026/7x8a_33056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x8a_33056/09_2026/7x8a_33056.map" } 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): 0.02s 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: 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: {'RNAv2': 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: 3.53, per 1000 atoms: 0.22 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: 1.54 Conformation dependent library (CDL) restraints added in 722.8 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: 2.12 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: 3.86 Time building geometry restraints manager: 2.03 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: 21734 1.61 - 3.22: 485 3.22 - 4.83: 122 4.83 - 6.44: 22 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=" O3' A C -2 " pdb=" C3' A C -2 " pdb=" C2' A C -2 " ideal model delta sigma weight residual 113.80 107.61 6.19 2.00e+00 2.50e-01 9.58e+00 ... (remaining 22365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 8785 17.91 - 35.83: 761 35.83 - 53.74: 133 53.74 - 71.65: 79 71.65 - 89.57: 35 Dihedral angle restraints: 9793 sinusoidal: 4204 harmonic: 5589 Sorted by residual: dihedral pdb=" C4' U C 5 " pdb=" C3' U C 5 " pdb=" C2' U C 5 " pdb=" C1' U C 5 " ideal model delta sinusoidal sigma weight residual 36.34 -37.29 73.63 1 3.10e+00 1.04e-01 7.17e+02 dihedral pdb=" C4' G C -18 " pdb=" C3' G C -18 " pdb=" C2' G C -18 " pdb=" C1' G C -18 " ideal model delta sinusoidal sigma weight residual 36.34 -37.06 73.40 1 3.10e+00 1.04e-01 7.14e+02 dihedral pdb=" C4' G C 11 " pdb=" C3' G C 11 " pdb=" C2' G C 11 " pdb=" C1' G C 11 " ideal model delta sinusoidal sigma weight residual 36.34 -36.59 72.93 1 3.10e+00 1.04e-01 7.06e+02 ... (remaining 9790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2104 0.063 - 0.126: 261 0.126 - 0.190: 8 0.190 - 0.253: 48 0.253 - 0.316: 28 Chirality restraints: 2449 Sorted by residual: chirality pdb=" C3' A C -2 " pdb=" C4' A C -2 " pdb=" O3' A C -2 " pdb=" C2' A C -2 " both_signs ideal model delta sigma weight residual False -2.50 -2.81 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" C2' G C -18 " pdb=" C3' G C -18 " pdb=" O2' G C -18 " pdb=" C1' G C -18 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" C3' G C 11 " pdb=" C4' G C 11 " pdb=" O3' G C 11 " pdb=" C2' G C 11 " both_signs ideal model delta sigma weight residual False -2.50 -2.79 0.29 2.00e-01 2.50e+01 2.14e+00 ... (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: 2.700 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.340 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 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= 0.142 Angle : 0.626 8.261 22391 Z= 0.305 Chirality : 0.059 0.316 2449 Planarity : 0.004 0.055 2759 Dihedral : 15.424 89.568 6199 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/Z covalent geometry : bond 0.00322 / 0.14 (16452) covalent geometry : angle 0.61656 / 0.30 (22370) hydrogen bonds : bond 0.18885 / 12.76 ( 649) hydrogen bonds : angle 6.92633 / 4.99 ( 1890) metal coordination : bond 0.00564 / 0.36 ( 16) metal coordination : angle 3.66776 / 2.32 ( 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 : 0.524 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: 0.6871 time to fit residues: 140.1420 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 : 0.528 ------------------------------------------------------------------------------- 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: 2.9990 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: 2.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3759 r_free = 0.3759 target = 0.132180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.099430 restraints weight = 21538.380| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.32 r_work: 0.3181 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16468 Z= 0.161 Angle : 0.865 16.626 22391 Z= 0.384 Chirality : 0.081 1.069 2449 Planarity : 0.004 0.047 2759 Dihedral : 11.518 139.126 2488 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.98 % Favored : 93.91 % Rotamer: Outliers : 1.18 % Allowed : 8.93 % Favored : 89.89 % 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: 0.38 (0.20), residues: 1922 helix: 1.55 (0.20), residues: 703 sheet: -0.23 (0.32), residues: 259 loop : -0.56 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 64 TYR 0.011 0.001 TYR A1481 PHE 0.017 0.001 PHE A 731 TRP 0.015 0.001 TRP A 612 HIS 0.003 0.001 HIS D 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (16452) covalent geometry : angle 0.85760 / 0.38 (22370) hydrogen bonds : bond 0.04135 / 2.69 ( 649) hydrogen bonds : angle 4.87424 / 3.56 ( 1890) metal coordination : bond 0.00521 / 0.34 ( 16) metal coordination : angle 3.76024 / 2.41 ( 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 167 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: D 35 ARG cc_start: 0.8632 (mtp-110) cc_final: 0.8419 (mpt-90) REVERT: D 136 ASP cc_start: 0.8525 (t0) cc_final: 0.8323 (t0) REVERT: D 139 LYS cc_start: 0.8616 (mttp) cc_final: 0.8293 (mttm) REVERT: A 337 THR cc_start: 0.8650 (m) cc_final: 0.8297 (t) REVERT: A 539 THR cc_start: 0.8805 (m) cc_final: 0.8556 (p) REVERT: A 901 ASN cc_start: 0.7702 (t0) cc_final: 0.6956 (t0) REVERT: A 925 TYR cc_start: 0.7854 (m-80) cc_final: 0.7639 (m-80) REVERT: A 1504 GLU cc_start: 0.7948 (pp20) cc_final: 0.7726 (pp20) REVERT: A 1589 GLU cc_start: 0.8026 (tp30) cc_final: 0.7758 (tp30) outliers start: 19 outliers final: 3 residues processed: 157 average time/residue: 0.5827 time to fit residues: 102.3019 Evaluate side-chains 125 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 163 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 167 optimal weight: 8.9990 chunk 131 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.129325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.096042 restraints weight = 21840.778| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.33 r_work: 0.3128 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16468 Z= 0.192 Angle : 0.766 15.276 22391 Z= 0.352 Chirality : 0.069 0.784 2449 Planarity : 0.004 0.066 2759 Dihedral : 12.091 150.196 2488 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.78 % Favored : 94.07 % Rotamer: Outliers : 1.43 % Allowed : 11.66 % Favored : 86.91 % 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: 0.27 (0.19), residues: 1922 helix: 1.48 (0.20), residues: 703 sheet: -0.32 (0.31), residues: 254 loop : -0.63 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 476 TYR 0.018 0.001 TYR A1595 PHE 0.022 0.002 PHE A 731 TRP 0.018 0.001 TRP A 612 HIS 0.004 0.001 HIS D 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (16452) covalent geometry : angle 0.75722 / 0.35 (22370) hydrogen bonds : bond 0.04057 / 2.62 ( 649) hydrogen bonds : angle 4.65284 / 3.39 ( 1890) metal coordination : bond 0.00637 / 0.42 ( 16) metal coordination : angle 3.90894 / 2.19 ( 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 160 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: D 136 ASP cc_start: 0.8504 (t0) cc_final: 0.8213 (t0) REVERT: D 139 LYS cc_start: 0.8603 (mttp) cc_final: 0.8202 (mttm) REVERT: D 665 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7749 (ptp-170) REVERT: A 453 ASN cc_start: 0.7583 (m-40) cc_final: 0.7372 (m-40) REVERT: A 539 THR cc_start: 0.8767 (m) cc_final: 0.8561 (p) REVERT: A 925 TYR cc_start: 0.7875 (m-80) cc_final: 0.7499 (m-80) REVERT: A 1589 GLU cc_start: 0.8118 (tp30) cc_final: 0.7782 (tp30) outliers start: 23 outliers final: 11 residues processed: 150 average time/residue: 0.6477 time to fit residues: 107.9585 Evaluate side-chains 133 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 665 ARG Chi-restraints excluded: chain D residue 710 ARG Chi-restraints excluded: chain A residue 59 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 996 LEU Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1565 ASP 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: 0.5980 chunk 160 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 154 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3749 r_free = 0.3749 target = 0.131323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.098437 restraints weight = 21460.621| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.31 r_work: 0.3166 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16468 Z= 0.147 Angle : 0.701 13.583 22391 Z= 0.322 Chirality : 0.062 0.617 2449 Planarity : 0.004 0.055 2759 Dihedral : 11.994 152.182 2488 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.88 % Favored : 94.02 % Rotamer: Outliers : 1.80 % Allowed : 12.90 % Favored : 85.30 % 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: 0.33 (0.19), residues: 1922 helix: 1.57 (0.20), residues: 706 sheet: -0.33 (0.31), residues: 250 loop : -0.62 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 476 TYR 0.011 0.001 TYR D 607 PHE 0.024 0.001 PHE A1520 TRP 0.016 0.001 TRP A 612 HIS 0.003 0.001 HIS A 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (16452) covalent geometry : angle 0.69266 / 0.32 (22370) hydrogen bonds : bond 0.03562 / 2.29 ( 649) hydrogen bonds : angle 4.38107 / 3.19 ( 1890) metal coordination : bond 0.00624 / 0.41 ( 16) metal coordination : angle 3.52534 / 2.03 ( 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 165 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 35 ARG cc_start: 0.8581 (mtp-110) cc_final: 0.8360 (mpt-90) REVERT: D 665 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7695 (ptp-170) REVERT: A 453 ASN cc_start: 0.7554 (m-40) cc_final: 0.7332 (m-40) REVERT: A 901 ASN cc_start: 0.7687 (t0) cc_final: 0.6911 (t0) REVERT: A 925 TYR cc_start: 0.7916 (m-80) cc_final: 0.7529 (m-80) REVERT: A 1581 ARG cc_start: 0.7677 (ptm160) cc_final: 0.7305 (ttt180) REVERT: A 1589 GLU cc_start: 0.8069 (tp30) cc_final: 0.7757 (tp30) outliers start: 29 outliers final: 11 residues processed: 151 average time/residue: 0.5637 time to fit residues: 95.8226 Evaluate side-chains 131 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain D residue 665 ARG Chi-restraints excluded: chain D residue 710 ARG Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 170 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 996 LEU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1509 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 131 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 129 optimal weight: 0.5980 chunk 144 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 183 HIS A 179 ASN A1506 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.132771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.100029 restraints weight = 21550.896| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.32 r_work: 0.3193 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16468 Z= 0.127 Angle : 0.658 12.031 22391 Z= 0.305 Chirality : 0.058 0.587 2449 Planarity : 0.004 0.049 2759 Dihedral : 11.997 153.951 2488 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.41 % Favored : 94.48 % Rotamer: Outliers : 2.11 % Allowed : 14.08 % Favored : 83.81 % 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: 0.43 (0.19), residues: 1922 helix: 1.68 (0.20), residues: 706 sheet: -0.30 (0.31), residues: 250 loop : -0.59 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 137 TYR 0.019 0.001 TYR A1595 PHE 0.014 0.001 PHE A 731 TRP 0.015 0.001 TRP A 612 HIS 0.003 0.001 HIS A 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (16452) covalent geometry : angle 0.65040 / 0.30 (22370) hydrogen bonds : bond 0.03340 / 2.13 ( 649) hydrogen bonds : angle 4.19008 / 3.05 ( 1890) metal coordination : bond 0.00486 / 0.31 ( 16) metal coordination : angle 3.25429 / 1.91 ( 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: 34 poor density : 134 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 139 LYS cc_start: 0.8593 (mttp) cc_final: 0.8079 (mttm) REVERT: D 665 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7695 (ptp-170) REVERT: A 776 ASN cc_start: 0.7946 (t0) cc_final: 0.7420 (p0) REVERT: A 821 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8571 (tttm) REVERT: A 901 ASN cc_start: 0.7623 (t0) cc_final: 0.6877 (t0) REVERT: A 925 TYR cc_start: 0.7889 (m-80) cc_final: 0.7470 (m-80) REVERT: A 969 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8438 (p) REVERT: A 1581 ARG cc_start: 0.7639 (ptm160) cc_final: 0.7350 (ttt180) REVERT: A 1589 GLU cc_start: 0.8093 (tp30) cc_final: 0.7783 (tp30) outliers start: 34 outliers final: 11 residues processed: 156 average time/residue: 0.5528 time to fit residues: 97.4018 Evaluate side-chains 137 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 665 ARG Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 545 LEU 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 950 LEU Chi-restraints excluded: chain A residue 969 THR Chi-restraints excluded: chain A residue 996 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: 1.9990 chunk 132 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 173 optimal weight: 0.0870 chunk 110 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3734 r_free = 0.3734 target = 0.130073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.096929 restraints weight = 21621.896| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.31 r_work: 0.3144 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16468 Z= 0.175 Angle : 0.693 14.074 22391 Z= 0.323 Chirality : 0.060 0.588 2449 Planarity : 0.004 0.048 2759 Dihedral : 12.107 153.229 2488 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.52 % Favored : 94.38 % Rotamer: Outliers : 1.86 % Allowed : 15.14 % Favored : 83.00 % 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: 0.36 (0.19), residues: 1922 helix: 1.60 (0.20), residues: 706 sheet: -0.31 (0.32), residues: 244 loop : -0.61 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 35 TYR 0.013 0.001 TYR D 607 PHE 0.014 0.001 PHE A 731 TRP 0.016 0.001 TRP A 612 HIS 0.004 0.001 HIS D 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (16452) covalent geometry : angle 0.68517 / 0.32 (22370) hydrogen bonds : bond 0.03580 / 2.30 ( 649) hydrogen bonds : angle 4.28392 / 3.11 ( 1890) metal coordination : bond 0.00677 / 0.43 ( 16) metal coordination : angle 3.56301 / 2.02 ( 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 154 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 35 ARG cc_start: 0.8526 (mtp-110) cc_final: 0.8293 (mpt-90) REVERT: D 139 LYS cc_start: 0.8492 (mttp) cc_final: 0.7929 (mttm) REVERT: D 665 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7765 (ptp-170) REVERT: A 214 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8176 (mp0) REVERT: A 454 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7951 (pt0) REVERT: A 776 ASN cc_start: 0.8021 (t0) cc_final: 0.7528 (p0) REVERT: A 821 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8635 (tttm) REVERT: A 901 ASN cc_start: 0.7648 (t0) cc_final: 0.6872 (t0) REVERT: A 925 TYR cc_start: 0.7991 (m-80) cc_final: 0.7590 (m-80) REVERT: A 985 LYS cc_start: 0.7662 (mmtt) cc_final: 0.7373 (mttm) REVERT: A 1581 ARG cc_start: 0.7707 (ptm160) cc_final: 0.7319 (ttt180) REVERT: A 1589 GLU cc_start: 0.8150 (tp30) cc_final: 0.7825 (tp30) outliers start: 30 outliers final: 14 residues processed: 145 average time/residue: 0.5808 time to fit residues: 95.0811 Evaluate side-chains 137 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 665 ARG 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 658 LEU 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 950 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 124 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 104 optimal weight: 0.0970 chunk 74 optimal weight: 3.9990 chunk 149 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 144 optimal weight: 0.4980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 699 HIS A1506 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.132506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.099891 restraints weight = 21511.755| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.30 r_work: 0.3190 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16468 Z= 0.126 Angle : 0.652 12.469 22391 Z= 0.303 Chirality : 0.056 0.533 2449 Planarity : 0.004 0.045 2759 Dihedral : 12.024 154.334 2488 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.52 % Favored : 94.43 % Rotamer: Outliers : 1.43 % Allowed : 16.25 % Favored : 82.32 % 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: 0.45 (0.19), residues: 1922 helix: 1.71 (0.20), residues: 706 sheet: -0.27 (0.31), residues: 252 loop : -0.58 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 137 TYR 0.011 0.001 TYR D 704 PHE 0.013 0.001 PHE D 491 TRP 0.014 0.001 TRP A 612 HIS 0.003 0.001 HIS A 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (16452) covalent geometry : angle 0.64475 / 0.30 (22370) hydrogen bonds : bond 0.03273 / 2.10 ( 649) hydrogen bonds : angle 4.16420 / 3.02 ( 1890) metal coordination : bond 0.00486 / 0.31 ( 16) metal coordination : angle 3.25057 / 1.92 ( 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 158 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 35 ARG cc_start: 0.8560 (mtp-110) cc_final: 0.8289 (mpt-90) REVERT: D 139 LYS cc_start: 0.8541 (mttp) cc_final: 0.8040 (mttm) REVERT: D 665 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7691 (ptp-170) REVERT: A 6 MET cc_start: 0.7159 (mmm) cc_final: 0.6926 (mmp) REVERT: A 214 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8165 (mp0) REVERT: A 454 GLU cc_start: 0.8230 (mt-10) cc_final: 0.8003 (pt0) REVERT: A 776 ASN cc_start: 0.7964 (t0) cc_final: 0.7525 (p0) REVERT: A 821 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8569 (tttm) REVERT: A 901 ASN cc_start: 0.7665 (t0) cc_final: 0.6934 (t0) REVERT: A 925 TYR cc_start: 0.7887 (m-80) cc_final: 0.7471 (m-80) REVERT: A 985 LYS cc_start: 0.7668 (mmtt) cc_final: 0.7407 (mttm) REVERT: A 1581 ARG cc_start: 0.7655 (ptm160) cc_final: 0.7404 (ttt180) REVERT: A 1589 GLU cc_start: 0.8148 (tp30) cc_final: 0.7809 (tp30) REVERT: A 1619 ILE cc_start: 0.7182 (mm) cc_final: 0.6897 (mm) outliers start: 23 outliers final: 10 residues processed: 150 average time/residue: 0.5908 time to fit residues: 99.3942 Evaluate side-chains 140 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 665 ARG 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 684 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 169 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 184 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 699 HIS A 39 GLN ** 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 = 0.3736 r_free = 0.3736 target = 0.130308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.097370 restraints weight = 21578.900| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.31 r_work: 0.3151 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16468 Z= 0.165 Angle : 0.683 13.578 22391 Z= 0.318 Chirality : 0.058 0.570 2449 Planarity : 0.004 0.044 2759 Dihedral : 12.088 154.206 2488 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.41 % Favored : 94.54 % Rotamer: Outliers : 1.49 % Allowed : 16.69 % Favored : 81.82 % 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: 0.39 (0.19), residues: 1922 helix: 1.63 (0.20), residues: 705 sheet: -0.22 (0.32), residues: 244 loop : -0.62 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 263 TYR 0.012 0.001 TYR D 607 PHE 0.012 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/Z covalent geometry : bond 0.00379 / 0.16 (16452) covalent geometry : angle 0.67541 / 0.32 (22370) hydrogen bonds : bond 0.03487 / 2.24 ( 649) hydrogen bonds : angle 4.23840 / 3.07 ( 1890) metal coordination : bond 0.00633 / 0.40 ( 16) metal coordination : angle 3.48305 / 1.99 ( 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 152 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 139 LYS cc_start: 0.8525 (mttp) cc_final: 0.8039 (mttm) REVERT: D 665 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7724 (ptp-170) REVERT: A 6 MET cc_start: 0.7193 (mmm) cc_final: 0.6991 (mmp) REVERT: A 214 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8195 (mp0) REVERT: A 454 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7996 (pt0) REVERT: A 776 ASN cc_start: 0.8085 (t0) cc_final: 0.7638 (p0) REVERT: A 821 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8633 (tttm) REVERT: A 901 ASN cc_start: 0.7623 (t0) cc_final: 0.6856 (t0) REVERT: A 925 TYR cc_start: 0.7975 (m-80) cc_final: 0.7627 (m-80) REVERT: A 1581 ARG cc_start: 0.7721 (ptm160) cc_final: 0.7422 (ttt180) REVERT: A 1589 GLU cc_start: 0.8191 (tp30) cc_final: 0.7865 (tp30) REVERT: A 1619 ILE cc_start: 0.7225 (mm) cc_final: 0.6937 (mm) outliers start: 24 outliers final: 13 residues processed: 144 average time/residue: 0.6081 time to fit residues: 98.2839 Evaluate side-chains 135 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 665 ARG 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 658 LEU 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 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: 0.7980 chunk 188 optimal weight: 0.2980 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 175 optimal weight: 6.9990 chunk 179 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 186 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 74 optimal weight: 0.0980 chunk 123 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 699 HIS ** A 786 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 = 0.3773 r_free = 0.3773 target = 0.133288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.100847 restraints weight = 21498.150| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.30 r_work: 0.3206 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16468 Z= 0.119 Angle : 0.649 11.130 22391 Z= 0.303 Chirality : 0.055 0.477 2449 Planarity : 0.004 0.050 2759 Dihedral : 11.983 155.531 2488 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.36 % Favored : 94.59 % Rotamer: Outliers : 1.30 % Allowed : 17.18 % Favored : 81.51 % 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: 0.51 (0.19), residues: 1922 helix: 1.78 (0.20), residues: 700 sheet: -0.19 (0.32), residues: 244 loop : -0.56 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 35 TYR 0.012 0.001 TYR D 607 PHE 0.013 0.001 PHE D 491 TRP 0.014 0.001 TRP A 612 HIS 0.003 0.001 HIS A1621 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (16452) covalent geometry : angle 0.64172 / 0.30 (22370) hydrogen bonds : bond 0.03160 / 2.02 ( 649) hydrogen bonds : angle 4.11747 / 2.98 ( 1890) metal coordination : bond 0.00461 / 0.29 ( 16) metal coordination : angle 3.14074 / 1.87 ( 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 154 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: D 35 ARG cc_start: 0.8594 (mtp-110) cc_final: 0.8306 (mpt-90) REVERT: D 139 LYS cc_start: 0.8543 (mttp) cc_final: 0.8095 (mttm) REVERT: A 6 MET cc_start: 0.7149 (mmm) cc_final: 0.6886 (mmp) REVERT: A 214 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8168 (mp0) REVERT: A 454 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7935 (pt0) REVERT: A 762 HIS cc_start: 0.8375 (m90) cc_final: 0.8170 (m90) REVERT: A 776 ASN cc_start: 0.8022 (t0) cc_final: 0.7602 (p0) REVERT: A 808 TYR cc_start: 0.8636 (t80) cc_final: 0.8226 (t80) REVERT: A 901 ASN cc_start: 0.7630 (t0) cc_final: 0.6894 (t0) REVERT: A 925 TYR cc_start: 0.7854 (m-80) cc_final: 0.7434 (m-80) REVERT: A 985 LYS cc_start: 0.7320 (mttm) cc_final: 0.7043 (mmtp) REVERT: A 1581 ARG cc_start: 0.7620 (ptm160) cc_final: 0.7378 (ttt180) REVERT: A 1589 GLU cc_start: 0.8165 (tp30) cc_final: 0.7886 (tp30) REVERT: A 1619 ILE cc_start: 0.7180 (mm) cc_final: 0.6890 (mm) outliers start: 21 outliers final: 10 residues processed: 148 average time/residue: 0.5681 time to fit residues: 94.8341 Evaluate side-chains 136 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 170 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 383 ILE 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 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: 4.9990 chunk 120 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 46 optimal weight: 0.0010 chunk 87 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 134 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 HIS ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 699 HIS ** A 786 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 = 0.3765 r_free = 0.3765 target = 0.132567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.099941 restraints weight = 21505.962| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.30 r_work: 0.3191 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16468 Z= 0.133 Angle : 0.658 11.655 22391 Z= 0.307 Chirality : 0.056 0.513 2449 Planarity : 0.004 0.055 2759 Dihedral : 11.991 155.696 2488 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.20 % Favored : 94.75 % Rotamer: Outliers : 1.12 % Allowed : 17.87 % Favored : 81.02 % 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: 0.52 (0.19), residues: 1922 helix: 1.80 (0.20), residues: 700 sheet: -0.16 (0.32), residues: 244 loop : -0.58 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 35 TYR 0.012 0.001 TYR D 607 PHE 0.012 0.001 PHE D 491 TRP 0.016 0.001 TRP A1487 HIS 0.012 0.001 HIS D 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (16452) covalent geometry : angle 0.65101 / 0.31 (22370) hydrogen bonds : bond 0.03223 / 2.07 ( 649) hydrogen bonds : angle 4.12491 / 2.98 ( 1890) metal coordination : bond 0.00478 / 0.30 ( 16) metal coordination : angle 3.20001 / 1.87 ( 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 149 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 35 ARG cc_start: 0.8612 (mtp-110) cc_final: 0.8349 (mpt-90) REVERT: D 139 LYS cc_start: 0.8552 (mttp) cc_final: 0.8098 (mttm) REVERT: D 210 HIS cc_start: 0.8125 (OUTLIER) cc_final: 0.7889 (t-90) REVERT: D 278 TRP cc_start: 0.8707 (OUTLIER) cc_final: 0.8436 (p-90) REVERT: D 327 ARG cc_start: 0.7744 (ptm-80) cc_final: 0.7374 (tmm-80) REVERT: A 214 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8179 (mp0) REVERT: A 454 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7978 (pt0) REVERT: A 776 ASN cc_start: 0.8004 (t0) cc_final: 0.7585 (p0) REVERT: A 808 TYR cc_start: 0.8729 (t80) cc_final: 0.8209 (t80) REVERT: A 821 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8562 (tttm) REVERT: A 901 ASN cc_start: 0.7638 (t0) cc_final: 0.6913 (t0) REVERT: A 925 TYR cc_start: 0.7875 (m-80) cc_final: 0.7455 (m-80) REVERT: A 985 LYS cc_start: 0.7353 (mttm) cc_final: 0.7057 (mmtp) REVERT: A 1581 ARG cc_start: 0.7625 (ptm160) cc_final: 0.7408 (ttt180) REVERT: A 1589 GLU cc_start: 0.8192 (tp30) cc_final: 0.7913 (tp30) REVERT: A 1619 ILE cc_start: 0.7197 (mm) cc_final: 0.6906 (mm) outliers start: 18 outliers final: 10 residues processed: 140 average time/residue: 0.5923 time to fit residues: 93.3707 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 : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 210 HIS Chi-restraints excluded: chain D residue 278 TRP Chi-restraints excluded: chain D residue 585 HIS 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 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: 0.9990 chunk 191 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 174 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 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 = 0.3759 r_free = 0.3759 target = 0.132177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.099393 restraints weight = 21529.861| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.31 r_work: 0.3183 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16468 Z= 0.140 Angle : 0.668 12.091 22391 Z= 0.312 Chirality : 0.056 0.527 2449 Planarity : 0.004 0.053 2759 Dihedral : 12.017 155.875 2488 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.67 % Favored : 94.28 % Rotamer: Outliers : 1.30 % Allowed : 17.56 % Favored : 81.14 % 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: 0.50 (0.19), residues: 1922 helix: 1.77 (0.20), residues: 700 sheet: -0.15 (0.32), residues: 244 loop : -0.58 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 35 TYR 0.012 0.001 TYR D 607 PHE 0.012 0.001 PHE D 491 TRP 0.017 0.001 TRP A1487 HIS 0.012 0.001 HIS D 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (16452) covalent geometry : angle 0.66097 / 0.31 (22370) hydrogen bonds : bond 0.03263 / 2.10 ( 649) hydrogen bonds : angle 4.13643 / 2.99 ( 1890) metal coordination : bond 0.00505 / 0.32 ( 16) metal coordination : angle 3.23912 / 1.88 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5657.23 seconds wall clock time: 97 minutes 25.27 seconds (5845.27 seconds total)