Starting phenix.real_space_refine on Mon Jun 23 13:28:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gur_51617/06_2025/9gur_51617.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gur_51617/06_2025/9gur_51617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gur_51617/06_2025/9gur_51617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gur_51617/06_2025/9gur_51617.map" model { file = "/net/cci-nas-00/data/ceres_data/9gur_51617/06_2025/9gur_51617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gur_51617/06_2025/9gur_51617.cif" } resolution = 4.2 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= 0.001 sd= 0.027 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 2 6.06 5 P 73 5.49 5 Mg 1 5.21 5 S 113 5.16 5 C 16773 2.51 5 N 4797 2.21 5 O 5369 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27128 Number of models: 1 Model: "" Number of chains: 10 Chain: "1" Number of atoms: 1776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1776 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 219} Chain: "5" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 567 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "6" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 567 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "7" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 596 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "X" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 345 Classifications: {'RNA': 16} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna2p': 5, 'rna3p': 10} Chain: "2" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1685 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Chain: "3" Number of atoms: 10415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1320, 10415 Classifications: {'peptide': 1320} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1264} Chain breaks: 1 Chain: "4" Number of atoms: 10376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1333, 10376 Classifications: {'peptide': 1333} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1277} Chain breaks: 2 Chain: "Z" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 798 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain breaks: 1 Chain: "4" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16409 SG CYS 4 70 56.017 113.302 81.835 1.00249.05 S ATOM 16423 SG CYS 4 72 57.615 116.058 80.089 1.00239.22 S ATOM 16531 SG CYS 4 85 54.507 114.180 78.482 1.00248.78 S ATOM 16555 SG CYS 4 88 57.622 112.718 78.178 1.00247.74 S ATOM 22243 SG CYS 4 814 18.683 57.522 78.522 1.00212.45 S ATOM 22808 SG CYS 4 888 22.135 58.976 78.729 1.00216.99 S ATOM 22859 SG CYS 4 895 20.133 58.244 81.929 1.00210.70 S ATOM 22880 SG CYS 4 898 21.391 55.337 79.821 1.00202.48 S Time building chain proxies: 19.31, per 1000 atoms: 0.71 Number of scatterers: 27128 At special positions: 0 Unit cell: (153.72, 127.68, 165.48, 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 2 29.99 S 113 16.00 P 73 15.00 Mg 1 11.99 O 5369 8.00 N 4797 7.00 C 16773 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.57 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 41502 " pdb="ZN ZN 41502 " - pdb=" SG CYS 4 85 " pdb="ZN ZN 41502 " - pdb=" SG CYS 4 72 " pdb="ZN ZN 41502 " - pdb=" SG CYS 4 88 " pdb="ZN ZN 41502 " - pdb=" SG CYS 4 70 " pdb=" ZN 41503 " pdb="ZN ZN 41503 " - pdb=" SG CYS 4 814 " pdb="ZN ZN 41503 " - pdb=" SG CYS 4 898 " pdb="ZN ZN 41503 " - pdb=" SG CYS 4 895 " pdb="ZN ZN 41503 " - pdb=" SG CYS 4 888 " Number of angles added : 12 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6038 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 51 sheets defined 41.5% alpha, 18.3% beta 13 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 10.59 Creating SS restraints... Processing helix chain '1' and resid 34 through 51 Processing helix chain '1' and resid 77 through 88 Processing helix chain '1' and resid 113 through 115 No H-bonds generated for 'chain '1' and resid 113 through 115' Processing helix chain '1' and resid 154 through 163 Processing helix chain '1' and resid 212 through 231 removed outlier: 3.518A pdb=" N GLN 1 227 " --> pdb=" O ILE 1 223 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA 1 230 " --> pdb=" O GLU 1 226 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE 1 231 " --> pdb=" O GLN 1 227 " (cutoff:3.500A) Processing helix chain '5' and resid 8 through 14 removed outlier: 3.931A pdb=" N LYS 5 12 " --> pdb=" O ASP 5 8 " (cutoff:3.500A) Processing helix chain '5' and resid 15 through 32 removed outlier: 3.807A pdb=" N GLN 5 29 " --> pdb=" O ARG 5 25 " (cutoff:3.500A) Processing helix chain '5' and resid 45 through 56 Processing helix chain '5' and resid 60 through 72 Processing helix chain '2' and resid 34 through 50 removed outlier: 3.630A pdb=" N THR 2 38 " --> pdb=" O GLY 2 34 " (cutoff:3.500A) Processing helix chain '2' and resid 77 through 87 removed outlier: 3.558A pdb=" N GLY 2 87 " --> pdb=" O LEU 2 83 " (cutoff:3.500A) Processing helix chain '2' and resid 113 through 115 No H-bonds generated for 'chain '2' and resid 113 through 115' Processing helix chain '2' and resid 212 through 230 removed outlier: 3.503A pdb=" N ARG 2 218 " --> pdb=" O GLU 2 214 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA 2 230 " --> pdb=" O GLU 2 226 " (cutoff:3.500A) Processing helix chain '3' and resid 28 through 40 Processing helix chain '3' and resid 47 through 57 removed outlier: 3.691A pdb=" N ALA 3 51 " --> pdb=" O TYR 3 47 " (cutoff:3.500A) Processing helix chain '3' and resid 62 through 64 No H-bonds generated for 'chain '3' and resid 62 through 64' Processing helix chain '3' and resid 81 through 89 Processing helix chain '3' and resid 206 through 213 removed outlier: 3.693A pdb=" N LEU 3 210 " --> pdb=" O ALA 3 206 " (cutoff:3.500A) Processing helix chain '3' and resid 216 through 225 Processing helix chain '3' and resid 242 through 247 Processing helix chain '3' and resid 270 through 280 Processing helix chain '3' and resid 288 through 295 removed outlier: 3.715A pdb=" N ILE 3 292 " --> pdb=" O PRO 3 288 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS 3 295 " --> pdb=" O TYR 3 291 " (cutoff:3.500A) Processing helix chain '3' and resid 318 through 328 Processing helix chain '3' and resid 345 through 354 Processing helix chain '3' and resid 358 through 371 Processing helix chain '3' and resid 377 through 390 removed outlier: 3.730A pdb=" N PHE 3 389 " --> pdb=" O PHE 3 385 " (cutoff:3.500A) Processing helix chain '3' and resid 398 through 409 Processing helix chain '3' and resid 421 through 437 Processing helix chain '3' and resid 447 through 449 No H-bonds generated for 'chain '3' and resid 447 through 449' Processing helix chain '3' and resid 455 through 482 removed outlier: 3.758A pdb=" N ALA 3 474 " --> pdb=" O ARG 3 470 " (cutoff:3.500A) Processing helix chain '3' and resid 488 through 493 Processing helix chain '3' and resid 495 through 509 Processing helix chain '3' and resid 519 through 528 Processing helix chain '3' and resid 544 through 549 Processing helix chain '3' and resid 551 through 555 Processing helix chain '3' and resid 565 through 569 removed outlier: 4.016A pdb=" N ASN 3 568 " --> pdb=" O GLU 3 565 " (cutoff:3.500A) Processing helix chain '3' and resid 607 through 612 Processing helix chain '3' and resid 656 through 661 removed outlier: 3.648A pdb=" N VAL 3 660 " --> pdb=" O THR 3 657 " (cutoff:3.500A) Processing helix chain '3' and resid 662 through 667 Processing helix chain '3' and resid 670 through 674 Processing helix chain '3' and resid 675 through 689 removed outlier: 3.908A pdb=" N ARG 3 687 " --> pdb=" O ALA 3 683 " (cutoff:3.500A) Processing helix chain '3' and resid 704 through 713 removed outlier: 3.751A pdb=" N GLY 3 713 " --> pdb=" O ALA 3 709 " (cutoff:3.500A) Processing helix chain '3' and resid 738 through 741 Processing helix chain '3' and resid 819 through 825 removed outlier: 4.006A pdb=" N VAL 3 823 " --> pdb=" O SER 3 819 " (cutoff:3.500A) Processing helix chain '3' and resid 858 through 865 Processing helix chain '3' and resid 942 through 980 removed outlier: 3.501A pdb=" N VAL 3 978 " --> pdb=" O ARG 3 974 " (cutoff:3.500A) Processing helix chain '3' and resid 985 through 989 Processing helix chain '3' and resid 995 through 1000 removed outlier: 3.878A pdb=" N LEU 31000 " --> pdb=" O TRP 3 997 " (cutoff:3.500A) Processing helix chain '3' and resid 1005 through 1038 Processing helix chain '3' and resid 1081 through 1085 Processing helix chain '3' and resid 1101 through 1107 removed outlier: 3.800A pdb=" N SER 31105 " --> pdb=" O LEU 31101 " (cutoff:3.500A) Processing helix chain '3' and resid 1109 through 1134 Processing helix chain '3' and resid 1137 through 1151 Processing helix chain '3' and resid 1160 through 1164 Processing helix chain '3' and resid 1167 through 1177 Processing helix chain '3' and resid 1191 through 1202 Processing helix chain '3' and resid 1238 through 1242 Processing helix chain '3' and resid 1271 through 1281 removed outlier: 3.504A pdb=" N TRP 31276 " --> pdb=" O GLU 31272 " (cutoff:3.500A) Processing helix chain '3' and resid 1284 through 1292 Processing helix chain '3' and resid 1297 through 1311 Processing helix chain '3' and resid 1320 through 1333 removed outlier: 3.844A pdb=" N ASN 31324 " --> pdb=" O PRO 31320 " (cutoff:3.500A) Processing helix chain '4' and resid 26 through 33 Processing helix chain '4' and resid 58 through 63 Processing helix chain '4' and resid 77 through 81 Processing helix chain '4' and resid 95 through 101 removed outlier: 3.946A pdb=" N ARG 4 99 " --> pdb=" O THR 4 95 " (cutoff:3.500A) Processing helix chain '4' and resid 113 through 119 removed outlier: 3.580A pdb=" N LEU 4 117 " --> pdb=" O HIS 4 113 " (cutoff:3.500A) Processing helix chain '4' and resid 122 through 129 Processing helix chain '4' and resid 131 through 140 removed outlier: 3.536A pdb=" N ARG 4 137 " --> pdb=" O ARG 4 133 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL 4 138 " --> pdb=" O ASP 4 134 " (cutoff:3.500A) Processing helix chain '4' and resid 148 through 152 removed outlier: 4.165A pdb=" N MET 4 151 " --> pdb=" O GLU 4 148 " (cutoff:3.500A) Processing helix chain '4' and resid 161 through 172 Processing helix chain '4' and resid 180 through 192 removed outlier: 3.527A pdb=" N ALA 4 184 " --> pdb=" O MET 4 180 " (cutoff:3.500A) Processing helix chain '4' and resid 193 through 208 removed outlier: 3.535A pdb=" N GLU 4 207 " --> pdb=" O GLU 4 203 " (cutoff:3.500A) Processing helix chain '4' and resid 210 through 230 removed outlier: 3.566A pdb=" N LYS 4 216 " --> pdb=" O THR 4 212 " (cutoff:3.500A) Processing helix chain '4' and resid 233 through 236 Processing helix chain '4' and resid 246 through 250 Processing helix chain '4' and resid 263 through 286 Processing helix chain '4' and resid 288 through 308 Processing helix chain '4' and resid 326 through 332 removed outlier: 3.811A pdb=" N MET 4 330 " --> pdb=" O SER 4 326 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE 4 331 " --> pdb=" O LEU 4 327 " (cutoff:3.500A) Processing helix chain '4' and resid 336 through 341 Processing helix chain '4' and resid 370 through 377 Processing helix chain '4' and resid 377 through 389 Processing helix chain '4' and resid 393 through 404 removed outlier: 3.693A pdb=" N ARG 4 403 " --> pdb=" O LYS 4 399 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU 4 404 " --> pdb=" O MET 4 400 " (cutoff:3.500A) Processing helix chain '4' and resid 405 through 416 Processing helix chain '4' and resid 430 through 432 No H-bonds generated for 'chain '4' and resid 430 through 432' Processing helix chain '4' and resid 450 through 458 removed outlier: 3.644A pdb=" N ALA 4 455 " --> pdb=" O PRO 4 451 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA 4 456 " --> pdb=" O LEU 4 452 " (cutoff:3.500A) Processing helix chain '4' and resid 473 through 483 Processing helix chain '4' and resid 485 through 490 removed outlier: 4.253A pdb=" N ILE 4 490 " --> pdb=" O THR 4 487 " (cutoff:3.500A) Processing helix chain '4' and resid 503 through 515 Processing helix chain '4' and resid 529 through 539 Processing helix chain '4' and resid 574 through 583 removed outlier: 3.824A pdb=" N ILE 4 582 " --> pdb=" O ILE 4 578 " (cutoff:3.500A) Processing helix chain '4' and resid 588 through 593 Processing helix chain '4' and resid 597 through 613 Processing helix chain '4' and resid 613 through 636 removed outlier: 3.789A pdb=" N THR 4 617 " --> pdb=" O GLY 4 613 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE 4 619 " --> pdb=" O LYS 4 615 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY 4 636 " --> pdb=" O ALA 4 632 " (cutoff:3.500A) Processing helix chain '4' and resid 640 through 644 Processing helix chain '4' and resid 648 through 670 removed outlier: 3.625A pdb=" N GLU 4 652 " --> pdb=" O GLU 4 648 " (cutoff:3.500A) Processing helix chain '4' and resid 674 through 704 Processing helix chain '4' and resid 720 through 728 Processing helix chain '4' and resid 733 through 742 Processing helix chain '4' and resid 768 through 805 removed outlier: 3.925A pdb=" N HIS 4 777 " --> pdb=" O PHE 4 773 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY 4 778 " --> pdb=" O ILE 4 774 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR 4 795 " --> pdb=" O ALA 4 791 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL 4 803 " --> pdb=" O ARG 4 799 " (cutoff:3.500A) Processing helix chain '4' and resid 834 through 840 removed outlier: 3.807A pdb=" N ARG 4 838 " --> pdb=" O PRO 4 834 " (cutoff:3.500A) Processing helix chain '4' and resid 865 through 875 Processing helix chain '4' and resid 896 through 900 Processing helix chain '4' and resid 914 through 928 removed outlier: 4.224A pdb=" N ILE 4 918 " --> pdb=" O ALA 4 914 " (cutoff:3.500A) Proline residue: 4 926 - end of helix Processing helix chain '4' and resid 1051 through 1055 removed outlier: 3.891A pdb=" N GLY 41055 " --> pdb=" O GLU 41052 " (cutoff:3.500A) Processing helix chain '4' and resid 1068 through 1074 removed outlier: 3.550A pdb=" N LYS 41072 " --> pdb=" O THR 41068 " (cutoff:3.500A) Processing helix chain '4' and resid 1137 through 1147 Processing helix chain '4' and resid 1216 through 1245 removed outlier: 7.772A pdb=" N VAL 41226 " --> pdb=" O ARG 41222 " (cutoff:3.500A) removed outlier: 9.156A pdb=" N HIS 41227 " --> pdb=" O LEU 41223 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA 41228 " --> pdb=" O ARG 41224 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR 41230 " --> pdb=" O VAL 41226 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL 41240 " --> pdb=" O GLU 41236 " (cutoff:3.500A) Processing helix chain '4' and resid 1250 through 1261 removed outlier: 3.509A pdb=" N ILE 41256 " --> pdb=" O HIS 41252 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN 41259 " --> pdb=" O VAL 41255 " (cutoff:3.500A) Processing helix chain '4' and resid 1282 through 1295 Processing helix chain '4' and resid 1308 through 1316 Processing helix chain '4' and resid 1318 through 1326 removed outlier: 3.686A pdb=" N ALA 41322 " --> pdb=" O SER 41318 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN 41326 " --> pdb=" O ALA 41322 " (cutoff:3.500A) Processing helix chain '4' and resid 1327 through 1339 Processing helix chain '4' and resid 1346 through 1354 removed outlier: 3.930A pdb=" N ASN 41350 " --> pdb=" O GLY 41346 " (cutoff:3.500A) Processing helix chain '4' and resid 1359 through 1373 removed outlier: 3.716A pdb=" N ALA 41364 " --> pdb=" O GLY 41360 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR 41365 " --> pdb=" O THR 41361 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 34 removed outlier: 4.221A pdb=" N ARG Z 21 " --> pdb=" O GLY Z 17 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ARG Z 27 " --> pdb=" O ALA Z 23 " (cutoff:3.500A) Processing helix chain 'Z' and resid 35 through 37 No H-bonds generated for 'chain 'Z' and resid 35 through 37' Processing helix chain 'Z' and resid 76 through 86 removed outlier: 4.018A pdb=" N VAL Z 86 " --> pdb=" O LEU Z 82 " (cutoff:3.500A) Processing helix chain 'Z' and resid 104 through 117 removed outlier: 3.571A pdb=" N ASN Z 113 " --> pdb=" O ASP Z 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 12 through 17 removed outlier: 5.187A pdb=" N LEU 1 13 " --> pdb=" O GLU 1 29 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLU 1 29 " --> pdb=" O LEU 1 13 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP 1 15 " --> pdb=" O THR 1 27 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASP 1 199 " --> pdb=" O PRO 1 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 53 through 56 Processing sheet with id=AA3, first strand: chain '1' and resid 59 through 60 Processing sheet with id=AA4, first strand: chain '1' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain '1' and resid 108 through 111 removed outlier: 3.709A pdb=" N VAL 1 110 " --> pdb=" O CYS 1 131 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N CYS 1 131 " --> pdb=" O VAL 1 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 152 through 153 Processing sheet with id=AA7, first strand: chain '2' and resid 17 through 20 removed outlier: 3.827A pdb=" N VAL 2 19 " --> pdb=" O HIS 2 23 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N HIS 2 23 " --> pdb=" O VAL 2 19 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA 2 24 " --> pdb=" O MET 2 205 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N MET 2 205 " --> pdb=" O ALA 2 24 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASP 2 199 " --> pdb=" O PRO 2 30 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N THR 2 196 " --> pdb=" O VAL 2 192 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL 2 192 " --> pdb=" O THR 2 196 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU 2 198 " --> pdb=" O ALA 2 190 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '2' and resid 52 through 56 Processing sheet with id=AA9, first strand: chain '2' and resid 90 through 92 Processing sheet with id=AB1, first strand: chain '2' and resid 109 through 111 removed outlier: 3.753A pdb=" N CYS 2 131 " --> pdb=" O VAL 2 110 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '2' and resid 152 through 153 Processing sheet with id=AB3, first strand: chain '3' and resid 59 through 61 removed outlier: 5.834A pdb=" N SER 3 66 " --> pdb=" O TYR 3 105 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N TYR 3 105 " --> pdb=" O SER 3 66 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LEU 3 68 " --> pdb=" O VAL 3 103 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL 3 103 " --> pdb=" O LEU 3 68 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N TYR 3 70 " --> pdb=" O ARG 3 101 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ARG 3 101 " --> pdb=" O TYR 3 70 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER 3 72 " --> pdb=" O LYS 3 99 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '3' and resid 59 through 61 removed outlier: 5.834A pdb=" N SER 3 66 " --> pdb=" O TYR 3 105 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N TYR 3 105 " --> pdb=" O SER 3 66 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LEU 3 68 " --> pdb=" O VAL 3 103 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL 3 103 " --> pdb=" O LEU 3 68 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N TYR 3 70 " --> pdb=" O ARG 3 101 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ARG 3 101 " --> pdb=" O TYR 3 70 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER 3 72 " --> pdb=" O LYS 3 99 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY 3 125 " --> pdb=" O LEU 3 96 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL 3 98 " --> pdb=" O TYR 3 123 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N TYR 3 123 " --> pdb=" O VAL 3 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '3' and resid 136 through 138 Processing sheet with id=AB6, first strand: chain '3' and resid 451 through 454 Processing sheet with id=AB7, first strand: chain '3' and resid 154 through 160 removed outlier: 4.029A pdb=" N LEU 3 171 " --> pdb=" O ASP 3 160 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N TYR 3 172 " --> pdb=" O PHE 3 188 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '3' and resid 180 through 181 Processing sheet with id=AB9, first strand: chain '3' and resid 238 through 239 Processing sheet with id=AC1, first strand: chain '3' and resid 255 through 257 removed outlier: 6.803A pdb=" N ILE 3 255 " --> pdb=" O TYR 3 262 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '3' and resid 580 through 581 removed outlier: 6.836A pdb=" N LEU 3 587 " --> pdb=" O LEU 3 606 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU 3 606 " --> pdb=" O LEU 3 587 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N THR 3 589 " --> pdb=" O HIS 3 604 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N HIS 3 604 " --> pdb=" O THR 3 589 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N TYR 3 591 " --> pdb=" O GLU 3 602 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLU 3 602 " --> pdb=" O TYR 3 591 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS 3 593 " --> pdb=" O THR 3 600 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '3' and resid 580 through 581 removed outlier: 3.542A pdb=" N ASP 3 654 " --> pdb=" O ALA 3 617 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '3' and resid 716 through 717 removed outlier: 6.281A pdb=" N ALA 3 716 " --> pdb=" O LEU 3 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '3' and resid 748 through 752 Processing sheet with id=AC6, first strand: chain '3' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain '3' and resid 817 through 818 removed outlier: 3.644A pdb=" N VAL 31097 " --> pdb=" O LEU 3 817 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N ILE 31096 " --> pdb=" O ASN 3 799 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG 3 801 " --> pdb=" O ILE 31096 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LEU 31098 " --> pdb=" O ARG 3 801 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA 3 803 " --> pdb=" O LEU 31098 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR 31226 " --> pdb=" O PHE 3 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '3' and resid 817 through 818 removed outlier: 3.644A pdb=" N VAL 31097 " --> pdb=" O LEU 3 817 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N ILE 31096 " --> pdb=" O ASN 3 799 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG 3 801 " --> pdb=" O ILE 31096 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LEU 31098 " --> pdb=" O ARG 3 801 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA 3 803 " --> pdb=" O LEU 31098 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR 31226 " --> pdb=" O PHE 3 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '3' and resid 830 through 841 removed outlier: 4.586A pdb=" N LYS 31048 " --> pdb=" O SER 3 840 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LYS 31057 " --> pdb=" O SER 3 925 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N SER 3 925 " --> pdb=" O LYS 31057 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '3' and resid 830 through 841 removed outlier: 4.586A pdb=" N LYS 31048 " --> pdb=" O SER 3 840 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '3' and resid 849 through 850 removed outlier: 3.619A pdb=" N GLU 3 849 " --> pdb=" O VAL 3 887 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '3' and resid 882 through 884 removed outlier: 6.768A pdb=" N LEU 3 918 " --> pdb=" O LEU 3 883 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '3' and resid 1244 through 1246 removed outlier: 3.625A pdb=" N GLN 4 435 " --> pdb=" O LEU 4 423 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE 4 447 " --> pdb=" O ARG 4 352 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL 4 354 " --> pdb=" O ILE 4 447 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LEU 4 449 " --> pdb=" O VAL 4 354 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR 4 356 " --> pdb=" O LEU 4 449 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '3' and resid 1269 through 1270 Processing sheet with id=AD6, first strand: chain '3' and resid 1335 through 1340 Processing sheet with id=AD7, first strand: chain '4' and resid 34 through 37 removed outlier: 4.535A pdb=" N SER 4 34 " --> pdb=" O MET 4 102 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N HIS 4 104 " --> pdb=" O SER 4 34 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLY 4 36 " --> pdb=" O HIS 4 104 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N GLU 4 106 " --> pdb=" O GLY 4 36 " (cutoff:3.500A) removed outlier: 10.072A pdb=" N LEU 4 107 " --> pdb=" O PRO 4 243 " (cutoff:3.500A) removed outlier: 9.901A pdb=" N SER 4 109 " --> pdb=" O VAL 4 241 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL 4 241 " --> pdb=" O SER 4 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '4' and resid 159 through 160 Processing sheet with id=AD9, first strand: chain '4' and resid 526 through 527 removed outlier: 6.870A pdb=" N LEU 4 527 " --> pdb=" O ARG 4 551 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N THR 4 553 " --> pdb=" O LEU 4 527 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '4' and resid 706 through 708 Processing sheet with id=AE2, first strand: chain '4' and resid 809 through 811 Processing sheet with id=AE3, first strand: chain '4' and resid 820 through 822 Processing sheet with id=AE4, first strand: chain '4' and resid 848 through 849 removed outlier: 6.332A pdb=" N VAL 4 848 " --> pdb=" O LEU 4 857 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain '4' and resid 990 through 991 Processing sheet with id=AE6, first strand: chain '4' and resid 990 through 991 Processing sheet with id=AE7, first strand: chain '4' and resid 965 through 967 removed outlier: 4.079A pdb=" N LEU 4 973 " --> pdb=" O LEU 41003 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '4' and resid 1024 through 1025 Processing sheet with id=AE9, first strand: chain '4' and resid 1028 through 1029 removed outlier: 3.521A pdb=" N ASP 41119 " --> pdb=" O THR 41029 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain '4' and resid 1099 through 1100 removed outlier: 4.043A pdb=" N LYS 41079 " --> pdb=" O ARG 41036 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL 41113 " --> pdb=" O VAL 41035 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain '4' and resid 1046 through 1049 removed outlier: 3.600A pdb=" N SER 41058 " --> pdb=" O GLN 41049 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU 41059 " --> pdb=" O VAL 41107 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain '4' and resid 1186 through 1190 removed outlier: 3.840A pdb=" N TYR 41186 " --> pdb=" O ILE 41177 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain '4' and resid 1277 through 1281 Processing sheet with id=AF5, first strand: chain 'Z' and resid 39 through 43 removed outlier: 3.769A pdb=" N GLU Z 41 " --> pdb=" O GLN Z 72 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY Z 91 " --> pdb=" O GLN Z 13 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Z' and resid 94 through 96 removed outlier: 3.654A pdb=" N THR Z 96 " --> pdb=" O ARG Z 99 " (cutoff:3.500A) 1175 hydrogen bonds defined for protein. 3243 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 13.26 Time building geometry restraints manager: 8.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8927 1.34 - 1.46: 3595 1.46 - 1.57: 14825 1.57 - 1.69: 143 1.69 - 1.81: 198 Bond restraints: 27688 Sorted by residual: bond pdb=" O3' DC 7 24 " pdb=" P DG 7 25 " ideal model delta sigma weight residual 1.607 1.676 -0.069 1.50e-02 4.44e+03 2.11e+01 bond pdb=" N VAL Z 69 " pdb=" CA VAL Z 69 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.17e-02 7.31e+03 1.05e+01 bond pdb=" N PHE Z 65 " pdb=" CA PHE Z 65 " ideal model delta sigma weight residual 1.462 1.493 -0.030 1.07e-02 8.73e+03 8.03e+00 bond pdb=" N PHE Z 64 " pdb=" CA PHE Z 64 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.53e+00 bond pdb=" C PHE Z 65 " pdb=" N PRO Z 66 " ideal model delta sigma weight residual 1.334 1.393 -0.059 2.34e-02 1.83e+03 6.37e+00 ... (remaining 27683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 37495 2.92 - 5.85: 205 5.85 - 8.77: 9 8.77 - 11.69: 3 11.69 - 14.62: 3 Bond angle restraints: 37715 Sorted by residual: angle pdb=" C2' DG 7 37 " pdb=" C1' DG 7 37 " pdb=" N9 DG 7 37 " ideal model delta sigma weight residual 113.50 128.12 -14.62 1.50e+00 4.44e-01 9.49e+01 angle pdb=" C2' DA 6 6 " pdb=" C1' DA 6 6 " pdb=" N9 DA 6 6 " ideal model delta sigma weight residual 113.50 126.17 -12.67 1.50e+00 4.44e-01 7.13e+01 angle pdb=" C2' DT 7 34 " pdb=" C1' DT 7 34 " pdb=" N1 DT 7 34 " ideal model delta sigma weight residual 113.50 125.45 -11.95 1.50e+00 4.44e-01 6.35e+01 angle pdb=" C2' DA 6 7 " pdb=" C1' DA 6 7 " pdb=" N9 DA 6 7 " ideal model delta sigma weight residual 113.50 125.16 -11.66 1.50e+00 4.44e-01 6.04e+01 angle pdb=" C2' DA 7 28 " pdb=" C1' DA 7 28 " pdb=" N9 DA 7 28 " ideal model delta sigma weight residual 113.50 124.42 -10.92 1.50e+00 4.44e-01 5.30e+01 ... (remaining 37710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.86: 16381 34.86 - 69.71: 457 69.71 - 104.57: 40 104.57 - 139.43: 2 139.43 - 174.28: 1 Dihedral angle restraints: 16881 sinusoidal: 7496 harmonic: 9385 Sorted by residual: dihedral pdb=" CA GLY 41166 " pdb=" C GLY 41166 " pdb=" N LYS 41167 " pdb=" CA LYS 41167 " ideal model delta harmonic sigma weight residual 180.00 136.78 43.22 0 5.00e+00 4.00e-02 7.47e+01 dihedral pdb=" CA PHE 41165 " pdb=" C PHE 41165 " pdb=" N GLY 41166 " pdb=" CA GLY 41166 " ideal model delta harmonic sigma weight residual 180.00 137.30 42.70 0 5.00e+00 4.00e-02 7.29e+01 dihedral pdb=" O4' C X 41 " pdb=" C1' C X 41 " pdb=" N1 C X 41 " pdb=" C2 C X 41 " ideal model delta sinusoidal sigma weight residual 200.00 78.86 121.14 1 1.50e+01 4.44e-03 6.47e+01 ... (remaining 16878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.172: 4300 0.172 - 0.345: 2 0.345 - 0.517: 1 0.517 - 0.689: 1 0.689 - 0.862: 4 Chirality restraints: 4308 Sorted by residual: chirality pdb=" C1' DG 7 37 " pdb=" O4' DG 7 37 " pdb=" C2' DG 7 37 " pdb=" N9 DG 7 37 " both_signs ideal model delta sigma weight residual False 2.42 1.56 0.86 2.00e-01 2.50e+01 1.86e+01 chirality pdb=" C1' DT 7 34 " pdb=" O4' DT 7 34 " pdb=" C2' DT 7 34 " pdb=" N1 DT 7 34 " both_signs ideal model delta sigma weight residual False 2.47 1.65 0.82 2.00e-01 2.50e+01 1.68e+01 chirality pdb=" C1' DA 6 6 " pdb=" O4' DA 6 6 " pdb=" C2' DA 6 6 " pdb=" N9 DA 6 6 " both_signs ideal model delta sigma weight residual False 2.42 1.66 0.76 2.00e-01 2.50e+01 1.45e+01 ... (remaining 4305 not shown) Planarity restraints: 4684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL Z 69 " 0.019 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C VAL Z 69 " -0.068 2.00e-02 2.50e+03 pdb=" O VAL Z 69 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU Z 70 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE Z 64 " 0.018 2.00e-02 2.50e+03 1.25e-02 2.74e+00 pdb=" CG PHE Z 64 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE Z 64 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE Z 64 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE Z 64 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE Z 64 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE Z 64 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS 3 551 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO 3 552 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO 3 552 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO 3 552 " 0.022 5.00e-02 4.00e+02 ... (remaining 4681 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 62 2.37 - 3.00: 17096 3.00 - 3.63: 42052 3.63 - 4.27: 63639 4.27 - 4.90: 101976 Nonbonded interactions: 224825 Sorted by model distance: nonbonded pdb=" OD1 ASP 4 460 " pdb="MG MG 41501 " model vdw 1.737 2.170 nonbonded pdb=" OD1 ASP 4 462 " pdb="MG MG 41501 " model vdw 1.789 2.170 nonbonded pdb=" OD1 ASP 4 464 " pdb="MG MG 41501 " model vdw 1.804 2.170 nonbonded pdb=" OG1 THR 3 595 " pdb=" OG1 THR 3 600 " model vdw 1.965 3.040 nonbonded pdb=" O2' A X 38 " pdb=" O2 C X 39 " model vdw 2.027 3.040 ... (remaining 224820 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '1' and (resid 6 through 157 or resid 169 through 233)) selection = (chain '2' and (resid 6 through 232 or (resid 233 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name OD2)))) } 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 group one per residue 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: 135.250 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: 0.040 Extract box with map and model: 1.050 Check model and map are aligned: 0.220 Set scattering table: 0.250 Process input model: 81.170 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.120 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 221.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 27696 Z= 0.154 Angle : 0.630 14.615 37727 Z= 0.360 Chirality : 0.049 0.862 4308 Planarity : 0.004 0.049 4684 Dihedral : 15.206 174.284 10843 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.91 % Favored : 93.97 % Rotamer: Outliers : 2.62 % Allowed : 8.10 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.13 (0.14), residues: 3249 helix: -0.25 (0.14), residues: 1131 sheet: -0.39 (0.23), residues: 439 loop : -1.15 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP 3 183 HIS 0.005 0.001 HIS 3 150 PHE 0.026 0.001 PHE Z 64 TYR 0.014 0.001 TYR 31251 ARG 0.003 0.000 ARG 4 250 Details of bonding type rmsd hydrogen bonds : bond 0.24473 ( 1182) hydrogen bonds : angle 8.51590 ( 3315) metal coordination : bond 0.00728 ( 8) metal coordination : angle 6.07420 ( 12) covalent geometry : bond 0.00304 (27688) covalent geometry : angle 0.62029 (37715) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 227 time to evaluate : 7.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 214 GLU cc_start: 0.9092 (tt0) cc_final: 0.8879 (tt0) REVERT: 5 66 VAL cc_start: 0.9737 (t) cc_final: 0.9390 (t) REVERT: 2 17 GLU cc_start: 0.9286 (OUTLIER) cc_final: 0.8815 (tm-30) REVERT: 2 118 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8012 (p0) REVERT: 2 205 MET cc_start: 0.9198 (ppp) cc_final: 0.8784 (ppp) REVERT: 2 228 LEU cc_start: 0.9159 (mt) cc_final: 0.8677 (pp) REVERT: 3 1 MET cc_start: 0.5475 (tpt) cc_final: 0.5164 (tpp) REVERT: 3 459 MET cc_start: 0.8784 (mtm) cc_final: 0.8457 (mtt) REVERT: 3 834 GLN cc_start: 0.9598 (mt0) cc_final: 0.9324 (mp10) REVERT: 3 1066 MET cc_start: 0.9314 (tpt) cc_final: 0.8864 (mmm) REVERT: 3 1233 LEU cc_start: 0.9445 (mp) cc_final: 0.8921 (mt) REVERT: 3 1243 MET cc_start: 0.9366 (tmm) cc_final: 0.9009 (tmm) REVERT: 3 1273 MET cc_start: 0.9641 (mtp) cc_final: 0.9420 (mtm) REVERT: 3 1329 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8801 (mt-10) REVERT: 4 102 MET cc_start: 0.8474 (mtm) cc_final: 0.7984 (ptm) REVERT: 4 192 MET cc_start: 0.9442 (mmm) cc_final: 0.9004 (tpp) REVERT: 4 338 PHE cc_start: 0.9408 (m-80) cc_final: 0.9207 (m-80) REVERT: 4 372 MET cc_start: 0.9123 (mtp) cc_final: 0.8711 (mtt) REVERT: 4 400 MET cc_start: 0.9269 (tpp) cc_final: 0.9026 (tpp) REVERT: 4 660 GLU cc_start: 0.9439 (OUTLIER) cc_final: 0.9151 (tp30) REVERT: 4 807 LEU cc_start: 0.8912 (mt) cc_final: 0.8509 (mp) REVERT: 4 895 CYS cc_start: 0.7717 (OUTLIER) cc_final: 0.6619 (p) REVERT: 4 986 ASP cc_start: 0.8977 (OUTLIER) cc_final: 0.8521 (p0) REVERT: 4 1025 MET cc_start: 0.8771 (mtm) cc_final: 0.8562 (mtm) REVERT: 4 1040 MET cc_start: 0.7876 (mtp) cc_final: 0.7435 (mtm) REVERT: 4 1075 ARG cc_start: 0.5559 (tpt170) cc_final: 0.4264 (ptt180) REVERT: 4 1260 MET cc_start: 0.9364 (mtp) cc_final: 0.9062 (mmm) REVERT: Z 68 TYR cc_start: 0.6474 (OUTLIER) cc_final: 0.6197 (m-80) REVERT: Z 90 MET cc_start: 0.9323 (mpp) cc_final: 0.8311 (mpp) outliers start: 73 outliers final: 27 residues processed: 287 average time/residue: 0.5265 time to fit residues: 240.6421 Evaluate side-chains 187 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 4.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 277 optimal weight: 9.9990 chunk 249 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 85 optimal weight: 20.0000 chunk 168 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 257 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 191 optimal weight: 6.9990 chunk 298 optimal weight: 2.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 132 HIS ** 2 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 235 ASN 3 357 ASN 3 568 ASN 3 573 ASN 3 628 HIS ** 3 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 824 GLN ** 3 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 31038 GLN 31146 GLN ** 31157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 477 GLN 4 488 ASN ** 4 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 910 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 41218 HIS ** 41279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.038302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.029504 restraints weight = 281398.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.030309 restraints weight = 182140.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.030879 restraints weight = 134535.828| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 27696 Z= 0.298 Angle : 0.829 14.223 37727 Z= 0.430 Chirality : 0.046 0.181 4308 Planarity : 0.005 0.061 4684 Dihedral : 15.182 169.194 4439 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.03 % Favored : 93.91 % Rotamer: Outliers : 0.18 % Allowed : 5.59 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.84 (0.14), residues: 3249 helix: 0.22 (0.14), residues: 1198 sheet: -0.59 (0.23), residues: 430 loop : -1.09 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP 3 997 HIS 0.008 0.002 HIS 4 430 PHE 0.028 0.003 PHE 3 186 TYR 0.026 0.003 TYR Z 68 ARG 0.013 0.001 ARG 1 91 Details of bonding type rmsd hydrogen bonds : bond 0.05801 ( 1182) hydrogen bonds : angle 6.06575 ( 3315) metal coordination : bond 0.01983 ( 8) metal coordination : angle 7.49732 ( 12) covalent geometry : bond 0.00613 (27688) covalent geometry : angle 0.81825 (37715) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 176 time to evaluate : 3.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 205 MET cc_start: 0.9216 (pmm) cc_final: 0.8987 (pmm) REVERT: 5 51 LEU cc_start: 0.9560 (tt) cc_final: 0.9095 (tt) REVERT: 5 55 GLU cc_start: 0.9356 (pt0) cc_final: 0.8986 (pt0) REVERT: 2 228 LEU cc_start: 0.9348 (mt) cc_final: 0.8882 (pp) REVERT: 3 1 MET cc_start: 0.5364 (tpt) cc_final: 0.5122 (tpp) REVERT: 3 403 MET cc_start: 0.9442 (tmm) cc_final: 0.9082 (tmm) REVERT: 3 492 MET cc_start: 0.8378 (mmp) cc_final: 0.7411 (tpp) REVERT: 3 515 MET cc_start: 0.8723 (tmm) cc_final: 0.7396 (tmm) REVERT: 3 604 HIS cc_start: 0.8289 (OUTLIER) cc_final: 0.8007 (m-70) REVERT: 3 1119 MET cc_start: 0.9178 (tpp) cc_final: 0.8944 (tpp) REVERT: 3 1233 LEU cc_start: 0.9434 (mp) cc_final: 0.8911 (mm) REVERT: 3 1235 LEU cc_start: 0.9503 (mp) cc_final: 0.9234 (mp) REVERT: 3 1243 MET cc_start: 0.9573 (tmm) cc_final: 0.9312 (tmm) REVERT: 3 1304 MET cc_start: 0.9370 (mmm) cc_final: 0.9143 (mmm) REVERT: 3 1329 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8732 (mt-10) REVERT: 4 400 MET cc_start: 0.9182 (tpp) cc_final: 0.8863 (tpp) REVERT: 4 424 ASN cc_start: 0.9352 (p0) cc_final: 0.9002 (p0) REVERT: 4 454 CYS cc_start: 0.8954 (p) cc_final: 0.8622 (p) REVERT: 4 466 MET cc_start: 0.9174 (mmm) cc_final: 0.8917 (tmm) REVERT: 4 807 LEU cc_start: 0.8875 (mt) cc_final: 0.8573 (mp) REVERT: 4 1025 MET cc_start: 0.8958 (mtm) cc_final: 0.8742 (mtm) REVERT: 4 1040 MET cc_start: 0.7974 (mtp) cc_final: 0.7687 (mtm) REVERT: 4 1075 ARG cc_start: 0.5823 (tpm170) cc_final: 0.4808 (ptt180) REVERT: 4 1256 ILE cc_start: 0.9692 (mp) cc_final: 0.9444 (tp) REVERT: 4 1332 LEU cc_start: 0.9924 (mm) cc_final: 0.9723 (mm) REVERT: Z 90 MET cc_start: 0.9215 (mpp) cc_final: 0.8709 (mpp) outliers start: 5 outliers final: 1 residues processed: 181 average time/residue: 0.3974 time to fit residues: 120.1601 Evaluate side-chains 137 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 135 time to evaluate : 3.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 4 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 286 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 308 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 153 optimal weight: 20.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 165 HIS 3 658 GLN ** 3 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 31157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 690 ASN ** 4 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 41279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.038962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.030112 restraints weight = 264143.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.030914 restraints weight = 175718.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.031484 restraints weight = 130987.826| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 27696 Z= 0.172 Angle : 0.658 10.986 37727 Z= 0.348 Chirality : 0.043 0.174 4308 Planarity : 0.004 0.043 4684 Dihedral : 14.884 174.261 4439 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.66 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.40 (0.14), residues: 3249 helix: 0.81 (0.15), residues: 1191 sheet: -0.63 (0.24), residues: 398 loop : -0.95 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 3 183 HIS 0.004 0.001 HIS 1 132 PHE 0.019 0.001 PHE 41145 TYR 0.023 0.002 TYR 31231 ARG 0.008 0.001 ARG 4 978 Details of bonding type rmsd hydrogen bonds : bond 0.04713 ( 1182) hydrogen bonds : angle 5.51901 ( 3315) metal coordination : bond 0.01017 ( 8) metal coordination : angle 6.12362 ( 12) covalent geometry : bond 0.00360 (27688) covalent geometry : angle 0.64945 (37715) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 5.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 205 MET cc_start: 0.9168 (pmm) cc_final: 0.8948 (pmm) REVERT: 5 19 LEU cc_start: 0.9761 (tp) cc_final: 0.9559 (tp) REVERT: 2 228 LEU cc_start: 0.9377 (mt) cc_final: 0.8839 (pp) REVERT: 3 403 MET cc_start: 0.9468 (tmm) cc_final: 0.9050 (tmm) REVERT: 3 492 MET cc_start: 0.8348 (mmp) cc_final: 0.7433 (tpp) REVERT: 3 963 GLU cc_start: 0.9490 (mm-30) cc_final: 0.9253 (mm-30) REVERT: 3 1233 LEU cc_start: 0.9299 (mp) cc_final: 0.9042 (mt) REVERT: 3 1241 ASP cc_start: 0.9324 (t0) cc_final: 0.9105 (t0) REVERT: 3 1304 MET cc_start: 0.9326 (mmm) cc_final: 0.9106 (mmm) REVERT: 3 1329 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8672 (mt-10) REVERT: 4 192 MET cc_start: 0.9121 (mmm) cc_final: 0.8626 (tpp) REVERT: 4 400 MET cc_start: 0.9210 (tpp) cc_final: 0.8917 (tpp) REVERT: 4 424 ASN cc_start: 0.9473 (p0) cc_final: 0.9248 (p0) REVERT: 4 454 CYS cc_start: 0.8952 (p) cc_final: 0.8492 (p) REVERT: 4 485 MET cc_start: 0.8948 (mtm) cc_final: 0.8616 (mtp) REVERT: 4 747 MET cc_start: 0.8109 (tpt) cc_final: 0.7875 (tpt) REVERT: 4 807 LEU cc_start: 0.8864 (mt) cc_final: 0.8542 (mp) REVERT: 4 1040 MET cc_start: 0.7872 (mtp) cc_final: 0.7640 (mtm) REVERT: 4 1314 LEU cc_start: 0.9289 (mt) cc_final: 0.8974 (pp) REVERT: Z 90 MET cc_start: 0.9212 (mpp) cc_final: 0.8500 (mpp) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.4503 time to fit residues: 137.8145 Evaluate side-chains 140 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 3.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 134 optimal weight: 7.9990 chunk 253 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 319 optimal weight: 0.8980 chunk 284 optimal weight: 0.0570 chunk 304 optimal weight: 10.0000 overall best weight: 2.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 31157 GLN ** 4 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 41252 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.038745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.029944 restraints weight = 268535.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.030760 restraints weight = 177832.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.031333 restraints weight = 131553.882| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27696 Z= 0.172 Angle : 0.647 10.004 37727 Z= 0.339 Chirality : 0.043 0.169 4308 Planarity : 0.004 0.045 4684 Dihedral : 14.834 173.916 4439 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.42 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.27 (0.15), residues: 3249 helix: 0.88 (0.15), residues: 1203 sheet: -0.63 (0.24), residues: 401 loop : -0.83 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 3 183 HIS 0.008 0.001 HIS 3 150 PHE 0.026 0.002 PHE 41165 TYR 0.023 0.001 TYR 31231 ARG 0.006 0.000 ARG 1 191 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 1182) hydrogen bonds : angle 5.33920 ( 3315) metal coordination : bond 0.00922 ( 8) metal coordination : angle 5.79659 ( 12) covalent geometry : bond 0.00362 (27688) covalent geometry : angle 0.63846 (37715) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 3.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 228 LEU cc_start: 0.9339 (mt) cc_final: 0.8757 (pp) REVERT: 3 1 MET cc_start: 0.6786 (tpp) cc_final: 0.6521 (tpp) REVERT: 3 403 MET cc_start: 0.9492 (tmm) cc_final: 0.9275 (tmm) REVERT: 3 492 MET cc_start: 0.8362 (mmp) cc_final: 0.7425 (tpp) REVERT: 3 825 GLU cc_start: 0.9309 (tp30) cc_final: 0.8791 (tm-30) REVERT: 3 963 GLU cc_start: 0.9452 (mm-30) cc_final: 0.9231 (mm-30) REVERT: 3 1064 ASP cc_start: 0.8872 (t0) cc_final: 0.8441 (t0) REVERT: 3 1119 MET cc_start: 0.9162 (tpp) cc_final: 0.8955 (tpp) REVERT: 3 1241 ASP cc_start: 0.9298 (t0) cc_final: 0.9072 (t0) REVERT: 3 1274 GLU cc_start: 0.8708 (mp0) cc_final: 0.8318 (mp0) REVERT: 3 1290 MET cc_start: 0.9348 (tmm) cc_final: 0.9110 (tmm) REVERT: 3 1329 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8655 (mt-10) REVERT: 4 102 MET cc_start: 0.8255 (ptt) cc_final: 0.8015 (ppp) REVERT: 4 192 MET cc_start: 0.9071 (mmm) cc_final: 0.8583 (tpp) REVERT: 4 400 MET cc_start: 0.9196 (tpp) cc_final: 0.8805 (tpt) REVERT: 4 454 CYS cc_start: 0.8901 (p) cc_final: 0.8391 (p) REVERT: 4 485 MET cc_start: 0.8978 (mtm) cc_final: 0.8714 (mtp) REVERT: 4 747 MET cc_start: 0.8149 (tpt) cc_final: 0.7916 (tpt) REVERT: 4 767 LEU cc_start: 0.9098 (mm) cc_final: 0.8894 (tp) REVERT: 4 807 LEU cc_start: 0.8832 (mt) cc_final: 0.8624 (mt) REVERT: 4 1025 MET cc_start: 0.8893 (mtm) cc_final: 0.8571 (mtm) REVERT: 4 1040 MET cc_start: 0.7774 (mtp) cc_final: 0.7546 (mtm) REVERT: 4 1196 LEU cc_start: 0.8494 (mt) cc_final: 0.8006 (pt) REVERT: Z 90 MET cc_start: 0.9219 (mpp) cc_final: 0.8382 (mpp) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.4808 time to fit residues: 143.8534 Evaluate side-chains 142 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 2.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 151 optimal weight: 7.9990 chunk 148 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 268 optimal weight: 6.9990 chunk 212 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 275 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 chunk 273 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 18 GLN ** 2 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 856 ASN ** 3 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 31023 HIS 31070 HIS 31313 HIS ** 4 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 910 ASN Z 33 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.036966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.028338 restraints weight = 276885.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.029129 restraints weight = 182020.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.029680 restraints weight = 134418.299| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 27696 Z= 0.274 Angle : 0.756 13.759 37727 Z= 0.393 Chirality : 0.044 0.180 4308 Planarity : 0.005 0.064 4684 Dihedral : 15.104 167.780 4439 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.65 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.63 (0.14), residues: 3249 helix: 0.50 (0.14), residues: 1207 sheet: -0.96 (0.24), residues: 400 loop : -0.92 (0.16), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP 4 580 HIS 0.009 0.002 HIS 3 150 PHE 0.018 0.002 PHE 3 390 TYR 0.021 0.002 TYR 31231 ARG 0.009 0.001 ARG 1 191 Details of bonding type rmsd hydrogen bonds : bond 0.04963 ( 1182) hydrogen bonds : angle 5.68962 ( 3315) metal coordination : bond 0.01662 ( 8) metal coordination : angle 7.02216 ( 12) covalent geometry : bond 0.00560 (27688) covalent geometry : angle 0.74568 (37715) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 3.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 55 GLU cc_start: 0.9362 (pt0) cc_final: 0.9002 (pp20) REVERT: 2 228 LEU cc_start: 0.9427 (mt) cc_final: 0.8878 (pp) REVERT: 3 403 MET cc_start: 0.9524 (tmm) cc_final: 0.9296 (tmm) REVERT: 3 492 MET cc_start: 0.8460 (mmp) cc_final: 0.7598 (tpp) REVERT: 3 1064 ASP cc_start: 0.8956 (t0) cc_final: 0.8292 (t0) REVERT: 3 1241 ASP cc_start: 0.9277 (t0) cc_final: 0.9040 (t0) REVERT: 3 1273 MET cc_start: 0.9458 (mtm) cc_final: 0.8394 (ptp) REVERT: 3 1274 GLU cc_start: 0.8940 (mp0) cc_final: 0.8563 (mp0) REVERT: 3 1290 MET cc_start: 0.9426 (tmm) cc_final: 0.9219 (tmm) REVERT: 4 192 MET cc_start: 0.9063 (mmm) cc_final: 0.8597 (tpp) REVERT: 4 454 CYS cc_start: 0.8905 (p) cc_final: 0.8583 (p) REVERT: 4 485 MET cc_start: 0.9019 (mtm) cc_final: 0.8738 (mtm) REVERT: 4 807 LEU cc_start: 0.8844 (mt) cc_final: 0.8590 (mp) REVERT: 4 1025 MET cc_start: 0.9028 (mtm) cc_final: 0.8697 (mtm) REVERT: Z 90 MET cc_start: 0.9263 (mpp) cc_final: 0.8315 (mpp) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.3534 time to fit residues: 93.2825 Evaluate side-chains 130 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 3.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 195 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 318 optimal weight: 10.0000 chunk 220 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 266 optimal weight: 6.9990 chunk 188 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 304 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 84 ASN ** 2 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 330 HIS ** 3 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.037400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.028702 restraints weight = 276164.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.029511 restraints weight = 179806.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.030085 restraints weight = 131986.672| |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 27696 Z= 0.213 Angle : 0.686 11.589 37727 Z= 0.359 Chirality : 0.043 0.173 4308 Planarity : 0.004 0.044 4684 Dihedral : 15.013 162.512 4439 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.16 % Favored : 93.78 % Rotamer: Outliers : 0.07 % Allowed : 2.83 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.15), residues: 3249 helix: 0.67 (0.15), residues: 1202 sheet: -1.01 (0.24), residues: 396 loop : -0.83 (0.16), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Z 9 HIS 0.007 0.001 HIS 3 150 PHE 0.038 0.002 PHE 5 17 TYR 0.022 0.002 TYR 1 68 ARG 0.007 0.001 ARG 1 191 Details of bonding type rmsd hydrogen bonds : bond 0.04559 ( 1182) hydrogen bonds : angle 5.49972 ( 3315) metal coordination : bond 0.01115 ( 8) metal coordination : angle 6.12910 ( 12) covalent geometry : bond 0.00441 (27688) covalent geometry : angle 0.67686 (37715) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 3.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 55 GLU cc_start: 0.9293 (pt0) cc_final: 0.8872 (pp20) REVERT: 3 403 MET cc_start: 0.9524 (tmm) cc_final: 0.9286 (tmm) REVERT: 3 492 MET cc_start: 0.8345 (mmp) cc_final: 0.7549 (tpp) REVERT: 3 653 MET cc_start: 0.7930 (tpp) cc_final: 0.7694 (tpp) REVERT: 3 1064 ASP cc_start: 0.9005 (t0) cc_final: 0.8463 (t0) REVERT: 3 1066 MET cc_start: 0.9253 (tpt) cc_final: 0.8422 (tpp) REVERT: 3 1230 MET cc_start: 0.8844 (ppp) cc_final: 0.8629 (ppp) REVERT: 3 1241 ASP cc_start: 0.9272 (t0) cc_final: 0.9012 (t0) REVERT: 3 1273 MET cc_start: 0.9552 (mtm) cc_final: 0.8543 (ptp) REVERT: 3 1274 GLU cc_start: 0.8895 (mp0) cc_final: 0.8630 (mp0) REVERT: 3 1290 MET cc_start: 0.9451 (tmm) cc_final: 0.9186 (tmm) REVERT: 4 151 MET cc_start: 0.8947 (mtp) cc_final: 0.8589 (mtp) REVERT: 4 192 MET cc_start: 0.9090 (mmm) cc_final: 0.8621 (tpp) REVERT: 4 454 CYS cc_start: 0.8864 (p) cc_final: 0.8325 (p) REVERT: 4 485 MET cc_start: 0.9096 (mtm) cc_final: 0.8816 (mtm) REVERT: 4 1025 MET cc_start: 0.8959 (mtm) cc_final: 0.8618 (mtm) REVERT: 4 1196 LEU cc_start: 0.8814 (mt) cc_final: 0.8080 (pt) REVERT: 4 1347 LEU cc_start: 0.9075 (mm) cc_final: 0.8835 (mt) REVERT: Z 73 MET cc_start: 0.8766 (tmm) cc_final: 0.7987 (tmm) REVERT: Z 90 MET cc_start: 0.9235 (mpp) cc_final: 0.8329 (mpp) outliers start: 2 outliers final: 0 residues processed: 162 average time/residue: 0.3638 time to fit residues: 100.1000 Evaluate side-chains 131 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 30 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 156 optimal weight: 0.4980 chunk 219 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 258 optimal weight: 5.9990 chunk 44 optimal weight: 20.0000 chunk 227 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 450 ASN 3 808 ASN ** 3 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 41108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.036999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.028384 restraints weight = 283138.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.029195 restraints weight = 182501.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.029770 restraints weight = 133308.510| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 27696 Z= 0.234 Angle : 0.714 13.602 37727 Z= 0.371 Chirality : 0.043 0.174 4308 Planarity : 0.004 0.050 4684 Dihedral : 15.030 154.429 4439 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.74 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.59 (0.15), residues: 3249 helix: 0.61 (0.15), residues: 1195 sheet: -1.07 (0.24), residues: 409 loop : -0.92 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP 4 580 HIS 0.007 0.001 HIS 3 150 PHE 0.033 0.002 PHE 5 17 TYR 0.026 0.002 TYR 1 68 ARG 0.009 0.001 ARG 4 312 Details of bonding type rmsd hydrogen bonds : bond 0.04634 ( 1182) hydrogen bonds : angle 5.56681 ( 3315) metal coordination : bond 0.01049 ( 8) metal coordination : angle 6.59032 ( 12) covalent geometry : bond 0.00482 (27688) covalent geometry : angle 0.70430 (37715) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 51 LEU cc_start: 0.9405 (tt) cc_final: 0.8700 (tt) REVERT: 5 55 GLU cc_start: 0.9308 (pt0) cc_final: 0.8858 (pt0) REVERT: 3 403 MET cc_start: 0.9535 (tmm) cc_final: 0.9281 (tmm) REVERT: 3 492 MET cc_start: 0.8376 (mmp) cc_final: 0.7505 (tpp) REVERT: 3 1230 MET cc_start: 0.8875 (ppp) cc_final: 0.8675 (ppp) REVERT: 3 1241 ASP cc_start: 0.9288 (t0) cc_final: 0.8996 (t0) REVERT: 3 1273 MET cc_start: 0.9572 (mtm) cc_final: 0.8551 (ptp) REVERT: 3 1274 GLU cc_start: 0.8921 (mp0) cc_final: 0.8658 (mp0) REVERT: 3 1290 MET cc_start: 0.9436 (tmm) cc_final: 0.9172 (tmm) REVERT: 4 192 MET cc_start: 0.9113 (mmm) cc_final: 0.8635 (tpp) REVERT: 4 454 CYS cc_start: 0.8819 (p) cc_final: 0.8290 (p) REVERT: 4 485 MET cc_start: 0.9148 (mtm) cc_final: 0.8876 (mtm) REVERT: 4 807 LEU cc_start: 0.8952 (mt) cc_final: 0.8623 (mp) REVERT: 4 1025 MET cc_start: 0.8978 (mtm) cc_final: 0.8642 (mtm) REVERT: 4 1196 LEU cc_start: 0.8928 (mt) cc_final: 0.8096 (pt) REVERT: 4 1347 LEU cc_start: 0.9014 (mm) cc_final: 0.8712 (mm) REVERT: Z 90 MET cc_start: 0.9263 (mpp) cc_final: 0.8376 (mpp) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.3489 time to fit residues: 92.1154 Evaluate side-chains 133 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 28 optimal weight: 1.9990 chunk 115 optimal weight: 8.9990 chunk 170 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 270 optimal weight: 6.9990 chunk 227 optimal weight: 1.9990 chunk 283 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 318 optimal weight: 0.8980 chunk 255 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 41268 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 = 0.3109 r_free = 0.3109 target = 0.037892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.029206 restraints weight = 270341.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.029997 restraints weight = 179354.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.030572 restraints weight = 132676.990| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27696 Z= 0.147 Angle : 0.639 9.631 37727 Z= 0.332 Chirality : 0.042 0.202 4308 Planarity : 0.004 0.058 4684 Dihedral : 14.831 142.800 4439 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.60 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.28 (0.15), residues: 3249 helix: 0.96 (0.15), residues: 1183 sheet: -0.89 (0.24), residues: 416 loop : -0.79 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 3 183 HIS 0.006 0.001 HIS 3 150 PHE 0.025 0.001 PHE 5 17 TYR 0.014 0.001 TYR 1 68 ARG 0.008 0.000 ARG 4 978 Details of bonding type rmsd hydrogen bonds : bond 0.04097 ( 1182) hydrogen bonds : angle 5.22739 ( 3315) metal coordination : bond 0.00679 ( 8) metal coordination : angle 5.34576 ( 12) covalent geometry : bond 0.00311 (27688) covalent geometry : angle 0.63235 (37715) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 2.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 51 LEU cc_start: 0.9377 (tt) cc_final: 0.8692 (tt) REVERT: 5 55 GLU cc_start: 0.9312 (pt0) cc_final: 0.8841 (pt0) REVERT: 3 403 MET cc_start: 0.9541 (tmm) cc_final: 0.9291 (tmm) REVERT: 3 492 MET cc_start: 0.8273 (mmp) cc_final: 0.7358 (tpp) REVERT: 3 653 MET cc_start: 0.7981 (tpp) cc_final: 0.7714 (tpp) REVERT: 3 681 MET cc_start: 0.9339 (ptp) cc_final: 0.9083 (ptp) REVERT: 3 825 GLU cc_start: 0.9453 (tp30) cc_final: 0.8918 (tm-30) REVERT: 3 1066 MET cc_start: 0.9433 (tpt) cc_final: 0.9220 (tpt) REVERT: 3 1212 LEU cc_start: 0.9556 (mt) cc_final: 0.9206 (mp) REVERT: 3 1241 ASP cc_start: 0.9260 (t0) cc_final: 0.8951 (t0) REVERT: 3 1273 MET cc_start: 0.9534 (mtm) cc_final: 0.8355 (ptp) REVERT: 3 1274 GLU cc_start: 0.8929 (mp0) cc_final: 0.8598 (mp0) REVERT: 3 1276 TRP cc_start: 0.9488 (m-10) cc_final: 0.9187 (m-90) REVERT: 3 1290 MET cc_start: 0.9445 (tmm) cc_final: 0.9131 (tmm) REVERT: 4 192 MET cc_start: 0.9063 (mmm) cc_final: 0.8609 (tpp) REVERT: 4 298 MET cc_start: 0.9343 (mmp) cc_final: 0.9126 (mmp) REVERT: 4 454 CYS cc_start: 0.8690 (p) cc_final: 0.8172 (p) REVERT: 4 485 MET cc_start: 0.9186 (mtm) cc_final: 0.8841 (mtm) REVERT: 4 747 MET cc_start: 0.8808 (tpt) cc_final: 0.8469 (tpp) REVERT: 4 1025 MET cc_start: 0.8888 (mtm) cc_final: 0.8560 (mtm) REVERT: 4 1196 LEU cc_start: 0.8762 (mt) cc_final: 0.7945 (pt) REVERT: Z 43 MET cc_start: 0.8899 (mmm) cc_final: 0.8222 (mmm) REVERT: Z 90 MET cc_start: 0.9274 (mpp) cc_final: 0.8403 (mpp) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.3485 time to fit residues: 96.0266 Evaluate side-chains 137 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 99 optimal weight: 20.0000 chunk 321 optimal weight: 8.9990 chunk 259 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 243 optimal weight: 2.9990 chunk 326 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 33 optimal weight: 20.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 41268 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 = 0.3097 r_free = 0.3097 target = 0.037512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.028951 restraints weight = 274170.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.029730 restraints weight = 182844.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.030291 restraints weight = 135947.490| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 27696 Z= 0.176 Angle : 0.660 14.504 37727 Z= 0.341 Chirality : 0.042 0.222 4308 Planarity : 0.004 0.048 4684 Dihedral : 14.831 139.287 4439 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.03 % Favored : 93.91 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.28 (0.15), residues: 3249 helix: 0.91 (0.15), residues: 1188 sheet: -0.89 (0.25), residues: 403 loop : -0.78 (0.16), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Z 9 HIS 0.006 0.001 HIS 3 150 PHE 0.024 0.002 PHE 5 17 TYR 0.021 0.001 TYR 1 68 ARG 0.007 0.000 ARG 4 312 Details of bonding type rmsd hydrogen bonds : bond 0.04158 ( 1182) hydrogen bonds : angle 5.26546 ( 3315) metal coordination : bond 0.00848 ( 8) metal coordination : angle 6.35445 ( 12) covalent geometry : bond 0.00370 (27688) covalent geometry : angle 0.65070 (37715) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 3.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 51 LEU cc_start: 0.9358 (tt) cc_final: 0.8611 (tt) REVERT: 5 55 GLU cc_start: 0.9316 (pt0) cc_final: 0.8845 (pt0) REVERT: 2 82 LEU cc_start: 0.9581 (tt) cc_final: 0.9273 (mt) REVERT: 3 403 MET cc_start: 0.9520 (tmm) cc_final: 0.9255 (tmm) REVERT: 3 492 MET cc_start: 0.8368 (mmp) cc_final: 0.7555 (tpp) REVERT: 3 653 MET cc_start: 0.7936 (tpp) cc_final: 0.7685 (tpp) REVERT: 3 681 MET cc_start: 0.9247 (ptp) cc_final: 0.9021 (ptp) REVERT: 3 1066 MET cc_start: 0.9355 (tpt) cc_final: 0.9154 (tpt) REVERT: 3 1230 MET cc_start: 0.8859 (ppp) cc_final: 0.8603 (ppp) REVERT: 3 1241 ASP cc_start: 0.9211 (t0) cc_final: 0.8903 (t0) REVERT: 3 1273 MET cc_start: 0.9516 (mtm) cc_final: 0.8501 (ptp) REVERT: 3 1274 GLU cc_start: 0.8928 (mp0) cc_final: 0.8674 (mp0) REVERT: 3 1290 MET cc_start: 0.9394 (tmm) cc_final: 0.9083 (tmm) REVERT: 4 192 MET cc_start: 0.9045 (mmm) cc_final: 0.8597 (tpp) REVERT: 4 454 CYS cc_start: 0.8875 (p) cc_final: 0.8268 (p) REVERT: 4 466 MET cc_start: 0.8819 (tpt) cc_final: 0.8410 (tpp) REVERT: 4 485 MET cc_start: 0.9166 (mtm) cc_final: 0.8848 (mtm) REVERT: 4 747 MET cc_start: 0.8722 (tpt) cc_final: 0.8361 (tpp) REVERT: 4 1025 MET cc_start: 0.8896 (mtm) cc_final: 0.8568 (mtm) REVERT: 4 1196 LEU cc_start: 0.8778 (mt) cc_final: 0.7890 (pt) REVERT: Z 37 ASP cc_start: 0.9056 (m-30) cc_final: 0.8643 (p0) REVERT: Z 43 MET cc_start: 0.8898 (mmm) cc_final: 0.8284 (mmm) REVERT: Z 90 MET cc_start: 0.9286 (mpp) cc_final: 0.8411 (mpp) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.3524 time to fit residues: 94.0281 Evaluate side-chains 132 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 109 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 288 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 chunk 220 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 93 GLN ** 2 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 69 GLN ** 4 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 41268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.037405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.028841 restraints weight = 272935.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.029616 restraints weight = 182236.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.030167 restraints weight = 135566.933| |-----------------------------------------------------------------------------| r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 27696 Z= 0.183 Angle : 0.667 14.106 37727 Z= 0.344 Chirality : 0.043 0.194 4308 Planarity : 0.004 0.044 4684 Dihedral : 14.822 134.648 4439 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.97 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.34 (0.15), residues: 3249 helix: 0.87 (0.15), residues: 1188 sheet: -1.00 (0.24), residues: 411 loop : -0.79 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 3 183 HIS 0.006 0.001 HIS 3 150 PHE 0.024 0.002 PHE 5 17 TYR 0.022 0.002 TYR 1 68 ARG 0.007 0.000 ARG 4 312 Details of bonding type rmsd hydrogen bonds : bond 0.04214 ( 1182) hydrogen bonds : angle 5.27124 ( 3315) metal coordination : bond 0.00820 ( 8) metal coordination : angle 6.27932 ( 12) covalent geometry : bond 0.00383 (27688) covalent geometry : angle 0.65806 (37715) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 51 LEU cc_start: 0.9352 (tt) cc_final: 0.8596 (tt) REVERT: 5 55 GLU cc_start: 0.9322 (pt0) cc_final: 0.8849 (pt0) REVERT: 3 403 MET cc_start: 0.9526 (tmm) cc_final: 0.9263 (tmm) REVERT: 3 492 MET cc_start: 0.8377 (mmp) cc_final: 0.7588 (tpp) REVERT: 3 653 MET cc_start: 0.7925 (tpp) cc_final: 0.7674 (tpp) REVERT: 3 681 MET cc_start: 0.9270 (ptp) cc_final: 0.9042 (ptp) REVERT: 3 1230 MET cc_start: 0.8851 (ppp) cc_final: 0.8605 (ppp) REVERT: 3 1273 MET cc_start: 0.9521 (mtm) cc_final: 0.8496 (ptp) REVERT: 3 1274 GLU cc_start: 0.8956 (mp0) cc_final: 0.8675 (mp0) REVERT: 3 1290 MET cc_start: 0.9439 (tmm) cc_final: 0.9116 (tmm) REVERT: 4 192 MET cc_start: 0.9064 (mmm) cc_final: 0.8617 (tpp) REVERT: 4 454 CYS cc_start: 0.8835 (p) cc_final: 0.8232 (p) REVERT: 4 466 MET cc_start: 0.8759 (tpt) cc_final: 0.8335 (tpp) REVERT: 4 485 MET cc_start: 0.9166 (mtm) cc_final: 0.8855 (mtm) REVERT: 4 747 MET cc_start: 0.8760 (tpt) cc_final: 0.8469 (tpt) REVERT: 4 1025 MET cc_start: 0.8910 (mtm) cc_final: 0.8581 (mtm) REVERT: 4 1196 LEU cc_start: 0.8796 (mt) cc_final: 0.7904 (pt) REVERT: Z 37 ASP cc_start: 0.9047 (m-30) cc_final: 0.8641 (p0) REVERT: Z 43 MET cc_start: 0.8920 (mmm) cc_final: 0.8280 (mmm) REVERT: Z 90 MET cc_start: 0.9309 (mpp) cc_final: 0.8400 (mpp) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.3372 time to fit residues: 86.6857 Evaluate side-chains 131 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 67 optimal weight: 1.9990 chunk 271 optimal weight: 0.1980 chunk 36 optimal weight: 0.7980 chunk 290 optimal weight: 30.0000 chunk 191 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 193 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 0.2980 chunk 312 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 69 GLN 3 688 GLN ** 4 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 41268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.038279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.029573 restraints weight = 267277.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.030372 restraints weight = 178178.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.030945 restraints weight = 132429.889| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27696 Z= 0.130 Angle : 0.630 11.198 37727 Z= 0.323 Chirality : 0.042 0.229 4308 Planarity : 0.004 0.046 4684 Dihedral : 14.646 131.549 4439 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.51 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.15), residues: 3249 helix: 1.17 (0.15), residues: 1177 sheet: -0.91 (0.25), residues: 419 loop : -0.72 (0.16), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 3 183 HIS 0.005 0.001 HIS 3 150 PHE 0.022 0.001 PHE 5 17 TYR 0.020 0.001 TYR 2 68 ARG 0.006 0.000 ARG 4 312 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 1182) hydrogen bonds : angle 5.05681 ( 3315) metal coordination : bond 0.00528 ( 8) metal coordination : angle 5.21381 ( 12) covalent geometry : bond 0.00277 (27688) covalent geometry : angle 0.62361 (37715) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8192.45 seconds wall clock time: 148 minutes 8.31 seconds (8888.31 seconds total)