Starting phenix.real_space_refine on Fri Sep 27 15:15:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8a_33056/09_2024/7x8a_33056.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8a_33056/09_2024/7x8a_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8a_33056/09_2024/7x8a_33056.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8a_33056/09_2024/7x8a_33056.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8a_33056/09_2024/7x8a_33056.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8a_33056/09_2024/7x8a_33056.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLN:plan1': 3, 'GLU:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4} 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: {'GLN:plan1': 2, 'HIS:plan': 3, 'ASN:plan1': 9, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 4} 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: 9.08, per 1000 atoms: 0.57 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: 3.81 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 5.66 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: 6.82 Time building geometry restraints manager: 4.50 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: 1.400 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: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 43.670 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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:10.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.000 ------------------------------------------------------------------------------- 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 16452 Z= 0.206 Angle : 0.531 8.054 22370 Z= 0.279 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.018 0.001 TRP D 278 HIS 0.004 0.001 HIS D 215 PHE 0.026 0.001 PHE A 731 TYR 0.023 0.001 TYR A1595 ARG 0.005 0.000 ARG A 697 *********************** 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 fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.901 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: 1.3918 time to fit residues: 284.3725 Evaluate side-chains 125 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.0670 chunk 148 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 153 optimal weight: 0.2980 chunk 59 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16452 Z= 0.183 Angle : 0.544 7.985 22370 Z= 0.287 Chirality : 0.041 0.186 2449 Planarity : 0.004 0.047 2759 Dihedral : 13.013 178.719 2602 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.83 % Favored : 94.07 % Rotamer: Outliers : 1.12 % Allowed : 8.56 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.20), residues: 1922 helix: 1.59 (0.20), residues: 703 sheet: -0.19 (0.33), residues: 244 loop : -0.54 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 612 HIS 0.003 0.001 HIS A 924 PHE 0.018 0.001 PHE A 731 TYR 0.011 0.001 TYR D 607 ARG 0.006 0.000 ARG D 35 *********************** 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 fitting. rotamer outliers: 18 poor density : 149 time to evaluate : 1.866 Fit side-chains revert: symmetry clash REVERT: D 139 LYS cc_start: 0.8516 (mttp) cc_final: 0.8292 (mttm) REVERT: A 677 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7532 (mp0) REVERT: A 901 ASN cc_start: 0.7715 (t0) cc_final: 0.7214 (t0) REVERT: A 959 GLU cc_start: 0.8448 (tt0) cc_final: 0.8117 (tt0) outliers start: 18 outliers final: 3 residues processed: 158 average time/residue: 1.2021 time to fit residues: 212.6069 Evaluate side-chains 123 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 119 time to evaluate : 1.806 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.3980 chunk 55 optimal weight: 0.4980 chunk 148 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 49 optimal weight: 20.0000 chunk 178 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 215 HIS A 7 ASN ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1506 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16452 Z= 0.294 Angle : 0.574 7.677 22370 Z= 0.299 Chirality : 0.043 0.199 2449 Planarity : 0.004 0.064 2759 Dihedral : 13.076 179.252 2602 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.88 % Favored : 93.96 % Rotamer: Outliers : 1.43 % Allowed : 11.35 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.19), residues: 1922 helix: 1.47 (0.20), residues: 703 sheet: -0.31 (0.31), residues: 254 loop : -0.59 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 612 HIS 0.004 0.001 HIS D 404 PHE 0.024 0.002 PHE A 129 TYR 0.020 0.001 TYR A1595 ARG 0.008 0.000 ARG D 35 *********************** 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 156 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 133 time to evaluate : 1.817 Fit side-chains revert: symmetry clash REVERT: D 139 LYS cc_start: 0.8515 (mttp) cc_final: 0.8294 (mttm) REVERT: D 665 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7598 (ptp-170) REVERT: A 901 ASN cc_start: 0.7708 (t0) cc_final: 0.7088 (t0) outliers start: 23 outliers final: 9 residues processed: 146 average time/residue: 1.2957 time to fit residues: 210.9243 Evaluate side-chains 127 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 1.826 ------------------------------------------------------------------------------- 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 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 176 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 92 optimal weight: 0.0050 chunk 19 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 178 optimal weight: 0.9990 chunk 189 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 169 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16452 Z= 0.173 Angle : 0.528 11.070 22370 Z= 0.275 Chirality : 0.041 0.213 2449 Planarity : 0.004 0.054 2759 Dihedral : 13.008 178.286 2602 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.78 % Favored : 94.12 % Rotamer: Outliers : 1.49 % Allowed : 13.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 1922 helix: 1.60 (0.20), residues: 706 sheet: -0.16 (0.31), residues: 252 loop : -0.57 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 612 HIS 0.003 0.001 HIS A1621 PHE 0.022 0.001 PHE A1520 TYR 0.010 0.001 TYR D 607 ARG 0.007 0.000 ARG D 137 *********************** 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 155 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 139 LYS cc_start: 0.8488 (mttp) cc_final: 0.8253 (mttm) REVERT: A 901 ASN cc_start: 0.7720 (t0) cc_final: 0.7202 (t0) outliers start: 24 outliers final: 4 residues processed: 145 average time/residue: 1.1060 time to fit residues: 181.7573 Evaluate side-chains 125 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 712 ASN Chi-restraints excluded: chain A residue 996 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 141 optimal weight: 0.5980 chunk 78 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 chunk 130 optimal weight: 0.0060 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 0.0020 chunk 170 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.1208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 924 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16452 Z= 0.248 Angle : 0.550 10.559 22370 Z= 0.286 Chirality : 0.042 0.212 2449 Planarity : 0.004 0.049 2759 Dihedral : 13.029 179.876 2602 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.78 % Favored : 94.12 % Rotamer: Outliers : 1.92 % Allowed : 14.33 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.19), residues: 1922 helix: 1.56 (0.20), residues: 707 sheet: -0.26 (0.31), residues: 252 loop : -0.59 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 612 HIS 0.004 0.001 HIS D 404 PHE 0.017 0.001 PHE A 731 TYR 0.014 0.001 TYR A1595 ARG 0.010 0.000 ARG D 35 *********************** 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 160 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 129 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 139 LYS cc_start: 0.8478 (mttp) cc_final: 0.8215 (mttm) REVERT: D 710 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8300 (ptt180) REVERT: A 821 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8294 (tttm) REVERT: A 901 ASN cc_start: 0.7721 (t0) cc_final: 0.7193 (t0) REVERT: A 969 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8672 (p) outliers start: 31 outliers final: 12 residues processed: 148 average time/residue: 1.1565 time to fit residues: 192.7796 Evaluate side-chains 137 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 710 ARG Chi-restraints excluded: chain A residue 11 GLU 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 950 LEU Chi-restraints excluded: chain A residue 969 THR 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 63 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 111 optimal weight: 0.5980 chunk 46 optimal weight: 0.2980 chunk 189 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 99 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 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 699 HIS A1506 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16452 Z= 0.169 Angle : 0.517 8.349 22370 Z= 0.271 Chirality : 0.041 0.268 2449 Planarity : 0.004 0.047 2759 Dihedral : 12.972 178.438 2602 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.62 % Favored : 94.28 % Rotamer: Outliers : 1.99 % Allowed : 15.32 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.19), residues: 1922 helix: 1.66 (0.20), residues: 707 sheet: -0.14 (0.31), residues: 250 loop : -0.55 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 612 HIS 0.003 0.001 HIS A1621 PHE 0.013 0.001 PHE D 491 TYR 0.011 0.001 TYR D 704 ARG 0.008 0.000 ARG A1452 *********************** 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 161 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 129 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 776 ASN cc_start: 0.7450 (t0) cc_final: 0.7188 (p0) REVERT: A 901 ASN cc_start: 0.7683 (t0) cc_final: 0.7173 (t0) REVERT: A 1581 ARG cc_start: 0.7679 (ptm160) cc_final: 0.7192 (ttt180) REVERT: A 1619 ILE cc_start: 0.7520 (mm) cc_final: 0.7248 (mm) outliers start: 32 outliers final: 12 residues processed: 150 average time/residue: 1.1405 time to fit residues: 193.6522 Evaluate side-chains 135 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 170 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 950 LEU 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 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 182 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 138 optimal weight: 0.4980 chunk 107 optimal weight: 0.0770 chunk 159 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- 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 A1506 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16452 Z= 0.176 Angle : 0.529 12.213 22370 Z= 0.273 Chirality : 0.040 0.210 2449 Planarity : 0.004 0.046 2759 Dihedral : 12.948 178.871 2602 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.41 % Favored : 94.54 % Rotamer: Outliers : 1.24 % Allowed : 16.69 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.19), residues: 1922 helix: 1.70 (0.20), residues: 707 sheet: -0.09 (0.31), residues: 250 loop : -0.55 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 612 HIS 0.003 0.001 HIS A 984 PHE 0.013 0.001 PHE D 491 TYR 0.011 0.001 TYR D 607 ARG 0.012 0.000 ARG D 35 *********************** 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 151 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 139 LYS cc_start: 0.8399 (mmtp) cc_final: 0.8028 (mttm) REVERT: A 776 ASN cc_start: 0.7459 (t0) cc_final: 0.7255 (p0) REVERT: A 901 ASN cc_start: 0.7710 (t0) cc_final: 0.7205 (t0) REVERT: A 1581 ARG cc_start: 0.7639 (ptm160) cc_final: 0.7089 (ttt180) REVERT: A 1619 ILE cc_start: 0.7530 (mm) cc_final: 0.7254 (mm) outliers start: 20 outliers final: 10 residues processed: 142 average time/residue: 1.1219 time to fit residues: 180.7148 Evaluate side-chains 128 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 390 LEU 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 996 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 116 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 112 optimal weight: 0.0770 chunk 56 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 147 ASN ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16452 Z= 0.218 Angle : 0.540 10.793 22370 Z= 0.279 Chirality : 0.041 0.197 2449 Planarity : 0.004 0.045 2759 Dihedral : 12.963 179.565 2602 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.67 % Favored : 94.28 % Rotamer: Outliers : 1.61 % Allowed : 16.75 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.19), residues: 1922 helix: 1.65 (0.20), residues: 707 sheet: -0.08 (0.32), residues: 244 loop : -0.58 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 612 HIS 0.003 0.001 HIS D 404 PHE 0.012 0.001 PHE D 491 TYR 0.013 0.001 TYR D 607 ARG 0.008 0.000 ARG A1452 *********************** 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 153 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 127 time to evaluate : 1.839 Fit side-chains revert: symmetry clash REVERT: D 139 LYS cc_start: 0.8354 (mmtp) cc_final: 0.7908 (mttm) REVERT: A 821 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8248 (tttm) REVERT: A 901 ASN cc_start: 0.7674 (t0) cc_final: 0.7163 (t0) REVERT: A 972 GLU cc_start: 0.7687 (tp30) cc_final: 0.7208 (tp30) REVERT: A 1581 ARG cc_start: 0.7671 (ptm160) cc_final: 0.7223 (ttt180) REVERT: A 1619 ILE cc_start: 0.7514 (mm) cc_final: 0.7224 (mm) outliers start: 26 outliers final: 14 residues processed: 145 average time/residue: 1.1378 time to fit residues: 186.7372 Evaluate side-chains 134 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 1.842 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.7980 chunk 180 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 176 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16452 Z= 0.212 Angle : 0.542 10.667 22370 Z= 0.281 Chirality : 0.041 0.198 2449 Planarity : 0.004 0.060 2759 Dihedral : 12.968 179.253 2602 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.62 % Favored : 94.33 % Rotamer: Outliers : 1.18 % Allowed : 17.49 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.19), residues: 1922 helix: 1.66 (0.20), residues: 707 sheet: 0.00 (0.32), residues: 242 loop : -0.60 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1487 HIS 0.009 0.001 HIS A 762 PHE 0.012 0.001 PHE D 491 TYR 0.015 0.001 TYR A 529 ARG 0.013 0.000 ARG D 35 *********************** 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 147 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 2.105 Fit side-chains revert: symmetry clash REVERT: D 139 LYS cc_start: 0.8420 (mmtp) cc_final: 0.8034 (mttm) REVERT: A 821 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8303 (tttm) REVERT: A 901 ASN cc_start: 0.7693 (t0) cc_final: 0.7187 (t0) REVERT: A 972 GLU cc_start: 0.7711 (tp30) cc_final: 0.7224 (tp30) REVERT: A 1581 ARG cc_start: 0.7666 (ptm160) cc_final: 0.7194 (ttt180) REVERT: A 1619 ILE cc_start: 0.7516 (mm) cc_final: 0.7220 (mm) outliers start: 19 outliers final: 14 residues processed: 141 average time/residue: 1.1913 time to fit residues: 190.5506 Evaluate side-chains 136 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 1.774 ------------------------------------------------------------------------------- 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 511 LEU 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 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 115 optimal weight: 1.9990 chunk 186 optimal weight: 0.1980 chunk 113 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 129 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 chunk 179 optimal weight: 0.6980 chunk 155 optimal weight: 5.9990 chunk 16 optimal weight: 0.3980 chunk 120 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 A1506 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16452 Z= 0.167 Angle : 0.526 10.599 22370 Z= 0.275 Chirality : 0.041 0.204 2449 Planarity : 0.004 0.043 2759 Dihedral : 12.922 178.465 2602 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.52 % Favored : 94.43 % Rotamer: Outliers : 1.05 % Allowed : 17.93 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.19), residues: 1922 helix: 1.73 (0.20), residues: 707 sheet: 0.04 (0.32), residues: 242 loop : -0.57 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1487 HIS 0.005 0.001 HIS A 762 PHE 0.013 0.001 PHE D 491 TYR 0.011 0.001 TYR D 607 ARG 0.008 0.000 ARG A 697 ********************** 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 148 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 1.722 Fit side-chains revert: symmetry clash REVERT: D 139 LYS cc_start: 0.8414 (mmtp) cc_final: 0.8065 (mttm) REVERT: A 821 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8247 (tttm) REVERT: A 901 ASN cc_start: 0.7672 (t0) cc_final: 0.7195 (t0) REVERT: A 1581 ARG cc_start: 0.7600 (ptm160) cc_final: 0.7176 (ttt180) REVERT: A 1619 ILE cc_start: 0.7489 (mm) cc_final: 0.7192 (mm) outliers start: 17 outliers final: 12 residues processed: 141 average time/residue: 1.0837 time to fit residues: 173.4833 Evaluate side-chains 134 residues out of total 1704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 1.835 ------------------------------------------------------------------------------- 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 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 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 123 optimal weight: 3.9990 chunk 165 optimal weight: 0.0570 chunk 47 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 159 optimal weight: 0.0030 chunk 19 optimal weight: 0.1980 chunk 28 optimal weight: 0.0670 overall best weight: 0.1846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 210 HIS ** D 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 612 ASN A 179 ASN A1506 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.133447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.100556 restraints weight = 21646.961| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.33 r_work: 0.3200 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16452 Z= 0.132 Angle : 0.525 10.279 22370 Z= 0.271 Chirality : 0.040 0.210 2449 Planarity : 0.004 0.044 2759 Dihedral : 12.821 177.136 2602 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.79 % Favored : 95.16 % Rotamer: Outliers : 0.93 % Allowed : 18.36 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.20), residues: 1922 helix: 1.87 (0.20), residues: 707 sheet: 0.08 (0.32), residues: 245 loop : -0.55 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1487 HIS 0.011 0.001 HIS D 210 PHE 0.013 0.001 PHE D 491 TYR 0.014 0.001 TYR A 529 ARG 0.013 0.000 ARG D 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4691.82 seconds wall clock time: 83 minutes 43.63 seconds (5023.63 seconds total)