Starting phenix.real_space_refine on Mon Sep 14 01:09:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6c6t_7350/09_2026/6c6t_7350_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c6t_7350/09_2026/6c6t_7350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6c6t_7350/09_2026/6c6t_7350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c6t_7350/09_2026/6c6t_7350.map" model { file = "/net/cci-nas-00/data/ceres_data/6c6t_7350/09_2026/6c6t_7350_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c6t_7350/09_2026/6c6t_7350_neut.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 66 5.49 5 Mg 1 5.21 5 S 109 5.16 5 C 16665 2.51 5 N 4766 2.21 5 O 5306 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26915 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 598 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "B" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 585 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "R" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 218 Classifications: {'RNA': 10} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "G" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1694 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1687 Classifications: {'peptide': 219} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Chain: "I" Number of atoms: 10407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1319, 10407 Classifications: {'peptide': 1319} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 54, 'TRANS': 1260} Chain breaks: 1 Chain: "J" Number of atoms: 10388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10388 Classifications: {'peptide': 1335} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 54, 'TRANS': 1277} Chain breaks: 2 Chain: "K" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 655 Classifications: {'peptide': 83} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 79} Chain: "D" Number of atoms: 680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 680 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Chain breaks: 1 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15638 SG CYS J 70 54.395 117.686 61.517 1.00 45.60 S ATOM 15652 SG CYS J 72 54.773 121.159 62.416 1.00 45.12 S ATOM 15760 SG CYS J 85 52.098 121.116 59.997 1.00 49.94 S ATOM 21472 SG CYS J 814 51.898 51.691 50.657 1.00 22.38 S ATOM 22037 SG CYS J 888 54.316 55.235 52.127 1.00 20.48 S ATOM 22088 SG CYS J 895 51.809 53.401 54.016 1.00 14.28 S ATOM 22109 SG CYS J 898 54.310 51.014 53.220 1.00 16.02 S Time building chain proxies: 5.27, per 1000 atoms: 0.20 Number of scatterers: 26915 At special positions: 0 Unit cell: (152.1, 140.4, 149.5, 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 109 16.00 P 66 15.00 Mg 1 11.99 O 5306 8.00 N 4766 7.00 C 16665 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: 2.15 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1501 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1501 " - pdb=" SG CYS J 72 " pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 898 " Number of angles added : 6 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6028 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 48 sheets defined 36.8% alpha, 16.0% beta 29 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 3.37 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.667A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 87 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 154 through 159 removed outlier: 4.286A pdb=" N ARG G 158 " --> pdb=" O PRO G 154 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE G 159 " --> pdb=" O ALA G 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 154 through 159' Processing helix chain 'G' and resid 212 through 228 Processing helix chain 'G' and resid 229 through 231 No H-bonds generated for 'chain 'G' and resid 229 through 231' Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.834A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.998A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 154 through 158 removed outlier: 3.539A pdb=" N THR H 157 " --> pdb=" O PRO H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 227 Processing helix chain 'I' and resid 28 through 39 Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.878A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 163 through 167 removed outlier: 3.993A pdb=" N SER I 166 " --> pdb=" O LYS I 163 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER I 167 " --> pdb=" O THR I 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 163 through 167' Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.916A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 247 removed outlier: 3.680A pdb=" N LEU I 246 " --> pdb=" O PRO I 243 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 280 Processing helix chain 'I' and resid 288 through 293 removed outlier: 4.287A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 288 through 293' Processing helix chain 'I' and resid 318 through 327 removed outlier: 3.853A pdb=" N GLN I 327 " --> pdb=" O ALA I 323 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 389 removed outlier: 4.305A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 removed outlier: 3.556A pdb=" N LEU I 409 " --> pdb=" O PHE I 405 " (cutoff:3.500A) Processing helix chain 'I' and resid 421 through 438 removed outlier: 3.757A pdb=" N ILE I 425 " --> pdb=" O SER I 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 481 removed outlier: 3.764A pdb=" N SER I 480 " --> pdb=" O LYS I 476 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 removed outlier: 3.636A pdb=" N SER I 499 " --> pdb=" O ALA I 495 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 527 Processing helix chain 'I' and resid 607 through 612 removed outlier: 3.613A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) Processing helix chain 'I' and resid 675 through 687 Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 738 through 741 Processing helix chain 'I' and resid 819 through 825 removed outlier: 4.232A pdb=" N VAL I 823 " --> pdb=" O SER I 819 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU I 825 " --> pdb=" O ARG I 821 " (cutoff:3.500A) Processing helix chain 'I' and resid 858 through 863 removed outlier: 3.976A pdb=" N LEU I 862 " --> pdb=" O GLY I 858 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 979 removed outlier: 3.518A pdb=" N LEU I 946 " --> pdb=" O ASP I 942 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.241A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.641A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) Processing helix chain 'I' and resid 1137 through 1151 removed outlier: 4.039A pdb=" N LEU I1141 " --> pdb=" O GLU I1137 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU I1151 " --> pdb=" O ARG I1147 " (cutoff:3.500A) Processing helix chain 'I' and resid 1160 through 1164 removed outlier: 3.827A pdb=" N THR I1163 " --> pdb=" O ASP I1160 " (cutoff:3.500A) Processing helix chain 'I' and resid 1167 through 1176 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1281 Processing helix chain 'I' and resid 1283 through 1292 removed outlier: 3.666A pdb=" N LEU I1287 " --> pdb=" O ALA I1283 " (cutoff:3.500A) Processing helix chain 'I' and resid 1297 through 1311 Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.690A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 94 through 99 Processing helix chain 'J' and resid 124 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 180 through 191 removed outlier: 3.882A pdb=" N ALA J 184 " --> pdb=" O MET J 180 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 207 removed outlier: 3.808A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 230 removed outlier: 3.954A pdb=" N SER J 230 " --> pdb=" O ALA J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 removed outlier: 3.521A pdb=" N TRP J 236 " --> pdb=" O LYS J 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 233 through 236' Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 286 removed outlier: 3.807A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 327 through 332 Processing helix chain 'J' and resid 337 through 342 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 389 Processing helix chain 'J' and resid 393 through 404 removed outlier: 3.968A pdb=" N ALA J 397 " --> pdb=" O THR J 393 " (cutoff:3.500A) Processing helix chain 'J' and resid 407 through 417 removed outlier: 3.567A pdb=" N ILE J 411 " --> pdb=" O VAL J 407 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG J 417 " --> pdb=" O ASP J 413 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 450 through 458 removed outlier: 3.647A pdb=" N CYS J 454 " --> pdb=" O HIS J 450 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA J 455 " --> pdb=" O PRO J 451 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA J 456 " --> pdb=" O LEU J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 504 through 514 removed outlier: 3.523A pdb=" N LEU J 508 " --> pdb=" O GLN J 504 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 573 through 581 removed outlier: 3.614A pdb=" N ALA J 577 " --> pdb=" O THR J 573 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 592 Processing helix chain 'J' and resid 598 through 613 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.645A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 670 removed outlier: 3.531A pdb=" N SER J 670 " --> pdb=" O GLU J 666 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 703 Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 removed outlier: 3.857A pdb=" N ILE J 737 " --> pdb=" O SER J 733 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 805 removed outlier: 3.845A pdb=" N GLY J 782 " --> pdb=" O GLY J 778 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ALA J 791 " --> pdb=" O ALA J 787 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN J 792 " --> pdb=" O LEU J 788 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN J 805 " --> pdb=" O VAL J 801 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 839 removed outlier: 3.644A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 876 removed outlier: 3.798A pdb=" N ASN J 875 " --> pdb=" O LEU J 871 " (cutoff:3.500A) Processing helix chain 'J' and resid 884 through 888 Processing helix chain 'J' and resid 895 through 900 removed outlier: 3.519A pdb=" N TYR J 899 " --> pdb=" O CYS J 895 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY J 900 " --> pdb=" O ALA J 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 895 through 900' Processing helix chain 'J' and resid 914 through 925 removed outlier: 4.003A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 928 No H-bonds generated for 'chain 'J' and resid 926 through 928' Processing helix chain 'J' and resid 1137 through 1146 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 4.195A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1261 Processing helix chain 'J' and resid 1282 through 1294 removed outlier: 3.546A pdb=" N ALA J1294 " --> pdb=" O ARG J1290 " (cutoff:3.500A) Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1327 through 1339 removed outlier: 3.829A pdb=" N VAL J1331 " --> pdb=" O GLU J1327 " (cutoff:3.500A) Processing helix chain 'J' and resid 1346 through 1353 removed outlier: 3.805A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1361 through 1372 removed outlier: 4.423A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 32 removed outlier: 4.068A pdb=" N LEU K 21 " --> pdb=" O PHE K 17 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL K 32 " --> pdb=" O ARG K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 56 removed outlier: 3.790A pdb=" N GLU K 56 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 84 Processing helix chain 'D' and resid 13 through 24 Processing helix chain 'D' and resid 65 through 71 Processing helix chain 'D' and resid 89 through 95 Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 17 removed outlier: 5.435A pdb=" N LEU G 13 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLU G 29 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP G 15 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASP G 199 " --> pdb=" O PRO G 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'G' and resid 97 through 104 removed outlier: 3.579A pdb=" N LYS G 104 " --> pdb=" O ILE G 140 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE G 140 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'G' and resid 108 through 111 Processing sheet with id=AA6, first strand: chain 'H' and resid 16 through 18 removed outlier: 6.231A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 16 through 18 removed outlier: 6.231A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA H 190 " --> pdb=" O LEU H 198 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 97 through 105 removed outlier: 7.787A pdb=" N SER H 141 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ILE H 61 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL H 59 " --> pdb=" O LEU H 171 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AB1, first strand: chain 'H' and resid 108 through 111 Processing sheet with id=AB2, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB3, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.395A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 59 through 60 removed outlier: 4.591A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB6, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.459A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 154 through 158 removed outlier: 3.776A pdb=" N ILE I 177 " --> pdb=" O GLY I 154 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN I 193 " --> pdb=" O ASP I 189 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 227 through 231 Processing sheet with id=AB9, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AC1, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.741A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 301 through 303 removed outlier: 7.213A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU I 308 " --> pdb=" O ASP I 303 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.670A pdb=" N GLU I 588 " --> pdb=" O GLN I 580 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 580 through 581 removed outlier: 3.670A pdb=" N GLU I 588 " --> pdb=" O GLN I 580 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 633 through 637 Processing sheet with id=AC6, first strand: chain 'I' and resid 748 through 752 removed outlier: 6.897A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 757 through 758 removed outlier: 3.550A pdb=" N THR I 757 " --> pdb=" O ILE I 765 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 768 through 769 Processing sheet with id=AC9, first strand: chain 'I' and resid 1209 through 1210 removed outlier: 7.457A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 830 through 841 removed outlier: 6.361A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 876 through 877 Processing sheet with id=AD3, first strand: chain 'I' and resid 882 through 884 removed outlier: 3.658A pdb=" N VAL I 884 " --> pdb=" O LEU I 918 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 887 through 888 Processing sheet with id=AD5, first strand: chain 'I' and resid 1244 through 1246 Processing sheet with id=AD6, first strand: chain 'I' and resid 1268 through 1270 Processing sheet with id=AD7, first strand: chain 'I' and resid 1335 through 1337 Processing sheet with id=AD8, first strand: chain 'J' and resid 34 through 37 removed outlier: 7.501A pdb=" N HIS J 104 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLU J 37 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N GLU J 106 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 9.874A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.896A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 145 through 146 Processing sheet with id=AE1, first strand: chain 'J' and resid 253 through 254 removed outlier: 4.416A pdb=" N VAL J 253 " --> pdb=" O ALA J 261 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 526 through 527 Processing sheet with id=AE3, first strand: chain 'J' and resid 706 through 708 removed outlier: 3.685A pdb=" N GLU J 714 " --> pdb=" O ILE J 707 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 821 through 822 Processing sheet with id=AE5, first strand: chain 'J' and resid 849 through 850 removed outlier: 4.608A pdb=" N ASP J 855 " --> pdb=" O LYS J 850 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 957 through 961 removed outlier: 3.803A pdb=" N THR J 980 " --> pdb=" O VAL J 997 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AE8, first strand: chain 'J' and resid 1034 through 1038 removed outlier: 3.618A pdb=" N ARG J1036 " --> pdb=" O LYS J1079 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS J1079 " --> pdb=" O ARG J1036 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 1046 through 1049 removed outlier: 4.088A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER J1058 " --> pdb=" O GLN J1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 1187 through 1190 Processing sheet with id=AF2, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 7.344A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 27 through 29 removed outlier: 3.847A pdb=" N PHE D 59 " --> pdb=" O SER D 3 " (cutoff:3.500A) 1022 hydrogen bonds defined for protein. 2892 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 7.02 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6049 1.33 - 1.45: 5646 1.45 - 1.57: 15447 1.57 - 1.69: 132 1.69 - 1.81: 188 Bond restraints: 27462 Sorted by residual: bond pdb=" C3' DC B 17 " pdb=" O3' DC B 17 " ideal model delta sigma weight residual 1.435 1.374 0.061 1.30e-02 5.92e+03 2.18e+01 bond pdb=" C3' DA A 11 " pdb=" O3' DA A 11 " ideal model delta sigma weight residual 1.435 1.491 -0.056 1.30e-02 5.92e+03 1.89e+01 bond pdb=" C3' DT B 15 " pdb=" O3' DT B 15 " ideal model delta sigma weight residual 1.435 1.380 0.055 1.30e-02 5.92e+03 1.81e+01 bond pdb=" C3' DG A 8 " pdb=" O3' DG A 8 " ideal model delta sigma weight residual 1.435 1.488 -0.053 1.30e-02 5.92e+03 1.69e+01 bond pdb=" N1 DT B 15 " pdb=" C2 DT B 15 " ideal model delta sigma weight residual 1.376 1.344 0.032 8.00e-03 1.56e+04 1.59e+01 ... (remaining 27457 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 36377 2.96 - 5.93: 900 5.93 - 8.89: 96 8.89 - 11.86: 20 11.86 - 14.82: 2 Bond angle restraints: 37395 Sorted by residual: angle pdb=" C LEU J 903 " pdb=" N ALA J 904 " pdb=" CA ALA J 904 " ideal model delta sigma weight residual 121.54 136.36 -14.82 1.91e+00 2.74e-01 6.02e+01 angle pdb=" O4' DG A 2 " pdb=" C4' DG A 2 " pdb=" C3' DG A 2 " ideal model delta sigma weight residual 106.00 102.35 3.65 6.00e-01 2.78e+00 3.70e+01 angle pdb=" O4' DG B 3 " pdb=" C4' DG B 3 " pdb=" C3' DG B 3 " ideal model delta sigma weight residual 106.00 102.70 3.30 6.00e-01 2.78e+00 3.03e+01 angle pdb=" C LYS I1158 " pdb=" N VAL I1159 " pdb=" CA VAL I1159 " ideal model delta sigma weight residual 121.97 131.61 -9.64 1.80e+00 3.09e-01 2.87e+01 angle pdb=" N ASP J1184 " pdb=" CA ASP J1184 " pdb=" C ASP J1184 " ideal model delta sigma weight residual 109.81 121.17 -11.36 2.21e+00 2.05e-01 2.64e+01 ... (remaining 37390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 16371 35.75 - 71.49: 323 71.49 - 107.24: 15 107.24 - 142.99: 0 142.99 - 178.73: 4 Dihedral angle restraints: 16713 sinusoidal: 7347 harmonic: 9366 Sorted by residual: dihedral pdb=" CA GLN I1157 " pdb=" C GLN I1157 " pdb=" N LYS I1158 " pdb=" CA LYS I1158 " ideal model delta harmonic sigma weight residual -180.00 -113.15 -66.85 0 5.00e+00 4.00e-02 1.79e+02 dihedral pdb=" CA THR I 595 " pdb=" C THR I 595 " pdb=" N ASP I 596 " pdb=" CA ASP I 596 " ideal model delta harmonic sigma weight residual -180.00 -135.19 -44.81 0 5.00e+00 4.00e-02 8.03e+01 dihedral pdb=" CA VAL K 32 " pdb=" C VAL K 32 " pdb=" N GLY K 33 " pdb=" CA GLY K 33 " ideal model delta harmonic sigma weight residual 0.00 -41.86 41.86 0 5.00e+00 4.00e-02 7.01e+01 ... (remaining 16710 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 3887 0.113 - 0.226: 366 0.226 - 0.340: 21 0.340 - 0.453: 1 0.453 - 0.566: 1 Chirality restraints: 4276 Sorted by residual: chirality pdb=" CB ILE I1079 " pdb=" CA ILE I1079 " pdb=" CG1 ILE I1079 " pdb=" CG2 ILE I1079 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.57 2.00e-01 2.50e+01 8.00e+00 chirality pdb=" CG LEU D 6 " pdb=" CB LEU D 6 " pdb=" CD1 LEU D 6 " pdb=" CD2 LEU D 6 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CB ILE H 144 " pdb=" CA ILE H 144 " pdb=" CG1 ILE H 144 " pdb=" CG2 ILE H 144 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 4273 not shown) Planarity restraints: 4655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP I 596 " -0.029 2.00e-02 2.50e+03 5.72e-02 3.27e+01 pdb=" C ASP I 596 " 0.099 2.00e-02 2.50e+03 pdb=" O ASP I 596 " -0.037 2.00e-02 2.50e+03 pdb=" N GLY I 597 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR I 595 " 0.025 2.00e-02 2.50e+03 5.01e-02 2.51e+01 pdb=" C THR I 595 " -0.087 2.00e-02 2.50e+03 pdb=" O THR I 595 " 0.032 2.00e-02 2.50e+03 pdb=" N ASP I 596 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 183 " -0.027 2.00e-02 2.50e+03 2.19e-02 1.20e+01 pdb=" CG TRP I 183 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP I 183 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP I 183 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP I 183 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP I 183 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP I 183 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 183 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 183 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP I 183 " -0.001 2.00e-02 2.50e+03 ... (remaining 4652 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 205 2.57 - 3.16: 20824 3.16 - 3.74: 40691 3.74 - 4.32: 56950 4.32 - 4.90: 93995 Nonbonded interactions: 212665 Sorted by model distance: nonbonded pdb=" OD2 ASP J 462 " pdb="MG MG R1501 " model vdw 1.993 2.170 nonbonded pdb=" O3' A R 20 " pdb="MG MG R1501 " model vdw 2.078 2.170 nonbonded pdb=" NH1 ARG J 425 " pdb=" O ASN J 458 " model vdw 2.084 3.120 nonbonded pdb=" OG1 THR I 207 " pdb=" OD2 ASP I 354 " model vdw 2.085 3.040 nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG R1501 " model vdw 2.087 2.170 ... (remaining 212660 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 'G' and (resid 7 through 158 or resid 169 through 232)) selection = (chain 'H' and (resid 7 through 190 or (resid 191 through 192 and (name N or nam \ e CA or name C or name O or name CB )) or resid 193 or (resid 194 and (name N or \ name CA or name C or name O or name CB )) or resid 195 through 232)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 31.080 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 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 : 0.011 0.208 27469 Z= 0.497 Angle : 1.172 29.502 37401 Z= 0.656 Chirality : 0.067 0.566 4276 Planarity : 0.008 0.072 4655 Dihedral : 13.490 178.733 10685 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.06 % Favored : 91.63 % Rotamer: Outliers : 0.72 % Allowed : 2.49 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.16 % Twisted Proline : 0.75 % Twisted General : 0.42 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.12 (0.12), residues: 3238 helix: -2.85 (0.11), residues: 1091 sheet: -2.16 (0.22), residues: 416 loop : -2.84 (0.12), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I1223 TYR 0.053 0.004 TYR I1229 PHE 0.041 0.004 PHE I 670 TRP 0.059 0.005 TRP I 183 HIS 0.019 0.003 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.01052 / 0.49 (27462) covalent geometry : angle 1.14960 / 0.65 (37395) hydrogen bonds : bond 0.13916 / 15.70 ( 1089) hydrogen bonds : angle 7.17016 / 8.41 ( 3040) metal coordination : bond 0.14866 / 16.83 ( 7) metal coordination : angle 18.04653 / 32.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 582 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 25 LYS cc_start: 0.8320 (mtmt) cc_final: 0.8014 (mttm) REVERT: G 117 HIS cc_start: 0.7212 (p-80) cc_final: 0.6799 (t70) REVERT: G 133 LEU cc_start: 0.9148 (mt) cc_final: 0.8870 (mt) REVERT: G 200 LYS cc_start: 0.8345 (ttmt) cc_final: 0.8129 (tttt) REVERT: H 157 THR cc_start: 0.8864 (m) cc_final: 0.8621 (m) REVERT: I 115 LYS cc_start: 0.5678 (pttt) cc_final: 0.4644 (tmmt) REVERT: I 515 MET cc_start: 0.8409 (ttp) cc_final: 0.8171 (ttp) REVERT: I 524 ILE cc_start: 0.8940 (tt) cc_final: 0.8683 (tt) REVERT: I 584 TYR cc_start: 0.8752 (m-80) cc_final: 0.8418 (m-80) REVERT: I 802 VAL cc_start: 0.9418 (OUTLIER) cc_final: 0.9029 (m) REVERT: I 829 THR cc_start: 0.9005 (m) cc_final: 0.8666 (t) REVERT: I 1124 ILE cc_start: 0.9263 (mm) cc_final: 0.8895 (mt) REVERT: J 50 LYS cc_start: 0.8213 (mttt) cc_final: 0.7610 (ptpp) REVERT: J 504 GLN cc_start: 0.8246 (pt0) cc_final: 0.8044 (pt0) REVERT: J 602 SER cc_start: 0.8755 (t) cc_final: 0.8525 (m) REVERT: J 709 ARG cc_start: 0.5875 (pmt170) cc_final: 0.4541 (tpt90) REVERT: J 737 ILE cc_start: 0.9166 (tt) cc_final: 0.8746 (mm) REVERT: J 743 MET cc_start: 0.8719 (ptp) cc_final: 0.8427 (ptp) REVERT: J 871 LEU cc_start: 0.7871 (mt) cc_final: 0.7650 (mt) REVERT: K 75 GLN cc_start: 0.6894 (mt0) cc_final: 0.6667 (tm-30) REVERT: D 79 VAL cc_start: 0.8654 (t) cc_final: 0.8414 (t) outliers start: 20 outliers final: 4 residues processed: 598 average time/residue: 0.1943 time to fit residues: 175.6415 Evaluate side-chains 323 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 318 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain J residue 60 ARG Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain K residue 4 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.4980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 23 HIS H 84 ASN H 103 ASN H 117 HIS H 128 HIS ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 150 HIS I 618 GLN I1116 HIS ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1268 GLN I1313 HIS J 450 HIS J 665 GLN J 805 GLN J1108 GLN J1268 ASN J1326 GLN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN D 20 HIS D 77 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.159045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.127782 restraints weight = 35298.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.126770 restraints weight = 57606.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.128048 restraints weight = 49255.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.128142 restraints weight = 37492.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.128115 restraints weight = 33080.882| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27469 Z= 0.157 Angle : 0.702 8.914 37401 Z= 0.374 Chirality : 0.046 0.274 4276 Planarity : 0.006 0.053 4655 Dihedral : 15.347 173.912 4334 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.21 % Favored : 93.64 % Rotamer: Outliers : 2.13 % Allowed : 8.03 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.16 % Twisted Proline : 0.75 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.13), residues: 3238 helix: -1.10 (0.14), residues: 1109 sheet: -1.92 (0.23), residues: 412 loop : -2.47 (0.13), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.001 ARG J 709 TYR 0.019 0.002 TYR D 8 PHE 0.020 0.002 PHE I 514 TRP 0.014 0.001 TRP I 183 HIS 0.011 0.001 HIS I1313 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (27462) covalent geometry : angle 0.69872 / 0.37 (37395) hydrogen bonds : bond 0.04951 / 5.60 ( 1089) hydrogen bonds : angle 5.55347 / 6.38 ( 3040) metal coordination : bond 0.01136 / 1.10 ( 7) metal coordination : angle 5.13234 / 9.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 387 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 133 LEU cc_start: 0.8953 (mt) cc_final: 0.8719 (mt) REVERT: H 103 ASN cc_start: 0.7393 (OUTLIER) cc_final: 0.7147 (m-40) REVERT: H 157 THR cc_start: 0.8931 (OUTLIER) cc_final: 0.8522 (m) REVERT: H 192 VAL cc_start: 0.7167 (OUTLIER) cc_final: 0.6858 (t) REVERT: I 44 GLU cc_start: 0.7232 (tm-30) cc_final: 0.6880 (tm-30) REVERT: I 115 LYS cc_start: 0.5948 (pttt) cc_final: 0.5049 (tttm) REVERT: I 479 LEU cc_start: 0.5680 (tp) cc_final: 0.5407 (tp) REVERT: I 488 MET cc_start: 0.5905 (mmt) cc_final: 0.5459 (tpp) REVERT: I 515 MET cc_start: 0.8414 (ttp) cc_final: 0.8178 (ttp) REVERT: I 524 ILE cc_start: 0.8993 (tt) cc_final: 0.8756 (tt) REVERT: I 622 ASN cc_start: 0.8206 (m110) cc_final: 0.7970 (m110) REVERT: I 802 VAL cc_start: 0.9351 (OUTLIER) cc_final: 0.9102 (m) REVERT: I 1151 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7598 (tt) REVERT: I 1231 TYR cc_start: 0.8489 (t80) cc_final: 0.8081 (t80) REVERT: J 60 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.7074 (ptt90) REVERT: J 669 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.6778 (tm-30) REVERT: J 737 ILE cc_start: 0.8875 (tt) cc_final: 0.8642 (mm) REVERT: J 743 MET cc_start: 0.8665 (ptp) cc_final: 0.8336 (ptp) REVERT: K 3 ARG cc_start: 0.8082 (tpp80) cc_final: 0.7723 (tpp-160) REVERT: K 58 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8622 (pp) REVERT: K 67 ARG cc_start: 0.8293 (mtp180) cc_final: 0.7998 (mtp-110) REVERT: K 75 GLN cc_start: 0.6869 (mt0) cc_final: 0.6651 (tm-30) REVERT: D 79 VAL cc_start: 0.8503 (t) cc_final: 0.8224 (t) outliers start: 59 outliers final: 23 residues processed: 429 average time/residue: 0.1922 time to fit residues: 128.4021 Evaluate side-chains 339 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 308 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 930 ASP Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain J residue 60 ARG Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 669 GLN Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 1187 GLU Chi-restraints excluded: chain J residue 1247 LYS Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1297 LYS Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain D residue 53 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 261 optimal weight: 4.9990 chunk 242 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 294 optimal weight: 7.9990 chunk 296 optimal weight: 0.9990 chunk 317 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 153 optimal weight: 0.4980 chunk 217 optimal weight: 7.9990 chunk 133 optimal weight: 0.0770 overall best weight: 0.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 69 GLN I 120 GLN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 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 = 0.3825 r_free = 0.3825 target = 0.159955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.126540 restraints weight = 35516.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.125117 restraints weight = 46672.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.126591 restraints weight = 41065.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.127073 restraints weight = 28880.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.127065 restraints weight = 24721.961| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 27469 Z= 0.134 Angle : 0.630 8.442 37401 Z= 0.336 Chirality : 0.045 0.290 4276 Planarity : 0.005 0.085 4655 Dihedral : 15.143 172.785 4332 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.15 % Favored : 93.76 % Rotamer: Outliers : 2.31 % Allowed : 10.34 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.75 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.14), residues: 3238 helix: -0.21 (0.15), residues: 1111 sheet: -1.76 (0.23), residues: 422 loop : -2.20 (0.14), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 709 TYR 0.015 0.001 TYR J 723 PHE 0.015 0.001 PHE I 514 TRP 0.009 0.001 TRP J 686 HIS 0.010 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (27462) covalent geometry : angle 0.62884 / 0.34 (37395) hydrogen bonds : bond 0.04329 / 4.90 ( 1089) hydrogen bonds : angle 5.09331 / 5.88 ( 3040) metal coordination : bond 0.00286 / 0.29 ( 7) metal coordination : angle 3.34365 / 6.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 352 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 133 LEU cc_start: 0.8970 (mt) cc_final: 0.8741 (mt) REVERT: H 25 LYS cc_start: 0.8358 (ttmm) cc_final: 0.7942 (ttmm) REVERT: H 99 ILE cc_start: 0.8367 (tt) cc_final: 0.8022 (pt) REVERT: H 157 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8574 (m) REVERT: I 115 LYS cc_start: 0.5841 (pttt) cc_final: 0.4879 (tttm) REVERT: I 524 ILE cc_start: 0.9033 (tt) cc_final: 0.8818 (tt) REVERT: I 930 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7450 (m-30) REVERT: I 1073 LYS cc_start: 0.7950 (mtpt) cc_final: 0.7688 (mtmm) REVERT: I 1119 MET cc_start: 0.7947 (tpt) cc_final: 0.7577 (ttt) REVERT: I 1229 TYR cc_start: 0.9087 (m-80) cc_final: 0.8736 (m-80) REVERT: I 1231 TYR cc_start: 0.8545 (t80) cc_final: 0.8056 (t80) REVERT: I 1341 ASP cc_start: 0.5633 (t0) cc_final: 0.5408 (t0) REVERT: J 60 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6933 (ttp-170) REVERT: J 743 MET cc_start: 0.8794 (ptp) cc_final: 0.8460 (ptp) REVERT: J 1148 ARG cc_start: 0.7972 (mpt-90) cc_final: 0.7666 (mpt-90) REVERT: K 3 ARG cc_start: 0.8025 (tpp80) cc_final: 0.7748 (tpp-160) REVERT: K 58 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8502 (pp) REVERT: K 67 ARG cc_start: 0.8194 (mtp180) cc_final: 0.7889 (mtp-110) REVERT: K 75 GLN cc_start: 0.7157 (mt0) cc_final: 0.6678 (tm-30) REVERT: D 79 VAL cc_start: 0.8581 (t) cc_final: 0.8334 (t) outliers start: 64 outliers final: 35 residues processed: 399 average time/residue: 0.1877 time to fit residues: 117.9539 Evaluate side-chains 336 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 297 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 18 GLN Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 ASN Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 930 ASP Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain J residue 60 ARG Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1187 GLU Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1297 LYS Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 96 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 84 optimal weight: 0.9980 chunk 184 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 179 optimal weight: 0.7980 chunk 235 optimal weight: 0.0000 chunk 178 optimal weight: 1.9990 chunk 265 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 253 optimal weight: 0.0670 chunk 229 optimal weight: 4.9990 chunk 245 optimal weight: 0.9980 overall best weight: 0.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 23 HIS H 103 ASN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 834 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.160578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.130193 restraints weight = 35247.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.128838 restraints weight = 68246.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.130083 restraints weight = 58653.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.130530 restraints weight = 37611.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.130583 restraints weight = 32543.941| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 27469 Z= 0.121 Angle : 0.595 9.249 37401 Z= 0.318 Chirality : 0.044 0.287 4276 Planarity : 0.004 0.050 4655 Dihedral : 15.008 173.437 4331 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.81 % Favored : 94.13 % Rotamer: Outliers : 2.20 % Allowed : 11.82 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.14), residues: 3238 helix: 0.39 (0.15), residues: 1101 sheet: -1.42 (0.23), residues: 409 loop : -2.04 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 542 TYR 0.016 0.001 TYR J 75 PHE 0.012 0.001 PHE J 620 TRP 0.012 0.001 TRP J 580 HIS 0.006 0.001 HIS H 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (27462) covalent geometry : angle 0.59426 / 0.32 (37395) hydrogen bonds : bond 0.04032 / 4.56 ( 1089) hydrogen bonds : angle 4.82475 / 5.61 ( 3040) metal coordination : bond 0.00305 / 0.32 ( 7) metal coordination : angle 2.36578 / 4.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 324 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 133 LEU cc_start: 0.8962 (mt) cc_final: 0.8719 (mt) REVERT: H 25 LYS cc_start: 0.8362 (ttmm) cc_final: 0.7932 (ttmm) REVERT: H 99 ILE cc_start: 0.8428 (tt) cc_final: 0.8172 (pt) REVERT: H 157 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8606 (m) REVERT: H 158 ARG cc_start: 0.7031 (ttm-80) cc_final: 0.6767 (ttm-80) REVERT: H 200 LYS cc_start: 0.8952 (tttt) cc_final: 0.8728 (ttpp) REVERT: I 115 LYS cc_start: 0.5910 (pttt) cc_final: 0.5036 (tttm) REVERT: I 488 MET cc_start: 0.6123 (mmt) cc_final: 0.5772 (tpp) REVERT: I 524 ILE cc_start: 0.8961 (tt) cc_final: 0.8731 (tt) REVERT: I 789 THR cc_start: 0.9337 (p) cc_final: 0.8868 (m) REVERT: I 925 SER cc_start: 0.8675 (OUTLIER) cc_final: 0.8291 (p) REVERT: I 930 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7323 (m-30) REVERT: I 1073 LYS cc_start: 0.7869 (mtpt) cc_final: 0.7404 (mtmm) REVERT: I 1119 MET cc_start: 0.7999 (tpt) cc_final: 0.7663 (ttt) REVERT: I 1231 TYR cc_start: 0.8558 (t80) cc_final: 0.8096 (t80) REVERT: J 60 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6877 (ttp-170) REVERT: J 743 MET cc_start: 0.8706 (ptp) cc_final: 0.8396 (ptp) REVERT: J 788 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8796 (mt) REVERT: J 1148 ARG cc_start: 0.8151 (mpt-90) cc_final: 0.7945 (mpt-90) REVERT: K 58 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8632 (pp) REVERT: K 75 GLN cc_start: 0.6974 (mt0) cc_final: 0.6671 (tm-30) REVERT: D 8 TYR cc_start: 0.8107 (t80) cc_final: 0.7472 (t80) REVERT: D 79 VAL cc_start: 0.8545 (t) cc_final: 0.8334 (t) outliers start: 61 outliers final: 38 residues processed: 371 average time/residue: 0.1599 time to fit residues: 94.9293 Evaluate side-chains 342 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 298 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 930 ASP Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain I residue 1155 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain J residue 60 ARG Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 677 GLU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1187 GLU Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1297 LYS Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1373 ARG Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 96 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 38 optimal weight: 9.9990 chunk 275 optimal weight: 30.0000 chunk 104 optimal weight: 1.9990 chunk 302 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 79 optimal weight: 20.0000 chunk 94 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 604 HIS I 760 ASN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 ASN J 450 HIS ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1366 HIS D 18 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.154695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.131316 restraints weight = 35407.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.125606 restraints weight = 71863.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.122335 restraints weight = 44990.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.122481 restraints weight = 44246.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.122624 restraints weight = 38131.389| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 27469 Z= 0.257 Angle : 0.702 8.451 37401 Z= 0.368 Chirality : 0.048 0.310 4276 Planarity : 0.005 0.056 4655 Dihedral : 15.093 175.766 4331 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.45 % Favored : 93.48 % Rotamer: Outliers : 3.42 % Allowed : 12.43 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.14), residues: 3238 helix: 0.38 (0.15), residues: 1102 sheet: -1.45 (0.24), residues: 425 loop : -1.97 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 322 TYR 0.019 0.002 TYR J 46 PHE 0.021 0.002 PHE I 514 TRP 0.011 0.002 TRP I 183 HIS 0.010 0.002 HIS J 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.26 (27462) covalent geometry : angle 0.70072 / 0.37 (37395) hydrogen bonds : bond 0.04615 / 5.20 ( 1089) hydrogen bonds : angle 4.91402 / 5.68 ( 3040) metal coordination : bond 0.01172 / 1.09 ( 7) metal coordination : angle 3.94357 / 7.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 295 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 23 HIS cc_start: 0.7983 (OUTLIER) cc_final: 0.7537 (t-90) REVERT: G 133 LEU cc_start: 0.9032 (mt) cc_final: 0.8751 (mt) REVERT: H 25 LYS cc_start: 0.8419 (ttmm) cc_final: 0.7972 (ttmm) REVERT: H 157 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8771 (m) REVERT: I 115 LYS cc_start: 0.5965 (pttt) cc_final: 0.4694 (tmmt) REVERT: I 390 PHE cc_start: 0.8004 (m-10) cc_final: 0.7625 (m-80) REVERT: I 453 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8541 (tt) REVERT: I 488 MET cc_start: 0.6066 (mmt) cc_final: 0.5530 (tpp) REVERT: I 1073 LYS cc_start: 0.8314 (mtpt) cc_final: 0.7961 (mtmm) REVERT: I 1119 MET cc_start: 0.8114 (tpt) cc_final: 0.7912 (ttt) REVERT: I 1231 TYR cc_start: 0.8849 (t80) cc_final: 0.8204 (t80) REVERT: J 60 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7203 (ptt90) REVERT: J 505 ASP cc_start: 0.7869 (t0) cc_final: 0.7471 (t0) REVERT: J 743 MET cc_start: 0.8774 (ptp) cc_final: 0.8515 (ptp) REVERT: J 802 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7606 (m-30) REVERT: J 1115 ILE cc_start: 0.1493 (OUTLIER) cc_final: 0.1064 (pp) REVERT: K 75 GLN cc_start: 0.6971 (mt0) cc_final: 0.6500 (tm-30) REVERT: D 8 TYR cc_start: 0.8300 (t80) cc_final: 0.7510 (t80) REVERT: D 79 VAL cc_start: 0.8704 (t) cc_final: 0.8487 (t) outliers start: 95 outliers final: 59 residues processed: 367 average time/residue: 0.1799 time to fit residues: 105.3658 Evaluate side-chains 339 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 274 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 867 GLU Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 60 ARG Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 292 VAL Chi-restraints excluded: chain J residue 400 MET Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 677 GLU Chi-restraints excluded: chain J residue 691 ASP Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1187 GLU Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1297 LYS Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1373 ARG Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 96 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 278 optimal weight: 9.9990 chunk 194 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 chunk 206 optimal weight: 0.9980 chunk 303 optimal weight: 0.9980 chunk 292 optimal weight: 20.0000 chunk 151 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 288 optimal weight: 20.0000 chunk 198 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 GLN J 300 GLN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 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 = 0.3795 r_free = 0.3795 target = 0.157044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.125935 restraints weight = 35458.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.125080 restraints weight = 48601.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.125842 restraints weight = 45576.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.126218 restraints weight = 32859.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.126331 restraints weight = 29714.597| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27469 Z= 0.151 Angle : 0.615 9.778 37401 Z= 0.324 Chirality : 0.045 0.336 4276 Planarity : 0.004 0.054 4655 Dihedral : 14.986 175.362 4331 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.87 % Favored : 94.07 % Rotamer: Outliers : 2.70 % Allowed : 13.98 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.14), residues: 3238 helix: 0.63 (0.15), residues: 1103 sheet: -1.42 (0.24), residues: 434 loop : -1.90 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 738 TYR 0.016 0.001 TYR J 75 PHE 0.019 0.001 PHE I 514 TRP 0.008 0.001 TRP J 115 HIS 0.006 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (27462) covalent geometry : angle 0.61356 / 0.32 (37395) hydrogen bonds : bond 0.04128 / 4.64 ( 1089) hydrogen bonds : angle 4.74863 / 5.50 ( 3040) metal coordination : bond 0.00500 / 0.48 ( 7) metal coordination : angle 2.90405 / 5.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 296 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 133 LEU cc_start: 0.9000 (mt) cc_final: 0.8735 (mt) REVERT: H 25 LYS cc_start: 0.8464 (ttmm) cc_final: 0.7992 (ttmm) REVERT: H 157 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8757 (m) REVERT: I 115 LYS cc_start: 0.6011 (pttt) cc_final: 0.4890 (tmmt) REVERT: I 390 PHE cc_start: 0.7962 (m-10) cc_final: 0.7538 (m-80) REVERT: I 488 MET cc_start: 0.6126 (mmt) cc_final: 0.5836 (tpp) REVERT: I 925 SER cc_start: 0.8740 (OUTLIER) cc_final: 0.8340 (p) REVERT: I 1073 LYS cc_start: 0.8254 (mtpt) cc_final: 0.7898 (mtmm) REVERT: I 1231 TYR cc_start: 0.8800 (t80) cc_final: 0.8214 (t80) REVERT: J 60 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6763 (ttp-170) REVERT: J 505 ASP cc_start: 0.7828 (t0) cc_final: 0.7415 (t0) REVERT: J 743 MET cc_start: 0.8712 (ptp) cc_final: 0.8414 (ptp) REVERT: J 751 ASP cc_start: 0.7986 (m-30) cc_final: 0.7719 (m-30) REVERT: J 802 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7521 (m-30) REVERT: J 1115 ILE cc_start: 0.2248 (OUTLIER) cc_final: 0.1511 (pp) REVERT: D 8 TYR cc_start: 0.8208 (t80) cc_final: 0.7530 (t80) REVERT: D 79 VAL cc_start: 0.8631 (t) cc_final: 0.8406 (t) outliers start: 75 outliers final: 55 residues processed: 357 average time/residue: 0.1778 time to fit residues: 102.0490 Evaluate side-chains 337 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 277 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 60 ARG Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 535 ARG Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 691 ASP Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 802 ASP Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1187 GLU Chi-restraints excluded: chain J residue 1247 LYS Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1297 LYS Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 96 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 139 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 chunk 202 optimal weight: 0.9990 chunk 219 optimal weight: 0.6980 chunk 192 optimal weight: 0.3980 chunk 262 optimal weight: 10.0000 chunk 234 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 78 optimal weight: 0.0980 chunk 42 optimal weight: 0.2980 chunk 52 optimal weight: 6.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 23 HIS I 69 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 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 = 0.3810 r_free = 0.3810 target = 0.158484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.127081 restraints weight = 35037.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.125064 restraints weight = 59771.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.126727 restraints weight = 51324.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.126957 restraints weight = 35404.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.126996 restraints weight = 30707.675| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 27469 Z= 0.115 Angle : 0.580 10.527 37401 Z= 0.308 Chirality : 0.044 0.330 4276 Planarity : 0.004 0.053 4655 Dihedral : 14.872 175.561 4331 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.78 % Favored : 94.16 % Rotamer: Outliers : 2.56 % Allowed : 14.30 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.14), residues: 3238 helix: 0.89 (0.16), residues: 1107 sheet: -1.28 (0.24), residues: 434 loop : -1.80 (0.14), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 542 TYR 0.017 0.001 TYR G 185 PHE 0.016 0.001 PHE I 337 TRP 0.011 0.001 TRP I 807 HIS 0.006 0.001 HIS H 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (27462) covalent geometry : angle 0.57948 / 0.31 (37395) hydrogen bonds : bond 0.03861 / 4.33 ( 1089) hydrogen bonds : angle 4.61106 / 5.37 ( 3040) metal coordination : bond 0.00341 / 0.34 ( 7) metal coordination : angle 2.09451 / 3.90 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 312 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 133 LEU cc_start: 0.8970 (mt) cc_final: 0.8708 (mt) REVERT: H 157 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8744 (m) REVERT: I 115 LYS cc_start: 0.5966 (pttt) cc_final: 0.4753 (tmmt) REVERT: I 390 PHE cc_start: 0.7994 (m-10) cc_final: 0.7592 (m-80) REVERT: I 488 MET cc_start: 0.5838 (mmt) cc_final: 0.5616 (tpp) REVERT: I 789 THR cc_start: 0.9393 (p) cc_final: 0.8890 (m) REVERT: I 925 SER cc_start: 0.8468 (OUTLIER) cc_final: 0.8173 (p) REVERT: I 930 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7330 (m-30) REVERT: I 1073 LYS cc_start: 0.7924 (mtpt) cc_final: 0.7492 (mtmm) REVERT: I 1231 TYR cc_start: 0.8720 (t80) cc_final: 0.7955 (t80) REVERT: J 505 ASP cc_start: 0.7844 (t0) cc_final: 0.7366 (t0) REVERT: J 743 MET cc_start: 0.8659 (ptp) cc_final: 0.8364 (ptp) REVERT: J 751 ASP cc_start: 0.7886 (m-30) cc_final: 0.7643 (m-30) REVERT: J 1115 ILE cc_start: 0.2135 (OUTLIER) cc_final: 0.1431 (pp) REVERT: D 8 TYR cc_start: 0.8103 (t80) cc_final: 0.7461 (t80) REVERT: D 79 VAL cc_start: 0.8622 (t) cc_final: 0.8405 (t) outliers start: 71 outliers final: 57 residues processed: 368 average time/residue: 0.1781 time to fit residues: 105.6776 Evaluate side-chains 348 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 287 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 297 VAL Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 930 ASP Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 691 ASP Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1187 GLU Chi-restraints excluded: chain J residue 1247 LYS Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 96 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 59 optimal weight: 0.5980 chunk 198 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 314 optimal weight: 7.9990 chunk 207 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 252 optimal weight: 0.5980 chunk 272 optimal weight: 10.0000 chunk 209 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 41 ASN I 387 ASN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 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 = 0.3798 r_free = 0.3798 target = 0.157420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.124872 restraints weight = 35667.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.123497 restraints weight = 53993.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.125300 restraints weight = 46015.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.125096 restraints weight = 28866.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.125306 restraints weight = 27118.012| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 27469 Z= 0.154 Angle : 0.609 10.767 37401 Z= 0.319 Chirality : 0.045 0.327 4276 Planarity : 0.004 0.053 4655 Dihedral : 14.846 176.286 4327 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.05 % Favored : 93.89 % Rotamer: Outliers : 2.63 % Allowed : 14.91 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.15), residues: 3238 helix: 0.94 (0.16), residues: 1103 sheet: -1.22 (0.24), residues: 434 loop : -1.78 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 738 TYR 0.025 0.001 TYR J 46 PHE 0.015 0.001 PHE I 514 TRP 0.007 0.001 TRP I 183 HIS 0.006 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (27462) covalent geometry : angle 0.60856 / 0.32 (37395) hydrogen bonds : bond 0.03953 / 4.44 ( 1089) hydrogen bonds : angle 4.59542 / 5.36 ( 3040) metal coordination : bond 0.00571 / 0.54 ( 7) metal coordination : angle 2.41979 / 4.48 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 287 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 23 HIS cc_start: 0.7948 (OUTLIER) cc_final: 0.7740 (t-90) REVERT: G 133 LEU cc_start: 0.9049 (mt) cc_final: 0.8768 (mt) REVERT: H 25 LYS cc_start: 0.8383 (ttmm) cc_final: 0.8000 (ttmm) REVERT: H 157 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8725 (m) REVERT: I 115 LYS cc_start: 0.5954 (pttt) cc_final: 0.4714 (tmmt) REVERT: I 239 MET cc_start: 0.5943 (tmm) cc_final: 0.5254 (tmm) REVERT: I 390 PHE cc_start: 0.8052 (m-10) cc_final: 0.7629 (m-80) REVERT: I 453 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8480 (tt) REVERT: I 488 MET cc_start: 0.5721 (mmt) cc_final: 0.5513 (tpp) REVERT: I 628 HIS cc_start: 0.6055 (m90) cc_final: 0.5836 (m-70) REVERT: I 704 MET cc_start: 0.7917 (mmm) cc_final: 0.7317 (ttm) REVERT: I 925 SER cc_start: 0.8474 (OUTLIER) cc_final: 0.8199 (p) REVERT: I 1073 LYS cc_start: 0.8182 (mtpt) cc_final: 0.7743 (mtmm) REVERT: I 1231 TYR cc_start: 0.8821 (t80) cc_final: 0.7911 (t80) REVERT: J 75 TYR cc_start: 0.6838 (m-80) cc_final: 0.6568 (m-80) REVERT: J 505 ASP cc_start: 0.7918 (t0) cc_final: 0.7546 (t0) REVERT: J 743 MET cc_start: 0.8785 (ptp) cc_final: 0.8470 (ptp) REVERT: J 751 ASP cc_start: 0.7968 (m-30) cc_final: 0.7704 (m-30) REVERT: J 1115 ILE cc_start: 0.1841 (OUTLIER) cc_final: 0.1346 (pp) REVERT: J 1187 GLU cc_start: 0.6128 (OUTLIER) cc_final: 0.5799 (mm-30) REVERT: D 8 TYR cc_start: 0.8175 (t80) cc_final: 0.7412 (t80) outliers start: 73 outliers final: 57 residues processed: 345 average time/residue: 0.1794 time to fit residues: 100.2135 Evaluate side-chains 339 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 276 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 545 PHE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1289 GLU Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 691 ASP Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 862 THR Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1187 GLU Chi-restraints excluded: chain J residue 1247 LYS Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 96 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 66 optimal weight: 2.9990 chunk 188 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 chunk 60 optimal weight: 0.0770 chunk 301 optimal weight: 0.2980 chunk 287 optimal weight: 30.0000 chunk 141 optimal weight: 2.9990 chunk 279 optimal weight: 20.0000 overall best weight: 0.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 628 HIS I 799 ASN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.159619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.126954 restraints weight = 35671.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.125328 restraints weight = 47063.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.126278 restraints weight = 40987.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.126818 restraints weight = 31884.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.126770 restraints weight = 28926.520| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 27469 Z= 0.117 Angle : 0.583 10.727 37401 Z= 0.306 Chirality : 0.044 0.341 4276 Planarity : 0.004 0.053 4655 Dihedral : 14.777 176.617 4327 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.56 % Favored : 94.41 % Rotamer: Outliers : 2.23 % Allowed : 15.49 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.15), residues: 3238 helix: 1.12 (0.16), residues: 1102 sheet: -1.09 (0.25), residues: 406 loop : -1.69 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J1148 TYR 0.013 0.001 TYR G 177 PHE 0.015 0.001 PHE D 56 TRP 0.009 0.001 TRP I 807 HIS 0.005 0.001 HIS H 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (27462) covalent geometry : angle 0.58251 / 0.31 (37395) hydrogen bonds : bond 0.03735 / 4.18 ( 1089) hydrogen bonds : angle 4.52028 / 5.27 ( 3040) metal coordination : bond 0.00275 / 0.26 ( 7) metal coordination : angle 1.84290 / 3.42 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 304 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 133 LEU cc_start: 0.9023 (mt) cc_final: 0.8749 (mt) REVERT: H 157 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8733 (m) REVERT: I 115 LYS cc_start: 0.5833 (pttt) cc_final: 0.4621 (tmmt) REVERT: I 390 PHE cc_start: 0.7953 (m-10) cc_final: 0.7521 (m-80) REVERT: I 453 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8457 (tt) REVERT: I 704 MET cc_start: 0.7782 (mmm) cc_final: 0.7233 (ttm) REVERT: I 789 THR cc_start: 0.9350 (p) cc_final: 0.8947 (m) REVERT: I 925 SER cc_start: 0.8447 (OUTLIER) cc_final: 0.8186 (p) REVERT: I 1073 LYS cc_start: 0.7987 (mppt) cc_final: 0.7491 (mtmm) REVERT: J 75 TYR cc_start: 0.6860 (m-80) cc_final: 0.6620 (m-80) REVERT: J 382 TYR cc_start: 0.8940 (m-10) cc_final: 0.8530 (m-10) REVERT: J 505 ASP cc_start: 0.7869 (t0) cc_final: 0.7515 (t0) REVERT: J 589 TYR cc_start: 0.9208 (t80) cc_final: 0.8892 (t80) REVERT: J 743 MET cc_start: 0.8736 (ptp) cc_final: 0.8416 (ptp) REVERT: J 751 ASP cc_start: 0.7930 (m-30) cc_final: 0.7691 (m-30) REVERT: J 821 MET cc_start: 0.7966 (mtp) cc_final: 0.7605 (mtp) REVERT: J 1115 ILE cc_start: 0.1754 (OUTLIER) cc_final: 0.1258 (pp) REVERT: D 8 TYR cc_start: 0.7965 (t80) cc_final: 0.7291 (t80) outliers start: 62 outliers final: 47 residues processed: 355 average time/residue: 0.1812 time to fit residues: 103.5605 Evaluate side-chains 340 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 289 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 545 PHE Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1273 MET Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 535 ARG Chi-restraints excluded: chain J residue 638 SER Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 691 ASP Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1187 GLU Chi-restraints excluded: chain J residue 1247 LYS Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain D residue 53 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 101 optimal weight: 0.4980 chunk 265 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 209 optimal weight: 0.8980 chunk 232 optimal weight: 2.9990 chunk 325 optimal weight: 4.9990 chunk 104 optimal weight: 0.1980 chunk 258 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 327 optimal weight: 0.5980 chunk 146 optimal weight: 8.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 103 ASN ** I 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 799 ASN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 ASN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN D 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.159336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.128238 restraints weight = 35462.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.127727 restraints weight = 47298.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.128348 restraints weight = 41297.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.129065 restraints weight = 31017.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.129005 restraints weight = 27608.267| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27469 Z= 0.116 Angle : 0.583 10.354 37401 Z= 0.306 Chirality : 0.044 0.342 4276 Planarity : 0.004 0.056 4655 Dihedral : 14.746 176.682 4327 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.68 % Favored : 94.29 % Rotamer: Outliers : 1.95 % Allowed : 16.25 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.15), residues: 3238 helix: 1.17 (0.16), residues: 1105 sheet: -1.01 (0.25), residues: 418 loop : -1.65 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J1148 TYR 0.025 0.001 TYR J 46 PHE 0.015 0.001 PHE J1037 TRP 0.007 0.001 TRP I 807 HIS 0.005 0.001 HIS H 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (27462) covalent geometry : angle 0.58234 / 0.31 (37395) hydrogen bonds : bond 0.03710 / 4.17 ( 1089) hydrogen bonds : angle 4.48721 / 5.23 ( 3040) metal coordination : bond 0.00279 / 0.28 ( 7) metal coordination : angle 1.67250 / 3.05 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 305 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 133 LEU cc_start: 0.9029 (mt) cc_final: 0.8764 (mt) REVERT: H 157 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8732 (m) REVERT: I 37 LYS cc_start: 0.7233 (tptt) cc_final: 0.6868 (tptt) REVERT: I 115 LYS cc_start: 0.5827 (pttt) cc_final: 0.4665 (tmmt) REVERT: I 704 MET cc_start: 0.7767 (mmm) cc_final: 0.7260 (ttm) REVERT: I 789 THR cc_start: 0.9363 (p) cc_final: 0.8962 (m) REVERT: I 925 SER cc_start: 0.8322 (OUTLIER) cc_final: 0.8094 (p) REVERT: I 930 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7462 (m-30) REVERT: I 1073 LYS cc_start: 0.7964 (mppt) cc_final: 0.7439 (mtmm) REVERT: I 1231 TYR cc_start: 0.8798 (t80) cc_final: 0.7163 (t80) REVERT: J 60 ARG cc_start: 0.7402 (ptt90) cc_final: 0.7190 (ttp-170) REVERT: J 382 TYR cc_start: 0.9009 (m-10) cc_final: 0.8588 (m-10) REVERT: J 505 ASP cc_start: 0.7968 (t0) cc_final: 0.7662 (t0) REVERT: J 589 TYR cc_start: 0.9181 (t80) cc_final: 0.8908 (t80) REVERT: J 743 MET cc_start: 0.8759 (ptp) cc_final: 0.8443 (ptp) REVERT: J 751 ASP cc_start: 0.7885 (m-30) cc_final: 0.7633 (m-30) REVERT: J 821 MET cc_start: 0.7985 (mtp) cc_final: 0.7627 (mtp) REVERT: J 1115 ILE cc_start: 0.1830 (OUTLIER) cc_final: 0.1303 (pp) REVERT: D 8 TYR cc_start: 0.7935 (t80) cc_final: 0.7226 (t80) outliers start: 54 outliers final: 39 residues processed: 345 average time/residue: 0.1790 time to fit residues: 99.4724 Evaluate side-chains 330 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 287 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 400 VAL Chi-restraints excluded: chain I residue 410 LEU Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 656 SER Chi-restraints excluded: chain I residue 839 VAL Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 930 ASP Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1096 ILE Chi-restraints excluded: chain I residue 1293 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 227 PHE Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 535 ARG Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 691 ASP Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 1115 ILE Chi-restraints excluded: chain J residue 1187 GLU Chi-restraints excluded: chain J residue 1247 LYS Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain D residue 53 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 328 random chunks: chunk 143 optimal weight: 30.0000 chunk 188 optimal weight: 0.5980 chunk 201 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 223 optimal weight: 0.2980 chunk 113 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 294 optimal weight: 7.9990 chunk 313 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 799 ASN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.159154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.125846 restraints weight = 35471.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.124782 restraints weight = 48338.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.126328 restraints weight = 41031.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.126550 restraints weight = 29641.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.126480 restraints weight = 25712.488| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27469 Z= 0.138 Angle : 0.597 10.258 37401 Z= 0.312 Chirality : 0.044 0.327 4276 Planarity : 0.004 0.060 4655 Dihedral : 14.751 177.158 4327 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.65 % Favored : 94.32 % Rotamer: Outliers : 1.87 % Allowed : 16.64 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.15), residues: 3238 helix: 1.17 (0.16), residues: 1107 sheet: -0.96 (0.25), residues: 418 loop : -1.64 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 738 TYR 0.030 0.001 TYR J 144 PHE 0.014 0.001 PHE I 514 TRP 0.007 0.001 TRP I 183 HIS 0.006 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (27462) covalent geometry : angle 0.59677 / 0.31 (37395) hydrogen bonds : bond 0.03794 / 4.27 ( 1089) hydrogen bonds : angle 4.50022 / 5.24 ( 3040) metal coordination : bond 0.00463 / 0.45 ( 7) metal coordination : angle 1.96446 / 3.60 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4018.97 seconds wall clock time: 70 minutes 33.69 seconds (4233.69 seconds total)