Starting phenix.real_space_refine on Fri Feb 16 19:37:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y83_33679/02_2024/7y83_33679.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y83_33679/02_2024/7y83_33679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y83_33679/02_2024/7y83_33679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y83_33679/02_2024/7y83_33679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y83_33679/02_2024/7y83_33679.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y83_33679/02_2024/7y83_33679.pdb" } resolution = 2.93 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= 0.194 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 59 5.49 5 Mg 1 5.21 5 S 54 5.16 5 C 10165 2.51 5 N 2832 2.21 5 O 3185 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 11": "OE1" <-> "OE2" Residue "A ASP 95": "OD1" <-> "OD2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "A ASP 386": "OD1" <-> "OD2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A GLU 454": "OE1" <-> "OE2" Residue "A GLU 508": "OE1" <-> "OE2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A GLU 611": "OE1" <-> "OE2" Residue "A TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 709": "OD1" <-> "OD2" Residue "A GLU 761": "OE1" <-> "OE2" Residue "A ASP 788": "OD1" <-> "OD2" Residue "A ASP 793": "OD1" <-> "OD2" Residue "A ASP 806": "OD1" <-> "OD2" Residue "A ASP 833": "OD1" <-> "OD2" Residue "A ASP 938": "OD1" <-> "OD2" Residue "A GLU 947": "OE1" <-> "OE2" Residue "A PHE 1019": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1400": "OD1" <-> "OD2" Residue "A GLU 1496": "OE1" <-> "OE2" Residue "A PHE 1570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 62": "OD1" <-> "OD2" Residue "D ASP 141": "OD1" <-> "OD2" Residue "D PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 217": "OD1" <-> "OD2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "D ASP 253": "OD1" <-> "OD2" Residue "D GLU 398": "OE1" <-> "OE2" Residue "D TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 678": "OE1" <-> "OE2" Residue "D GLU 686": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16300 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1221, 9841 Classifications: {'peptide': 1221} Link IDs: {'PTRANS': 57, 'TRANS': 1163} Chain breaks: 10 Chain: "B" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 757 Classifications: {'RNA': 36} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 10, 'rna3p_pur': 5, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 15} Chain: "C" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 499 Classifications: {'RNA': 23} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 13, 'rna3p_pyr': 5} Link IDs: {'rna2p': 4, 'rna3p': 18} Chain: "D" Number of atoms: 5198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5198 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 18, 'TRANS': 621} Chain breaks: 7 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 1, ' ZN': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5607 SG CYS A 750 57.794 37.629 86.522 1.00 61.47 S ATOM 5620 SG CYS A 752 60.495 38.229 84.299 1.00 70.59 S ATOM 5642 SG CYS A 755 58.314 41.212 85.509 1.00 55.64 S ATOM 3532 SG CYS A 491 51.998 54.037 109.845 1.00 58.61 S ATOM 3600 SG CYS A 501 50.556 53.661 113.214 1.00 52.17 S ATOM 3614 SG CYS A 503 53.912 55.703 112.412 1.00 34.79 S ATOM 3636 SG CYS A 506 50.622 57.124 111.245 1.00 19.20 S ATOM 7502 SG CYS A1018 48.595 37.915 50.331 1.00 73.90 S ATOM 7698 SG CYS A1406 48.536 36.234 53.762 1.00 67.74 S ATOM 7749 SG CYS A1414 51.772 36.647 51.673 1.00 66.74 S ATOM 7766 SG CYS A1417 50.371 39.562 53.406 1.00 69.54 S ATOM 668 SG CYS A 88 39.646 69.655 135.709 1.00 45.02 S ATOM 939 SG CYS A 121 37.304 71.424 138.127 1.00 67.64 S ATOM 985 SG CYS A 127 38.123 72.925 134.705 1.00 56.97 S ATOM 1009 SG CYS A 130 35.985 69.764 134.962 1.00 42.23 S Time building chain proxies: 8.76, per 1000 atoms: 0.54 Number of scatterers: 16300 At special positions: 0 Unit cell: (105.6, 102.3, 160.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 54 16.00 P 59 15.00 Mg 1 11.99 O 3185 8.00 N 2832 7.00 C 10165 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 - 3.50 Amino acid : False - 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: 6.51 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" ND1 HIS A 747 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 750 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 752 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 755 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 491 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 506 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 503 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 501 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1414 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1417 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1018 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1406 " pdb=" ZN A1805 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 88 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 127 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 121 " Number of angles added : 21 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3442 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 25 sheets defined 43.1% alpha, 15.9% beta 15 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 6.32 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 removed outlier: 3.972A pdb=" N LYS A 30 " --> pdb=" O TRP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 59 through 78 Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 145 through 149 removed outlier: 3.643A pdb=" N ASP A 148 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR A 149 " --> pdb=" O ASN A 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 145 through 149' Processing helix chain 'A' and resid 168 through 172 removed outlier: 3.740A 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 269 through 287 Processing helix chain 'A' and resid 291 through 303 removed outlier: 4.198A pdb=" N ILE A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 307 removed outlier: 3.823A pdb=" N GLY A 307 " --> pdb=" O ARG A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 304 through 307' Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 354 through 374 Processing helix chain 'A' and resid 471 through 488 Processing helix chain 'A' and resid 503 through 511 Processing helix chain 'A' and resid 569 through 580 Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 617 through 625 Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 630 through 637 Processing helix chain 'A' and resid 654 through 657 Processing helix chain 'A' and resid 658 through 664 Processing helix chain 'A' and resid 686 through 693 removed outlier: 3.770A pdb=" N THR A 692 " --> pdb=" O ILE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 739 Processing helix chain 'A' and resid 752 through 759 Processing helix chain 'A' and resid 776 through 780 removed outlier: 3.644A pdb=" N PHE A 780 " --> pdb=" O GLY A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 847 Processing helix chain 'A' and resid 855 through 859 removed outlier: 3.684A pdb=" N GLY A 859 " --> pdb=" O GLY A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 914 removed outlier: 3.786A pdb=" N LYS A 912 " --> pdb=" O HIS A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1015 Processing helix chain 'A' and resid 1394 through 1399 removed outlier: 3.648A pdb=" N LYS A1398 " --> pdb=" O THR A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1421 Processing helix chain 'A' and resid 1463 through 1468 removed outlier: 3.610A pdb=" N SER A1467 " --> pdb=" O ARG A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1485 through 1493 removed outlier: 3.926A pdb=" N ILE A1489 " --> pdb=" O ASN A1485 " (cutoff:3.500A) Processing helix chain 'A' and resid 1493 through 1501 Processing helix chain 'A' and resid 1528 through 1540 Processing helix chain 'A' and resid 1552 through 1556 Processing helix chain 'A' and resid 1583 through 1603 Processing helix chain 'A' and resid 1615 through 1618 removed outlier: 3.619A pdb=" N VAL A1618 " --> pdb=" O GLN A1615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1615 through 1618' Processing helix chain 'A' and resid 1619 through 1629 Processing helix chain 'A' and resid 1662 through 1668 removed outlier: 3.962A pdb=" N ASP A1668 " --> pdb=" O LYS A1664 " (cutoff:3.500A) Processing helix chain 'A' and resid 1673 through 1682 Processing helix chain 'D' and resid 16 through 33 removed outlier: 3.629A pdb=" N ASN D 33 " --> pdb=" O ASP D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 60 removed outlier: 3.589A pdb=" N LYS D 43 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 81 Processing helix chain 'D' and resid 90 through 110 removed outlier: 3.507A pdb=" N LYS D 94 " --> pdb=" O PRO D 90 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS D 110 " --> pdb=" O ARG D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 136 Processing helix chain 'D' and resid 141 through 155 Processing helix chain 'D' and resid 163 through 177 removed outlier: 3.695A pdb=" N ILE D 167 " --> pdb=" O TYR D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 182 No H-bonds generated for 'chain 'D' and resid 180 through 182' Processing helix chain 'D' and resid 183 through 190 Processing helix chain 'D' and resid 194 through 205 removed outlier: 3.616A pdb=" N ILE D 205 " --> pdb=" O ALA D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 224 removed outlier: 3.650A pdb=" N LYS D 224 " --> pdb=" O THR D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 246 removed outlier: 4.153A pdb=" N ASP D 234 " --> pdb=" O HIS D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 267 Processing helix chain 'D' and resid 270 through 277 removed outlier: 4.012A pdb=" N ARG D 275 " --> pdb=" O THR D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 281 through 296 removed outlier: 3.864A pdb=" N TYR D 285 " --> pdb=" O HIS D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 320 removed outlier: 3.740A pdb=" N LEU D 320 " --> pdb=" O ILE D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 329 Processing helix chain 'D' and resid 342 through 357 Processing helix chain 'D' and resid 433 through 450 Processing helix chain 'D' and resid 451 through 453 No H-bonds generated for 'chain 'D' and resid 451 through 453' Processing helix chain 'D' and resid 454 through 469 Processing helix chain 'D' and resid 470 through 474 Processing helix chain 'D' and resid 489 through 495 Processing helix chain 'D' and resid 496 through 500 removed outlier: 3.632A pdb=" N SER D 500 " --> pdb=" O LEU D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 514 removed outlier: 3.998A pdb=" N ASN D 513 " --> pdb=" O LEU D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 525 Processing helix chain 'D' and resid 566 through 572 Processing helix chain 'D' and resid 592 through 595 Processing helix chain 'D' and resid 607 through 611 Processing helix chain 'D' and resid 644 through 652 removed outlier: 3.528A pdb=" N ILE D 652 " --> pdb=" O ALA D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 675 removed outlier: 3.675A pdb=" N THR D 669 " --> pdb=" O ARG D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 691 removed outlier: 3.704A pdb=" N TRP D 687 " --> pdb=" O LYS D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 708 removed outlier: 3.884A pdb=" N ALA D 708 " --> pdb=" O TYR D 704 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 153 removed outlier: 6.701A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ARG A 19 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N TRP A 44 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL A 21 " --> pdb=" O TRP A 44 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N TRP A 46 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N GLU A 22 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 12.858A pdb=" N ARG A 193 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 111 Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 181 removed outlier: 6.927A pdb=" N ARG A 180 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 333 through 334 Processing sheet with id=AA7, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 514 removed outlier: 6.623A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 431 through 432 removed outlier: 3.945A pdb=" N ASN A 459 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AB2, first strand: chain 'A' and resid 526 through 533 removed outlier: 9.989A pdb=" N GLU A 526 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N ASP A 547 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 10.802A pdb=" N ARG A 528 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N LEU A 545 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 10.234A pdb=" N ARG A 530 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N GLY A 543 " --> pdb=" O ARG A 530 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ALA A 532 " --> pdb=" O GLU A 541 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 610 through 612 Processing sheet with id=AB4, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.764A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.764A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 707 through 708 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 920 through 921 Processing sheet with id=AB9, first strand: chain 'A' and resid 924 through 927 Processing sheet with id=AC1, first strand: chain 'A' and resid 991 through 992 removed outlier: 6.223A pdb=" N LEU A 996 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL A1517 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN A1516 " --> pdb=" O THR A 960 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASN A1526 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU A 950 " --> pdb=" O ASN A1526 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1429 through 1431 removed outlier: 3.852A pdb=" N ASN A1516 " --> pdb=" O THR A 960 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASN A1526 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU A 950 " --> pdb=" O ASN A1526 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 985 through 987 removed outlier: 6.345A pdb=" N LYS A 985 " --> pdb=" O THR A1508 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N GLU A1510 " --> pdb=" O LYS A 985 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N TYR A 987 " --> pdb=" O GLU A1510 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 425 through 427 removed outlier: 6.111A pdb=" N VAL D 484 " --> pdb=" O CYS D 517 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 406 through 407 Processing sheet with id=AC6, first strand: chain 'D' and resid 580 through 582 removed outlier: 6.213A pdb=" N LEU D 580 " --> pdb=" O ILE D 623 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 585 through 587 removed outlier: 4.184A pdb=" N HIS D 585 " --> pdb=" O LYS D 599 " (cutoff:3.500A) 652 hydrogen bonds defined for protein. 1827 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 7.79 Time building geometry restraints manager: 7.04 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: 4595 1.33 - 1.45: 3256 1.45 - 1.57: 8737 1.57 - 1.69: 116 1.69 - 1.81: 74 Bond restraints: 16778 Sorted by residual: bond pdb=" CB PRO D 397 " pdb=" CG PRO D 397 " ideal model delta sigma weight residual 1.492 1.573 -0.081 5.00e-02 4.00e+02 2.64e+00 bond pdb=" CG1 ILE D 169 " pdb=" CD1 ILE D 169 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.09e+00 bond pdb=" C THR A 556 " pdb=" N PHE A 557 " ideal model delta sigma weight residual 1.333 1.296 0.036 2.74e-02 1.33e+03 1.75e+00 bond pdb=" CB PRO A 694 " pdb=" CG PRO A 694 " ideal model delta sigma weight residual 1.492 1.557 -0.065 5.00e-02 4.00e+02 1.71e+00 bond pdb=" CG1 ILE D 712 " pdb=" CD1 ILE D 712 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.59e+00 ... (remaining 16773 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.88: 571 105.88 - 112.96: 9068 112.96 - 120.04: 5832 120.04 - 127.12: 7111 127.12 - 134.19: 314 Bond angle restraints: 22896 Sorted by residual: angle pdb=" CA PRO D 397 " pdb=" N PRO D 397 " pdb=" CD PRO D 397 " ideal model delta sigma weight residual 112.00 106.54 5.46 1.40e+00 5.10e-01 1.52e+01 angle pdb=" O4' G B 47 " pdb=" C1' G B 47 " pdb=" N9 G B 47 " ideal model delta sigma weight residual 108.20 113.76 -5.56 1.50e+00 4.44e-01 1.38e+01 angle pdb=" CA TYR D 696 " pdb=" CB TYR D 696 " pdb=" CG TYR D 696 " ideal model delta sigma weight residual 113.90 120.14 -6.24 1.80e+00 3.09e-01 1.20e+01 angle pdb=" CG ARG A 208 " pdb=" CD ARG A 208 " pdb=" NE ARG A 208 " ideal model delta sigma weight residual 112.00 118.46 -6.46 2.20e+00 2.07e-01 8.61e+00 angle pdb=" CA ARG A 51 " pdb=" CB ARG A 51 " pdb=" CG ARG A 51 " ideal model delta sigma weight residual 114.10 119.83 -5.73 2.00e+00 2.50e-01 8.21e+00 ... (remaining 22891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 9471 35.69 - 71.37: 608 71.37 - 107.06: 47 107.06 - 142.75: 0 142.75 - 178.43: 2 Dihedral angle restraints: 10128 sinusoidal: 4778 harmonic: 5350 Sorted by residual: dihedral pdb=" O4' U C 20 " pdb=" C1' U C 20 " pdb=" N1 U C 20 " pdb=" C2 U C 20 " ideal model delta sinusoidal sigma weight residual -128.00 50.43 -178.43 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U C 14 " pdb=" C1' U C 14 " pdb=" N1 U C 14 " pdb=" C2 U C 14 " ideal model delta sinusoidal sigma weight residual 232.00 64.47 167.53 1 1.70e+01 3.46e-03 6.57e+01 dihedral pdb=" O4' U B 41 " pdb=" C1' U B 41 " pdb=" N1 U B 41 " pdb=" C2 U B 41 " ideal model delta sinusoidal sigma weight residual -128.00 -69.65 -58.35 1 1.70e+01 3.46e-03 1.58e+01 ... (remaining 10125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2157 0.059 - 0.117: 315 0.117 - 0.176: 31 0.176 - 0.234: 1 0.234 - 0.293: 2 Chirality restraints: 2506 Sorted by residual: chirality pdb=" CB ILE D 169 " pdb=" CA ILE D 169 " pdb=" CG1 ILE D 169 " pdb=" CG2 ILE D 169 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" C1' G B 47 " pdb=" O4' G B 47 " pdb=" C2' G B 47 " pdb=" N9 G B 47 " both_signs ideal model delta sigma weight residual False 2.44 2.16 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CB ILE A1619 " pdb=" CA ILE A1619 " pdb=" CG1 ILE A1619 " pdb=" CG2 ILE A1619 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.15e-01 ... (remaining 2503 not shown) Planarity restraints: 2709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 687 " -0.031 2.00e-02 2.50e+03 2.55e-02 1.62e+01 pdb=" CG TRP D 687 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP D 687 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP D 687 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 687 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 687 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 687 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 687 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 687 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP D 687 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 396 " 0.052 5.00e-02 4.00e+02 7.59e-02 9.22e+00 pdb=" N PRO D 397 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO D 397 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 397 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G B 47 " -0.031 2.00e-02 2.50e+03 1.48e-02 6.57e+00 pdb=" N9 G B 47 " 0.040 2.00e-02 2.50e+03 pdb=" C8 G B 47 " -0.000 2.00e-02 2.50e+03 pdb=" N7 G B 47 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G B 47 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B 47 " 0.000 2.00e-02 2.50e+03 pdb=" O6 G B 47 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G B 47 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G B 47 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B 47 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G B 47 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G B 47 " 0.001 2.00e-02 2.50e+03 ... (remaining 2706 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 190 2.52 - 3.11: 11976 3.11 - 3.71: 28543 3.71 - 4.30: 40777 4.30 - 4.90: 66897 Nonbonded interactions: 148383 Sorted by model distance: nonbonded pdb=" OD1 ASP A 137 " pdb="MG MG A1804 " model vdw 1.923 2.170 nonbonded pdb=" OP2 U B 26 " pdb="MG MG A1804 " model vdw 1.930 2.170 nonbonded pdb=" OG1 THR A 941 " pdb=" OE1 GLU A 943 " model vdw 2.101 2.440 nonbonded pdb=" O ALA D 588 " pdb=" OG SER D 596 " model vdw 2.129 2.440 nonbonded pdb=" OG SER A1001 " pdb=" OP1 G B 47 " model vdw 2.137 2.440 ... (remaining 148378 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.240 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: 0.030 Extract box with map and model: 4.880 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 52.890 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 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:12.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 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 : 0.004 0.081 16778 Z= 0.233 Angle : 0.575 7.741 22896 Z= 0.303 Chirality : 0.041 0.293 2506 Planarity : 0.005 0.085 2709 Dihedral : 20.604 178.432 6686 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.52 % Allowed : 32.09 % Favored : 62.39 % 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: 0.07 (0.20), residues: 1823 helix: 0.99 (0.20), residues: 680 sheet: -1.41 (0.30), residues: 258 loop : -0.12 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP D 687 HIS 0.004 0.001 HIS A 924 PHE 0.028 0.002 PHE D 477 TYR 0.017 0.001 TYR D 696 ARG 0.019 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 185 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 752 CYS cc_start: 0.7263 (m) cc_final: 0.6911 (m) REVERT: A 773 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7466 (mt-10) REVERT: D 216 MET cc_start: 0.7532 (tpt) cc_final: 0.7101 (tpt) REVERT: D 687 TRP cc_start: 0.8000 (t60) cc_final: 0.7384 (t60) outliers start: 90 outliers final: 87 residues processed: 268 average time/residue: 1.0701 time to fit residues: 326.4564 Evaluate side-chains 266 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 178 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 611 GLU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 762 HIS Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 987 TYR Chi-restraints excluded: chain A residue 1029 SER Chi-restraints excluded: chain A residue 1424 ASP Chi-restraints excluded: chain A residue 1443 LEU Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain A residue 1649 ASN Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 474 CYS Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 618 LYS Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 667 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 0.7980 chunk 144 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 173 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 HIS ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 ASN D 699 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.0643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16778 Z= 0.228 Angle : 0.529 6.548 22896 Z= 0.276 Chirality : 0.041 0.277 2506 Planarity : 0.004 0.051 2709 Dihedral : 17.159 178.056 3075 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 6.50 % Allowed : 29.69 % Favored : 63.80 % 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: 0.24 (0.20), residues: 1823 helix: 1.24 (0.20), residues: 685 sheet: -1.40 (0.31), residues: 254 loop : -0.11 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D 687 HIS 0.004 0.001 HIS D 457 PHE 0.023 0.001 PHE D 703 TYR 0.017 0.001 TYR D 76 ARG 0.011 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 207 time to evaluate : 1.725 Fit side-chains revert: symmetry clash REVERT: A 8 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7026 (pt) REVERT: A 123 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7837 (tmtt) REVERT: A 145 ARG cc_start: 0.7316 (mtm-85) cc_final: 0.7052 (mtm-85) REVERT: A 217 LYS cc_start: 0.6534 (OUTLIER) cc_final: 0.6198 (tptm) REVERT: A 218 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7463 (pttp) REVERT: A 464 LYS cc_start: 0.7260 (OUTLIER) cc_final: 0.6780 (mmtt) REVERT: A 506 CYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8019 (m) REVERT: A 752 CYS cc_start: 0.7295 (m) cc_final: 0.6872 (m) REVERT: A 852 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8492 (mt) REVERT: A 1004 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.7064 (ttp-170) REVERT: A 1504 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7488 (pm20) REVERT: A 1581 ARG cc_start: 0.7330 (ttt180) cc_final: 0.7062 (ttt180) REVERT: D 494 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8752 (mpt180) REVERT: D 640 ASP cc_start: 0.7551 (t70) cc_final: 0.7235 (t70) REVERT: D 687 TRP cc_start: 0.8257 (t60) cc_final: 0.7636 (t60) outliers start: 106 outliers final: 54 residues processed: 286 average time/residue: 1.0645 time to fit residues: 345.0646 Evaluate side-chains 250 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 186 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 987 TYR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1004 ARG Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1504 GLU Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 343 HIS Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 533 SER Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain D residue 667 ASN Chi-restraints excluded: chain D residue 714 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 7.9990 chunk 53 optimal weight: 0.0870 chunk 144 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 173 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 overall best weight: 2.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 699 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 16778 Z= 0.428 Angle : 0.634 8.518 22896 Z= 0.325 Chirality : 0.045 0.292 2506 Planarity : 0.004 0.050 2709 Dihedral : 16.951 177.571 2988 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 7.85 % Allowed : 29.14 % Favored : 63.01 % 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: -0.09 (0.19), residues: 1823 helix: 0.91 (0.20), residues: 685 sheet: -1.64 (0.31), residues: 260 loop : -0.20 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 687 HIS 0.006 0.001 HIS D 457 PHE 0.023 0.002 PHE D 324 TYR 0.019 0.002 TYR D 607 ARG 0.012 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 186 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7345 (pt) REVERT: A 51 ARG cc_start: 0.7517 (ttm110) cc_final: 0.7267 (ttm-80) REVERT: A 117 ASN cc_start: 0.5920 (OUTLIER) cc_final: 0.5446 (p0) REVERT: A 123 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7820 (tmtt) REVERT: A 145 ARG cc_start: 0.7375 (mtm-85) cc_final: 0.7090 (mtm-85) REVERT: A 217 LYS cc_start: 0.6650 (OUTLIER) cc_final: 0.6330 (tptm) REVERT: A 464 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.6682 (mmtt) REVERT: A 835 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.7014 (tmtt) REVERT: A 852 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8495 (mt) REVERT: A 961 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.6776 (pp) REVERT: A 1004 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.7145 (ttp-170) REVERT: A 1504 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7464 (pm20) REVERT: D 40 ASP cc_start: 0.6940 (m-30) cc_final: 0.6422 (p0) REVERT: D 290 LEU cc_start: 0.8240 (mt) cc_final: 0.8016 (mt) REVERT: D 578 ARG cc_start: 0.7052 (ptt180) cc_final: 0.6179 (tpp-160) REVERT: D 687 TRP cc_start: 0.8483 (t60) cc_final: 0.8123 (t60) outliers start: 128 outliers final: 72 residues processed: 290 average time/residue: 1.0850 time to fit residues: 356.4001 Evaluate side-chains 258 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 176 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 987 TYR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1004 ARG Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1016 LYS Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1504 GLU Chi-restraints excluded: chain A residue 1580 LYS Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain A residue 1649 ASN Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 533 SER Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 563 ASP Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 667 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 171 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 174 optimal weight: 8.9990 chunk 184 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 165 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 699 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16778 Z= 0.220 Angle : 0.534 7.436 22896 Z= 0.277 Chirality : 0.041 0.309 2506 Planarity : 0.004 0.057 2709 Dihedral : 16.764 178.558 2987 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 7.30 % Allowed : 30.37 % Favored : 62.33 % 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: 0.11 (0.20), residues: 1823 helix: 1.16 (0.20), residues: 686 sheet: -1.53 (0.31), residues: 257 loop : -0.17 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 687 HIS 0.006 0.001 HIS D 457 PHE 0.020 0.001 PHE D 703 TYR 0.016 0.001 TYR D 76 ARG 0.012 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 189 time to evaluate : 1.890 Fit side-chains revert: symmetry clash REVERT: A 8 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7081 (pt) REVERT: A 117 ASN cc_start: 0.5884 (OUTLIER) cc_final: 0.5431 (p0) REVERT: A 123 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7809 (tmtt) REVERT: A 145 ARG cc_start: 0.7295 (mtm-85) cc_final: 0.6985 (mtm-85) REVERT: A 217 LYS cc_start: 0.6595 (OUTLIER) cc_final: 0.6378 (tptm) REVERT: A 279 VAL cc_start: 0.8032 (OUTLIER) cc_final: 0.7788 (m) REVERT: A 464 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6576 (mmtt) REVERT: A 852 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8469 (mt) REVERT: A 1004 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.7102 (ttp-170) REVERT: A 1504 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7421 (pm20) REVERT: A 1581 ARG cc_start: 0.7184 (ttt180) cc_final: 0.6861 (ttt180) REVERT: D 40 ASP cc_start: 0.6890 (m-30) cc_final: 0.6363 (p0) REVERT: D 125 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.7666 (tptm) REVERT: D 290 LEU cc_start: 0.8208 (mt) cc_final: 0.7964 (mt) REVERT: D 687 TRP cc_start: 0.8378 (t60) cc_final: 0.7958 (t60) outliers start: 119 outliers final: 68 residues processed: 279 average time/residue: 1.0981 time to fit residues: 347.2067 Evaluate side-chains 259 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 181 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 704 LYS Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 762 HIS Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 987 TYR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1004 ARG Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1504 GLU Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain A residue 1649 ASN Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 533 SER Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 667 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 153 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 127 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 699 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 16778 Z= 0.386 Angle : 0.611 10.248 22896 Z= 0.314 Chirality : 0.044 0.301 2506 Planarity : 0.004 0.063 2709 Dihedral : 16.729 177.902 2979 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 7.48 % Allowed : 30.12 % Favored : 62.39 % 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: -0.08 (0.19), residues: 1823 helix: 0.96 (0.20), residues: 684 sheet: -1.66 (0.31), residues: 260 loop : -0.23 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 612 HIS 0.006 0.001 HIS D 457 PHE 0.024 0.002 PHE D 184 TYR 0.018 0.002 TYR D 76 ARG 0.013 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 187 time to evaluate : 1.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7287 (pt) REVERT: A 117 ASN cc_start: 0.5878 (OUTLIER) cc_final: 0.5421 (p0) REVERT: A 123 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7791 (tmtt) REVERT: A 145 ARG cc_start: 0.7363 (mtm-85) cc_final: 0.7103 (mtm-85) REVERT: A 464 LYS cc_start: 0.7342 (OUTLIER) cc_final: 0.6731 (mmtt) REVERT: A 835 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.7040 (tmtt) REVERT: A 852 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8468 (mt) REVERT: A 961 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.6710 (pp) REVERT: A 1004 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.7061 (ttp-170) REVERT: A 1504 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7434 (pm20) REVERT: D 40 ASP cc_start: 0.6931 (m-30) cc_final: 0.6422 (p0) REVERT: D 125 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.7649 (tptm) REVERT: D 184 PHE cc_start: 0.7779 (t80) cc_final: 0.7548 (t80) REVERT: D 357 GLN cc_start: 0.8558 (mt0) cc_final: 0.8324 (mm110) REVERT: D 578 ARG cc_start: 0.7079 (ptt180) cc_final: 0.6270 (tpp-160) REVERT: D 687 TRP cc_start: 0.8388 (t60) cc_final: 0.8036 (t60) outliers start: 122 outliers final: 76 residues processed: 289 average time/residue: 1.1051 time to fit residues: 361.2825 Evaluate side-chains 267 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 181 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 704 LYS Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 987 TYR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1004 ARG Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1504 GLU Chi-restraints excluded: chain A residue 1549 LEU Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain A residue 1649 ASN Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 533 SER Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 667 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 62 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 184 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 699 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16778 Z= 0.234 Angle : 0.547 9.695 22896 Z= 0.283 Chirality : 0.041 0.289 2506 Planarity : 0.004 0.069 2709 Dihedral : 16.612 178.627 2979 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 6.99 % Allowed : 31.10 % Favored : 61.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.12 (0.20), residues: 1823 helix: 1.17 (0.20), residues: 685 sheet: -1.50 (0.31), residues: 254 loop : -0.18 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 612 HIS 0.005 0.001 HIS A 924 PHE 0.026 0.001 PHE D 703 TYR 0.015 0.002 TYR D 76 ARG 0.015 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 191 time to evaluate : 1.850 Fit side-chains revert: symmetry clash REVERT: A 8 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7114 (pt) REVERT: A 117 ASN cc_start: 0.5766 (OUTLIER) cc_final: 0.5305 (p0) REVERT: A 123 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7808 (tmtt) REVERT: A 145 ARG cc_start: 0.7377 (mtm-85) cc_final: 0.7112 (mtm-85) REVERT: A 464 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6657 (mmtt) REVERT: A 835 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6914 (tmtt) REVERT: A 852 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8452 (mt) REVERT: A 961 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6519 (pp) REVERT: A 1004 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.7068 (ttp-170) REVERT: A 1504 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7389 (pm20) REVERT: D 40 ASP cc_start: 0.6930 (m-30) cc_final: 0.6386 (p0) REVERT: D 125 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.7636 (tptm) REVERT: D 181 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6627 (tp30) REVERT: D 184 PHE cc_start: 0.7788 (t80) cc_final: 0.7537 (t80) REVERT: D 290 LEU cc_start: 0.8202 (mt) cc_final: 0.7985 (mt) REVERT: D 357 GLN cc_start: 0.8535 (mt0) cc_final: 0.8330 (mm110) REVERT: D 578 ARG cc_start: 0.7093 (ptt180) cc_final: 0.6285 (tpp-160) REVERT: D 687 TRP cc_start: 0.8367 (t60) cc_final: 0.8098 (t60) outliers start: 114 outliers final: 66 residues processed: 279 average time/residue: 1.1470 time to fit residues: 361.9176 Evaluate side-chains 252 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 175 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 704 LYS Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 987 TYR Chi-restraints excluded: chain A residue 1004 ARG Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1017 SER Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1443 LEU Chi-restraints excluded: chain A residue 1504 GLU Chi-restraints excluded: chain A residue 1549 LEU Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain A residue 1649 ASN Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 563 ASP Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 667 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 178 optimal weight: 7.9990 chunk 20 optimal weight: 0.4980 chunk 105 optimal weight: 20.0000 chunk 134 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 184 optimal weight: 1.9990 chunk 115 optimal weight: 0.2980 chunk 112 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 699 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16778 Z= 0.237 Angle : 0.551 9.173 22896 Z= 0.284 Chirality : 0.041 0.287 2506 Planarity : 0.004 0.074 2709 Dihedral : 16.551 178.454 2973 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 6.69 % Allowed : 31.29 % Favored : 62.02 % 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: 0.18 (0.20), residues: 1823 helix: 1.22 (0.20), residues: 686 sheet: -1.42 (0.32), residues: 252 loop : -0.18 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 612 HIS 0.006 0.001 HIS D 457 PHE 0.019 0.001 PHE A 926 TYR 0.016 0.001 TYR D 76 ARG 0.017 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 191 time to evaluate : 1.826 Fit side-chains revert: symmetry clash REVERT: A 8 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7087 (pt) REVERT: A 123 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7811 (tmtt) REVERT: A 145 ARG cc_start: 0.7341 (mtm-85) cc_final: 0.7064 (mtm-85) REVERT: A 464 LYS cc_start: 0.7206 (OUTLIER) cc_final: 0.6541 (mmtt) REVERT: A 752 CYS cc_start: 0.7400 (m) cc_final: 0.6868 (m) REVERT: A 835 LYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6958 (tmtt) REVERT: A 950 LEU cc_start: 0.8452 (pt) cc_final: 0.8177 (pp) REVERT: A 961 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6578 (pp) REVERT: A 1004 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.7052 (ttp-170) REVERT: A 1463 ARG cc_start: 0.7218 (mmt90) cc_final: 0.7009 (mmt90) REVERT: A 1504 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7422 (pm20) REVERT: D 40 ASP cc_start: 0.6951 (m-30) cc_final: 0.6393 (p0) REVERT: D 80 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7222 (tp) REVERT: D 125 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.7657 (tptm) REVERT: D 184 PHE cc_start: 0.8017 (t80) cc_final: 0.7779 (t80) REVERT: D 290 LEU cc_start: 0.8195 (mt) cc_final: 0.7990 (mt) REVERT: D 357 GLN cc_start: 0.8537 (mt0) cc_final: 0.8326 (mm110) REVERT: D 578 ARG cc_start: 0.7100 (ptt180) cc_final: 0.6268 (tpp-160) REVERT: D 687 TRP cc_start: 0.8393 (t60) cc_final: 0.8138 (t60) outliers start: 109 outliers final: 75 residues processed: 275 average time/residue: 1.0641 time to fit residues: 333.0325 Evaluate side-chains 264 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 180 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 704 LYS Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 987 TYR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1004 ARG Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1504 GLU Chi-restraints excluded: chain A residue 1549 LEU Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain A residue 1649 ASN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 343 HIS Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 533 SER Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 563 ASP Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 667 ASN Chi-restraints excluded: chain D residue 686 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 113 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 chunk 35 optimal weight: 0.7980 chunk 117 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16778 Z= 0.266 Angle : 0.564 9.494 22896 Z= 0.290 Chirality : 0.041 0.281 2506 Planarity : 0.004 0.079 2709 Dihedral : 16.524 178.346 2966 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 6.50 % Allowed : 31.23 % Favored : 62.27 % 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: 0.13 (0.20), residues: 1823 helix: 1.20 (0.20), residues: 686 sheet: -1.56 (0.31), residues: 258 loop : -0.17 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 612 HIS 0.006 0.001 HIS D 457 PHE 0.025 0.002 PHE D 703 TYR 0.017 0.002 TYR D 76 ARG 0.018 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 185 time to evaluate : 1.813 Fit side-chains revert: symmetry clash REVERT: A 8 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7132 (pt) REVERT: A 117 ASN cc_start: 0.5957 (OUTLIER) cc_final: 0.5740 (p0) REVERT: A 123 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7803 (tmtt) REVERT: A 145 ARG cc_start: 0.7340 (mtm-85) cc_final: 0.7056 (mtm-85) REVERT: A 464 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6558 (mmtt) REVERT: A 752 CYS cc_start: 0.7484 (m) cc_final: 0.6949 (m) REVERT: A 835 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6973 (tmtt) REVERT: A 950 LEU cc_start: 0.8461 (pt) cc_final: 0.8184 (pp) REVERT: A 961 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6563 (pp) REVERT: A 1004 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.7038 (ttp-170) REVERT: A 1463 ARG cc_start: 0.7216 (mmt90) cc_final: 0.7007 (mmt90) REVERT: A 1504 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7441 (pm20) REVERT: D 40 ASP cc_start: 0.6904 (m-30) cc_final: 0.6358 (p0) REVERT: D 80 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7264 (tp) REVERT: D 125 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.7652 (tptm) REVERT: D 184 PHE cc_start: 0.8084 (t80) cc_final: 0.7854 (t80) REVERT: D 357 GLN cc_start: 0.8530 (mt0) cc_final: 0.8321 (mm110) REVERT: D 578 ARG cc_start: 0.7052 (ptt180) cc_final: 0.6291 (tpp-160) REVERT: D 687 TRP cc_start: 0.8349 (t60) cc_final: 0.8094 (t60) outliers start: 106 outliers final: 78 residues processed: 264 average time/residue: 1.0449 time to fit residues: 313.3377 Evaluate side-chains 263 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 175 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 704 LYS Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 987 TYR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1004 ARG Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1504 GLU Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain A residue 1649 ASN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 533 SER Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 563 ASP Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 597 MET Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 667 ASN Chi-restraints excluded: chain D residue 686 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 167 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 160 optimal weight: 7.9990 chunk 171 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 134 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16778 Z= 0.208 Angle : 0.551 9.569 22896 Z= 0.283 Chirality : 0.041 0.279 2506 Planarity : 0.004 0.085 2709 Dihedral : 16.465 178.600 2966 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 5.58 % Allowed : 32.39 % Favored : 62.02 % 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: 0.24 (0.20), residues: 1823 helix: 1.31 (0.20), residues: 686 sheet: -1.42 (0.32), residues: 251 loop : -0.17 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 612 HIS 0.005 0.001 HIS D 457 PHE 0.017 0.001 PHE A 926 TYR 0.016 0.001 TYR D 76 ARG 0.019 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 193 time to evaluate : 1.838 Fit side-chains revert: symmetry clash REVERT: A 8 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.6963 (pt) REVERT: A 51 ARG cc_start: 0.7475 (ttm110) cc_final: 0.7274 (ttm-80) REVERT: A 117 ASN cc_start: 0.5890 (OUTLIER) cc_final: 0.5682 (p0) REVERT: A 123 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7793 (tmtt) REVERT: A 145 ARG cc_start: 0.7325 (mtm-85) cc_final: 0.7043 (mtm-85) REVERT: A 464 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6575 (mmtt) REVERT: A 752 CYS cc_start: 0.7363 (m) cc_final: 0.6842 (m) REVERT: A 835 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.7011 (tmtt) REVERT: A 950 LEU cc_start: 0.8429 (pt) cc_final: 0.8153 (pp) REVERT: A 961 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6582 (pp) REVERT: A 1004 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.6987 (ttp-170) REVERT: A 1463 ARG cc_start: 0.7266 (mmt90) cc_final: 0.7061 (mmt90) REVERT: A 1496 GLU cc_start: 0.6819 (mm-30) cc_final: 0.6516 (mt-10) REVERT: A 1504 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7416 (pm20) REVERT: D 40 ASP cc_start: 0.6882 (m-30) cc_final: 0.6335 (p0) REVERT: D 80 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7216 (tp) REVERT: D 125 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.7653 (tptm) REVERT: D 184 PHE cc_start: 0.8034 (t80) cc_final: 0.7798 (t80) REVERT: D 216 MET cc_start: 0.7370 (tpt) cc_final: 0.7019 (tpt) REVERT: D 578 ARG cc_start: 0.7094 (ptt180) cc_final: 0.6266 (tpp-160) REVERT: D 687 TRP cc_start: 0.8367 (t60) cc_final: 0.8056 (t60) outliers start: 91 outliers final: 65 residues processed: 258 average time/residue: 1.1009 time to fit residues: 323.0441 Evaluate side-chains 254 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 179 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 704 LYS Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 762 HIS Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 987 TYR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1004 ARG Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1443 LEU Chi-restraints excluded: chain A residue 1504 GLU Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 667 ASN Chi-restraints excluded: chain D residue 686 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 112 optimal weight: 8.9990 chunk 181 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 190 optimal weight: 1.9990 chunk 175 optimal weight: 9.9990 chunk 151 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 117 optimal weight: 0.0670 chunk 92 optimal weight: 5.9990 overall best weight: 1.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16778 Z= 0.315 Angle : 0.594 10.038 22896 Z= 0.303 Chirality : 0.043 0.285 2506 Planarity : 0.004 0.066 2709 Dihedral : 16.495 178.171 2962 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.09 % Allowed : 33.13 % Favored : 61.78 % 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: 0.08 (0.20), residues: 1823 helix: 1.14 (0.20), residues: 686 sheet: -1.57 (0.31), residues: 254 loop : -0.19 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 612 HIS 0.006 0.001 HIS D 457 PHE 0.028 0.002 PHE D 703 TYR 0.018 0.002 TYR D 76 ARG 0.012 0.001 ARG A 168 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 180 time to evaluate : 1.767 Fit side-chains revert: symmetry clash REVERT: A 8 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7152 (pt) REVERT: A 117 ASN cc_start: 0.5967 (OUTLIER) cc_final: 0.5742 (p0) REVERT: A 123 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7801 (tmtt) REVERT: A 145 ARG cc_start: 0.7396 (mtm-85) cc_final: 0.7099 (mtm-85) REVERT: A 464 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6572 (mmtt) REVERT: A 752 CYS cc_start: 0.7498 (m) cc_final: 0.6998 (m) REVERT: A 835 LYS cc_start: 0.7168 (OUTLIER) cc_final: 0.6967 (tmtt) REVERT: A 961 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.6546 (pp) REVERT: A 1004 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.7193 (ttp-170) REVERT: A 1463 ARG cc_start: 0.7287 (mmt90) cc_final: 0.7065 (mmt90) REVERT: A 1496 GLU cc_start: 0.6743 (mm-30) cc_final: 0.6449 (mt-10) REVERT: A 1504 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7418 (pm20) REVERT: D 40 ASP cc_start: 0.6938 (m-30) cc_final: 0.6377 (p0) REVERT: D 80 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.7222 (tp) REVERT: D 125 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.7666 (tptm) REVERT: D 184 PHE cc_start: 0.8059 (t80) cc_final: 0.7760 (t80) REVERT: D 578 ARG cc_start: 0.7064 (ptt180) cc_final: 0.6258 (tpp-160) REVERT: D 640 ASP cc_start: 0.7524 (t70) cc_final: 0.7176 (t70) REVERT: D 687 TRP cc_start: 0.8410 (t60) cc_final: 0.8114 (t60) outliers start: 83 outliers final: 65 residues processed: 244 average time/residue: 1.1443 time to fit residues: 314.7597 Evaluate side-chains 249 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 174 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 704 LYS Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 987 TYR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1004 ARG Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1443 LEU Chi-restraints excluded: chain A residue 1504 GLU Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1649 ASN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 563 ASP Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 667 ASN Chi-restraints excluded: chain D residue 686 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 120 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 139 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.181731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.146388 restraints weight = 18231.689| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.75 r_work: 0.3602 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16778 Z= 0.201 Angle : 0.553 9.103 22896 Z= 0.284 Chirality : 0.041 0.276 2506 Planarity : 0.004 0.058 2709 Dihedral : 16.421 178.695 2962 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.79 % Allowed : 33.62 % Favored : 61.60 % 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: 0.25 (0.20), residues: 1823 helix: 1.31 (0.20), residues: 687 sheet: -1.35 (0.32), residues: 245 loop : -0.19 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 612 HIS 0.005 0.001 HIS D 457 PHE 0.021 0.001 PHE A 926 TYR 0.017 0.001 TYR D 704 ARG 0.012 0.000 ARG A 168 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5875.18 seconds wall clock time: 106 minutes 13.88 seconds (6373.88 seconds total)