Starting phenix.real_space_refine (version: dev) on Wed Feb 22 02:48:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y83_33679/02_2023/7y83_33679.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y83_33679/02_2023/7y83_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_2023/7y83_33679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y83_33679/02_2023/7y83_33679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y83_33679/02_2023/7y83_33679.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y83_33679/02_2023/7y83_33679.pdb" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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-4877/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: 9.42, per 1000 atoms: 0.58 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: 7.55 Conformation dependent library (CDL) restraints added in 2.2 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: 5.13 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: 7.20 Time building geometry restraints manager: 7.99 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: 9373 35.69 - 71.37: 509 71.37 - 107.06: 32 107.06 - 142.75: 0 142.75 - 178.43: 2 Dihedral angle restraints: 9916 sinusoidal: 4566 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 9913 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 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. 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.210 Check model and map are aligned: 0.280 Process input model: 53.280 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.140 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 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 : 19.417 178.432 6474 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 5.52 % 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 *********************** 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 : 1.919 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 87 residues processed: 268 average time/residue: 1.0463 time to fit residues: 319.4277 Evaluate side-chains 265 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 178 time to evaluate : 1.844 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 83 residues processed: 6 average time/residue: 0.7981 time to fit residues: 8.1681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 97 optimal weight: 0.0470 chunk 77 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 173 optimal weight: 5.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 HIS ** A 776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7910 moved from start: 0.0660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 16778 Z= 0.182 Angle : 0.510 6.424 22896 Z= 0.267 Chirality : 0.040 0.268 2506 Planarity : 0.004 0.052 2709 Dihedral : 12.015 178.469 2713 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 9.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.31 (0.20), residues: 1823 helix: 1.33 (0.20), residues: 686 sheet: -1.29 (0.31), residues: 251 loop : -0.13 (0.21), residues: 886 *********************** 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 362 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 211 time to evaluate : 1.745 Fit side-chains outliers start: 151 outliers final: 96 residues processed: 328 average time/residue: 1.0317 time to fit residues: 385.7118 Evaluate side-chains 285 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 189 time to evaluate : 1.692 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 80 residues processed: 17 average time/residue: 0.3089 time to fit residues: 10.0421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 173 optimal weight: 7.9990 chunk 187 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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** ** A1568 HIS ** 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: 0.8045 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.082 16778 Z= 0.509 Angle : 0.677 8.588 22896 Z= 0.347 Chirality : 0.047 0.290 2506 Planarity : 0.005 0.051 2709 Dihedral : 12.253 176.762 2713 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 9.57 % 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: -0.20 (0.19), residues: 1823 helix: 0.78 (0.19), residues: 685 sheet: -1.66 (0.31), residues: 260 loop : -0.25 (0.21), residues: 878 *********************** 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 345 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 189 time to evaluate : 2.142 Fit side-chains outliers start: 156 outliers final: 102 residues processed: 319 average time/residue: 1.0727 time to fit residues: 389.2000 Evaluate side-chains 273 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 171 time to evaluate : 1.965 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 90 residues processed: 13 average time/residue: 0.5234 time to fit residues: 11.3619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 171 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 174 optimal weight: 8.9990 chunk 184 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 165 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 269 HIS ** A1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 ASN D 699 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 16778 Z= 0.207 Angle : 0.531 7.242 22896 Z= 0.277 Chirality : 0.041 0.300 2506 Planarity : 0.004 0.059 2709 Dihedral : 12.094 178.496 2713 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 8.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.20), residues: 1823 helix: 1.14 (0.20), residues: 685 sheet: -1.47 (0.31), residues: 255 loop : -0.15 (0.21), residues: 883 *********************** 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 333 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 191 time to evaluate : 1.696 Fit side-chains outliers start: 142 outliers final: 98 residues processed: 309 average time/residue: 1.0332 time to fit residues: 364.6074 Evaluate side-chains 275 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 177 time to evaluate : 1.786 Switching outliers to nearest non-outliers outliers start: 98 outliers final: 87 residues processed: 12 average time/residue: 0.3581 time to fit residues: 8.7082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 153 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 165 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 991 ASN ** A1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 699 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.082 16778 Z= 0.556 Angle : 0.709 8.961 22896 Z= 0.362 Chirality : 0.048 0.286 2506 Planarity : 0.005 0.065 2709 Dihedral : 12.372 176.967 2713 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer Outliers : 9.20 % 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: -0.44 (0.19), residues: 1823 helix: 0.56 (0.19), residues: 692 sheet: -1.77 (0.30), residues: 261 loop : -0.38 (0.21), residues: 870 *********************** 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 328 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 178 time to evaluate : 1.858 Fit side-chains outliers start: 150 outliers final: 102 residues processed: 309 average time/residue: 1.0741 time to fit residues: 376.6355 Evaluate side-chains 272 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 170 time to evaluate : 2.011 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 94 residues processed: 9 average time/residue: 0.4965 time to fit residues: 8.3238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 62 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 108 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 184 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** 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: 0.7945 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 16778 Z= 0.203 Angle : 0.546 8.955 22896 Z= 0.284 Chirality : 0.041 0.287 2506 Planarity : 0.004 0.068 2709 Dihedral : 12.137 178.852 2713 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 7.79 % 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: 0.00 (0.20), residues: 1823 helix: 1.08 (0.20), residues: 685 sheet: -1.66 (0.30), residues: 259 loop : -0.21 (0.21), residues: 879 *********************** 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 319 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 192 time to evaluate : 1.847 Fit side-chains outliers start: 127 outliers final: 100 residues processed: 301 average time/residue: 1.0506 time to fit residues: 360.7198 Evaluate side-chains 270 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 170 time to evaluate : 1.815 Switching outliers to nearest non-outliers outliers start: 100 outliers final: 91 residues processed: 10 average time/residue: 0.3215 time to fit residues: 7.0893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 178 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 134 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 699 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 16778 Z= 0.234 Angle : 0.555 9.446 22896 Z= 0.286 Chirality : 0.041 0.290 2506 Planarity : 0.004 0.074 2709 Dihedral : 12.067 178.602 2713 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 8.16 % 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: 1.18 (0.20), residues: 685 sheet: -1.49 (0.31), residues: 246 loop : -0.20 (0.21), residues: 892 *********************** 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 314 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 181 time to evaluate : 1.776 Fit side-chains outliers start: 133 outliers final: 103 residues processed: 293 average time/residue: 1.0320 time to fit residues: 345.8149 Evaluate side-chains 274 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 171 time to evaluate : 1.612 Switching outliers to nearest non-outliers outliers start: 103 outliers final: 94 residues processed: 10 average time/residue: 0.4177 time to fit residues: 7.9198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 113 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 17 optimal weight: 0.0980 chunk 144 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 16778 Z= 0.219 Angle : 0.553 9.986 22896 Z= 0.285 Chirality : 0.041 0.271 2506 Planarity : 0.004 0.079 2709 Dihedral : 12.003 178.698 2713 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 7.48 % 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: 0.20 (0.20), residues: 1823 helix: 1.23 (0.20), residues: 685 sheet: -1.38 (0.32), residues: 240 loop : -0.18 (0.21), residues: 898 *********************** 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 304 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 182 time to evaluate : 1.788 Fit side-chains outliers start: 122 outliers final: 100 residues processed: 289 average time/residue: 1.0164 time to fit residues: 336.9253 Evaluate side-chains 273 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 173 time to evaluate : 1.859 Switching outliers to nearest non-outliers outliers start: 100 outliers final: 90 residues processed: 11 average time/residue: 0.2935 time to fit residues: 7.3532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 167 optimal weight: 0.7980 chunk 176 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 171 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 16778 Z= 0.269 Angle : 0.574 10.221 22896 Z= 0.296 Chirality : 0.042 0.272 2506 Planarity : 0.004 0.083 2709 Dihedral : 12.021 178.454 2713 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 6.69 % 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: 0.15 (0.20), residues: 1823 helix: 1.17 (0.20), residues: 685 sheet: -1.42 (0.32), residues: 240 loop : -0.20 (0.21), residues: 898 *********************** 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: 109 poor density : 175 time to evaluate : 1.946 Fit side-chains outliers start: 109 outliers final: 98 residues processed: 275 average time/residue: 1.0381 time to fit residues: 327.6507 Evaluate side-chains 266 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 168 time to evaluate : 1.987 Switching outliers to nearest non-outliers outliers start: 98 outliers final: 93 residues processed: 6 average time/residue: 0.3646 time to fit residues: 5.7446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 112 optimal weight: 7.9990 chunk 181 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 190 optimal weight: 0.5980 chunk 175 optimal weight: 10.0000 chunk 151 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 16778 Z= 0.312 Angle : 0.600 10.570 22896 Z= 0.307 Chirality : 0.043 0.275 2506 Planarity : 0.004 0.064 2709 Dihedral : 12.056 178.297 2713 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 6.63 % 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: 0.01 (0.19), residues: 1823 helix: 1.07 (0.20), residues: 685 sheet: -1.63 (0.31), residues: 254 loop : -0.21 (0.21), residues: 884 ********************** 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 283 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 175 time to evaluate : 1.893 Fit side-chains outliers start: 108 outliers final: 101 residues processed: 273 average time/residue: 1.0221 time to fit residues: 320.0093 Evaluate side-chains 269 residues out of total 1630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 168 time to evaluate : 1.668 Switching outliers to nearest non-outliers outliers start: 101 outliers final: 95 residues processed: 7 average time/residue: 0.4074 time to fit residues: 7.1961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 120 optimal weight: 5.9990 chunk 161 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 139 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 155 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.181966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.146876 restraints weight = 18255.807| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.74 r_work: 0.3605 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 16778 Z= 0.209 Angle : 0.563 10.438 22896 Z= 0.291 Chirality : 0.041 0.350 2506 Planarity : 0.004 0.084 2709 Dihedral : 11.991 178.799 2713 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 6.56 % 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: 685 sheet: -1.41 (0.32), residues: 240 loop : -0.20 (0.21), residues: 898 =============================================================================== Job complete usr+sys time: 5847.71 seconds wall clock time: 104 minutes 56.17 seconds (6296.17 seconds total)