Starting phenix.real_space_refine on Mon Jul 6 04:20:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7x74_33031/07_2026/7x74_33031.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x74_33031/07_2026/7x74_33031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7x74_33031/07_2026/7x74_33031.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7x74_33031/07_2026/7x74_33031.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x74_33031/07_2026/7x74_33031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x74_33031/07_2026/7x74_33031.map" model { file = "/net/cci-nas-00/data/ceres_data/7x74_33031/07_2026/7x74_33031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x74_33031/07_2026/7x74_33031.cif" } resolution = 3.7 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= 0.002 sd= 0.048 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 14 6.06 5 P 172 5.49 5 Mg 1 5.21 5 S 112 5.16 5 C 19811 2.51 5 N 5834 2.21 5 O 6606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32550 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1742 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 13, 'TRANS': 212} Chain: "B" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1792 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 13, 'TRANS': 219} Chain: "C" Number of atoms: 8692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 8692 Classifications: {'peptide': 1116} Link IDs: {'PTRANS': 58, 'TRANS': 1057} Chain: "D" Number of atoms: 9846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1259, 9846 Classifications: {'peptide': 1259} Link IDs: {'PTRANS': 56, 'TRANS': 1202} Chain: "E" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 597 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "F" Number of atoms: 2379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2379 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 285} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "H" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "M" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "N" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "O" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1714 Classifications: {'DNA': 84} Link IDs: {'rna3p': 83} Chain: "P" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1729 Classifications: {'DNA': 84} Link IDs: {'rna3p': 83} Chain: "Q" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 108 Classifications: {'RNA': 5} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12673 SG CYS D 60 79.405 105.081 115.600 1.00 89.92 S ATOM 12691 SG CYS D 62 78.425 106.446 118.672 1.00 92.64 S ATOM 12800 SG CYS D 75 81.725 105.107 118.292 1.00 92.95 S ATOM 12826 SG CYS D 78 79.543 102.402 118.777 1.00 89.64 S ATOM 19225 SG CYS D 886 108.319 51.187 83.854 1.00 89.23 S ATOM 19789 SG CYS D 962 105.034 51.322 85.140 1.00 75.30 S ATOM 19837 SG CYS D 969 105.603 53.110 81.641 1.00 66.75 S ATOM 19856 SG CYS D 972 105.394 49.445 81.961 1.00 74.56 S ATOM 25704 SG CYS G 90 86.606 185.316 86.727 1.00190.55 S ATOM 25726 SG CYS G 93 84.097 187.108 84.454 1.00191.16 S ATOM 25999 SG CYS G 130 85.156 188.165 88.144 1.00181.18 S ATOM 26018 SG CYS G 133 82.623 185.515 87.499 1.00174.23 S ATOM 25618 SG CYS G 79 102.355 191.689 83.182 1.00192.00 S ATOM 26688 SG CYS H 90 116.446 168.898 96.542 1.00190.67 S ATOM 26710 SG CYS H 93 118.318 166.112 98.232 1.00190.26 S ATOM 26983 SG CYS H 130 118.500 169.682 99.670 1.00187.29 S ATOM 27002 SG CYS H 133 120.323 168.508 96.384 1.00182.07 S ATOM 26602 SG CYS H 79 101.099 167.249 103.859 1.00179.93 S ATOM 27672 SG CYS M 90 83.012 176.677 42.752 1.00186.96 S ATOM 27694 SG CYS M 93 79.996 177.992 44.807 1.00185.83 S ATOM 27967 SG CYS M 130 79.557 176.422 41.337 1.00187.59 S ATOM 27986 SG CYS M 133 81.166 179.882 41.828 1.00182.16 S ATOM 27586 SG CYS M 79 82.168 161.855 47.847 1.00184.71 S ATOM 28656 SG CYS N 90 106.872 152.110 37.598 1.00184.39 S ATOM 28678 SG CYS N 93 110.500 150.877 37.218 1.00182.76 S ATOM 28951 SG CYS N 130 107.828 150.174 34.553 1.00182.02 S ATOM 28970 SG CYS N 133 107.755 148.369 37.846 1.00175.03 S ATOM 28570 SG CYS N 79 106.598 164.781 28.454 1.00186.86 S Time building chain proxies: 7.39, per 1000 atoms: 0.23 Number of scatterers: 32550 At special positions: 0 Unit cell: (147.4, 220, 200.2, 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 14 29.99 S 112 16.00 P 172 15.00 Mg 1 11.99 O 6606 8.00 N 5834 7.00 C 19811 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: 2.92 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1402 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 78 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 75 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 62 " pdb="ZN ZN D1402 " - pdb=" SG CYS D 60 " pdb=" ZN D1403 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 972 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 969 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 886 " pdb="ZN ZN D1403 " - pdb=" SG CYS D 962 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 130 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 90 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 93 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 133 " pdb=" ZN G 202 " pdb="ZN ZN G 202 " - pdb=" NE2 HIS G 85 " pdb="ZN ZN G 202 " - pdb=" NE2 HIS G 87 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 79 " pdb=" ZN G 203 " pdb="ZN ZN G 203 " - pdb=" NE2 HIS G 122 " pdb="ZN ZN G 203 " - pdb=" NE2 HIS G 86 " pdb="ZN ZN G 203 " - pdb=" NE2 HIS G 84 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 93 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 90 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 133 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 130 " pdb=" ZN H 202 " pdb="ZN ZN H 202 " - pdb=" NE2 HIS H 85 " pdb="ZN ZN H 202 " - pdb=" NE2 HIS H 87 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 79 " pdb=" ZN H 203 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 86 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 84 " pdb="ZN ZN H 203 " - pdb=" NE2 HIS H 122 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 133 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 130 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 93 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 90 " pdb=" ZN M 202 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 79 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 85 " pdb="ZN ZN M 202 " - pdb=" NE2 HIS M 87 " pdb=" ZN M 203 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 122 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 84 " pdb="ZN ZN M 203 " - pdb=" NE2 HIS M 86 " pdb=" ZN N 201 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 130 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 133 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 93 " pdb="ZN ZN N 201 " - pdb=" SG CYS N 90 " pdb=" ZN N 202 " pdb="ZN ZN N 202 " - pdb=" SG CYS N 79 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 85 " pdb="ZN ZN N 202 " - pdb=" NE2 HIS N 87 " pdb=" ZN N 203 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 86 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 122 " pdb="ZN ZN N 203 " - pdb=" NE2 HIS N 84 " Number of angles added : 36 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6876 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 48 sheets defined 44.1% alpha, 13.3% beta 68 base pairs and 116 stacking pairs defined. Time for finding SS restraints: 5.00 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 Processing helix chain 'A' and resid 72 through 82 removed outlier: 4.273A pdb=" N GLN A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 203 through 225 removed outlier: 4.166A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 45 removed outlier: 3.757A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 83 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 203 through 221 Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'C' and resid 38 through 50 removed outlier: 3.829A pdb=" N THR C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER C 44 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'C' and resid 221 through 229 removed outlier: 3.905A pdb=" N LEU C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 241 Processing helix chain 'C' and resid 243 through 253 Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'C' and resid 276 through 289 Processing helix chain 'C' and resid 297 through 309 removed outlier: 3.716A pdb=" N LYS C 306 " --> pdb=" O TYR C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 337 removed outlier: 3.595A pdb=" N GLY C 337 " --> pdb=" O LYS C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 360 No H-bonds generated for 'chain 'C' and resid 358 through 360' Processing helix chain 'C' and resid 366 through 392 Processing helix chain 'C' and resid 399 through 404 removed outlier: 3.738A pdb=" N ILE C 404 " --> pdb=" O PRO C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 418 removed outlier: 3.524A pdb=" N VAL C 410 " --> pdb=" O ILE C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 440 removed outlier: 3.619A pdb=" N ARG C 440 " --> pdb=" O THR C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 460 removed outlier: 3.558A pdb=" N ARG C 459 " --> pdb=" O GLY C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 4.016A pdb=" N ARG C 524 " --> pdb=" O ASP C 520 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N PHE C 525 " --> pdb=" O GLU C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 525' Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 576 through 580 Processing helix chain 'C' and resid 587 through 599 removed outlier: 4.076A pdb=" N ARG C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 623 Processing helix chain 'C' and resid 725 through 731 Processing helix chain 'C' and resid 765 through 769 removed outlier: 4.508A pdb=" N ASP C 769 " --> pdb=" O VAL C 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 812 Processing helix chain 'C' and resid 906 through 912 removed outlier: 4.211A pdb=" N SER C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 928 removed outlier: 3.508A pdb=" N LEU C 918 " --> pdb=" O PRO C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 947 Processing helix chain 'C' and resid 966 through 976 removed outlier: 3.554A pdb=" N LEU C 970 " --> pdb=" O ARG C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 1021 through 1026 removed outlier: 3.995A pdb=" N LYS C1025 " --> pdb=" O LEU C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1044 through 1048 Processing helix chain 'C' and resid 1054 through 1064 removed outlier: 3.683A pdb=" N TYR C1064 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing helix chain 'C' and resid 1067 through 1075 Processing helix chain 'C' and resid 1080 through 1094 removed outlier: 3.838A pdb=" N VAL C1085 " --> pdb=" O VAL C1081 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS C1086 " --> pdb=" O THR C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1104 through 1115 Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 121 through 127 removed outlier: 3.529A pdb=" N LEU D 125 " --> pdb=" O ALA D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 147 through 188 Processing helix chain 'D' and resid 192 through 228 Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 256 through 268 removed outlier: 3.905A pdb=" N ALA D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.867A pdb=" N THR D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 removed outlier: 3.695A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 339 through 360 removed outlier: 3.513A pdb=" N LEU D 360 " --> pdb=" O ARG D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 402 through 407 removed outlier: 3.938A pdb=" N LYS D 407 " --> pdb=" O ASP D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 417 removed outlier: 3.512A pdb=" N LEU D 417 " --> pdb=" O PHE D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 480 through 491 Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 533 removed outlier: 3.629A pdb=" N CYS D 529 " --> pdb=" O HIS D 525 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR D 530 " --> pdb=" O PRO D 526 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ALA D 531 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE D 532 " --> pdb=" O VAL D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 580 through 589 removed outlier: 3.677A pdb=" N GLY D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 617 Processing helix chain 'D' and resid 636 through 640 removed outlier: 3.555A pdb=" N GLU D 640 " --> pdb=" O ARG D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 672 removed outlier: 3.508A pdb=" N LEU D 672 " --> pdb=" O PHE D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 699 Processing helix chain 'D' and resid 700 through 723 removed outlier: 3.937A pdb=" N GLY D 723 " --> pdb=" O ALA D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 757 removed outlier: 3.611A pdb=" N ARG D 757 " --> pdb=" O LYS D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 788 Processing helix chain 'D' and resid 792 through 800 Processing helix chain 'D' and resid 805 through 814 removed outlier: 3.511A pdb=" N MET D 809 " --> pdb=" O ASN D 805 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 877 removed outlier: 3.989A pdb=" N GLY D 850 " --> pdb=" O ILE D 846 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS D 853 " --> pdb=" O HIS D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 950 Processing helix chain 'D' and resid 969 through 974 removed outlier: 3.544A pdb=" N TYR D 973 " --> pdb=" O CYS D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 988 through 999 removed outlier: 3.676A pdb=" N ILE D 992 " --> pdb=" O ALA D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1005 removed outlier: 4.479A pdb=" N THR D1005 " --> pdb=" O GLY D1001 " (cutoff:3.500A) Processing helix chain 'D' and resid 1022 through 1031 Processing helix chain 'D' and resid 1100 through 1108 removed outlier: 3.626A pdb=" N VAL D1104 " --> pdb=" O ASN D1100 " (cutoff:3.500A) Processing helix chain 'D' and resid 1109 through 1127 removed outlier: 3.556A pdb=" N SER D1127 " --> pdb=" O LYS D1123 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1145 removed outlier: 4.129A pdb=" N ILE D1137 " --> pdb=" O HIS D1133 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE D1140 " --> pdb=" O HIS D1136 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D1145 " --> pdb=" O ILE D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1166 through 1180 Processing helix chain 'D' and resid 1192 through 1199 Processing helix chain 'D' and resid 1202 through 1209 Processing helix chain 'D' and resid 1212 through 1223 Processing helix chain 'D' and resid 1231 through 1238 removed outlier: 4.282A pdb=" N ILE D1236 " --> pdb=" O LYS D1232 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE D1237 " --> pdb=" O GLU D1233 " (cutoff:3.500A) Processing helix chain 'D' and resid 1258 through 1265 Processing helix chain 'E' and resid 15 through 24 removed outlier: 4.174A pdb=" N LEU E 19 " --> pdb=" O PRO E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 45 Processing helix chain 'E' and resid 66 through 78 removed outlier: 3.635A pdb=" N ILE E 70 " --> pdb=" O LYS E 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 223 Processing helix chain 'F' and resid 229 through 252 Processing helix chain 'F' and resid 257 through 294 removed outlier: 5.091A pdb=" N ARG F 284 " --> pdb=" O GLU F 280 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU F 285 " --> pdb=" O ALA F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 317 Processing helix chain 'F' and resid 325 through 345 removed outlier: 4.016A pdb=" N TYR F 329 " --> pdb=" O LYS F 325 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR F 331 " --> pdb=" O SER F 327 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TRP F 332 " --> pdb=" O THR F 328 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TRP F 333 " --> pdb=" O TYR F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 374 Processing helix chain 'F' and resid 378 through 387 Processing helix chain 'F' and resid 389 through 400 Processing helix chain 'F' and resid 417 through 421 removed outlier: 3.739A pdb=" N LEU F 421 " --> pdb=" O PHE F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 450 Processing helix chain 'F' and resid 451 through 463 Processing helix chain 'F' and resid 471 through 476 removed outlier: 3.511A pdb=" N GLY F 476 " --> pdb=" O LEU F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 498 removed outlier: 3.642A pdb=" N ARG F 487 " --> pdb=" O ARG F 483 " (cutoff:3.500A) Processing helix chain 'F' and resid 500 through 502 No H-bonds generated for 'chain 'F' and resid 500 through 502' Processing helix chain 'F' and resid 503 through 508 removed outlier: 4.078A pdb=" N ASP F 508 " --> pdb=" O GLN F 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 26 removed outlier: 3.840A pdb=" N ALA G 17 " --> pdb=" O THR G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 43 Processing helix chain 'G' and resid 47 through 62 removed outlier: 4.050A pdb=" N VAL G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 116 Processing helix chain 'G' and resid 130 through 135 Processing helix chain 'H' and resid 13 through 26 Processing helix chain 'H' and resid 32 through 43 Processing helix chain 'H' and resid 47 through 62 Processing helix chain 'H' and resid 101 through 115 removed outlier: 3.840A pdb=" N GLU H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 135 removed outlier: 4.228A pdb=" N ALA H 134 " --> pdb=" O CYS H 130 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY H 135 " --> pdb=" O ALA H 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 130 through 135' Processing helix chain 'M' and resid 13 through 26 removed outlier: 3.509A pdb=" N VAL M 26 " --> pdb=" O ALA M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 43 Processing helix chain 'M' and resid 47 through 62 Processing helix chain 'M' and resid 101 through 116 removed outlier: 3.892A pdb=" N GLU M 105 " --> pdb=" O GLY M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 135 Processing helix chain 'N' and resid 13 through 26 Processing helix chain 'N' and resid 32 through 43 Processing helix chain 'N' and resid 47 through 62 Processing helix chain 'N' and resid 101 through 116 removed outlier: 4.201A pdb=" N GLU N 105 " --> pdb=" O GLY N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 135 removed outlier: 4.123A pdb=" N ALA N 134 " --> pdb=" O CYS N 130 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 removed outlier: 5.622A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 3.634A pdb=" N SER A 53 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLU A 141 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL A 51 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY A 143 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ALA A 49 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 removed outlier: 4.370A pdb=" N ASP B 188 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N THR B 181 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ASP B 190 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU B 179 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LEU B 192 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYS B 177 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL B 194 " --> pdb=" O THR B 175 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR B 175 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL B 196 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LYS B 173 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR B 198 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B 171 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 93 through 99 removed outlier: 3.742A pdb=" N SER B 53 " --> pdb=" O THR B 139 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N GLU B 141 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N VAL B 51 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLY B 143 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ALA B 49 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA8, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.668A pdb=" N GLY B 103 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 147 removed outlier: 3.787A pdb=" N VAL B 147 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 166 " --> pdb=" O VAL B 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.363A pdb=" N ILE C 23 " --> pdb=" O ALA C 958 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 91 through 100 removed outlier: 5.242A pdb=" N LEU C 93 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR C 128 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N PHE C 95 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N GLU C 126 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASP C 97 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA C 119 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASP C 144 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU C 121 " --> pdb=" O MET C 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 154 through 156 Processing sheet with id=AB4, first strand: chain 'C' and resid 166 through 169 Processing sheet with id=AB5, first strand: chain 'C' and resid 172 through 180 removed outlier: 3.601A pdb=" N ASP C 180 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS C 185 " --> pdb=" O ASP C 180 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE C 188 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU C 200 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 340 through 342 Processing sheet with id=AB7, first strand: chain 'C' and resid 441 through 442 Processing sheet with id=AB8, first strand: chain 'C' and resid 491 through 492 removed outlier: 6.922A pdb=" N ILE C 498 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU C 517 " --> pdb=" O ILE C 498 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR C 500 " --> pdb=" O ASP C 515 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP C 515 " --> pdb=" O THR C 500 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TYR C 502 " --> pdb=" O ASP C 513 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASP C 513 " --> pdb=" O TYR C 502 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS C 504 " --> pdb=" O THR C 511 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 491 through 492 Processing sheet with id=AC1, first strand: chain 'C' and resid 628 through 629 removed outlier: 6.997A pdb=" N VAL C 628 " --> pdb=" O LEU C 688 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 634 through 639 removed outlier: 7.093A pdb=" N THR C 645 " --> pdb=" O GLN C 637 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N VAL C 639 " --> pdb=" O TYR C 643 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N TYR C 643 " --> pdb=" O VAL C 639 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 694 through 695 Processing sheet with id=AC4, first strand: chain 'C' and resid 870 through 872 removed outlier: 7.148A pdb=" N ILE C 721 " --> pdb=" O SER C 882 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE C 884 " --> pdb=" O ILE C 721 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU C 723 " --> pdb=" O ILE C 884 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE C 722 " --> pdb=" O ILE C 902 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N ILE C 901 " --> pdb=" O ASN C 704 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU C 706 " --> pdb=" O ILE C 901 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LEU C 903 " --> pdb=" O LEU C 706 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA C 708 " --> pdb=" O LEU C 903 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N SER C1009 " --> pdb=" O PHE C 709 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 734 through 744 removed outlier: 4.288A pdb=" N GLY C 835 " --> pdb=" O TYR C 858 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA C 860 " --> pdb=" O VAL C 833 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N VAL C 833 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N LYS C 862 " --> pdb=" O GLY C 831 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N GLY C 831 " --> pdb=" O LYS C 862 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY C 831 " --> pdb=" O VAL C 782 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 754 through 755 Processing sheet with id=AC7, first strand: chain 'C' and resid 787 through 789 removed outlier: 3.541A pdb=" N LEU C 788 " --> pdb=" O LEU C 823 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU C 823 " --> pdb=" O LEU C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 892 through 893 Processing sheet with id=AC9, first strand: chain 'C' and resid 1027 through 1029 removed outlier: 3.714A pdb=" N ALA D 426 " --> pdb=" O VAL D 543 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER D 428 " --> pdb=" O MET D 541 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1052 through 1053 Processing sheet with id=AD2, first strand: chain 'C' and resid 1123 through 1124 Processing sheet with id=AD3, first strand: chain 'D' and resid 9 through 10 removed outlier: 3.797A pdb=" N ASP D1226 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 94 through 96 Processing sheet with id=AD5, first strand: chain 'D' and resid 234 through 235 removed outlier: 5.300A pdb=" N ILE D 136 " --> pdb=" O SER D 255 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N SER D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 336 through 337 removed outlier: 3.679A pdb=" N THR D 337 " --> pdb=" O ILE F 404 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 430 through 432 Processing sheet with id=AD8, first strand: chain 'D' and resid 443 through 444 removed outlier: 5.643A pdb=" N LEU D 443 " --> pdb=" O VAL D 517 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 566 through 567 removed outlier: 3.872A pdb=" N ARG D 572 " --> pdb=" O LYS D 567 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 603 through 604 Processing sheet with id=AE2, first strand: chain 'D' and resid 820 through 821 removed outlier: 3.676A pdb=" N GLU D 825 " --> pdb=" O ASN D 821 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 892 through 895 removed outlier: 4.099A pdb=" N MET D 919 " --> pdb=" O ARG D 957 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1070 through 1073 removed outlier: 3.635A pdb=" N GLY D1046 " --> pdb=" O VAL D1088 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1163 through 1165 Processing sheet with id=AE6, first strand: chain 'D' and resid 1253 through 1257 removed outlier: 3.595A pdb=" N ARG D1254 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU E 83 " --> pdb=" O ARG D1254 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 30 through 31 Processing sheet with id=AE8, first strand: chain 'G' and resid 96 through 99 removed outlier: 5.174A pdb=" N HIS G 87 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE G 126 " --> pdb=" O HIS G 87 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N HIS H 87 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N GLY H 128 " --> pdb=" O HIS H 87 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL H 89 " --> pdb=" O GLY H 128 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 30 through 31 Processing sheet with id=AF1, first strand: chain 'M' and resid 65 through 68 Processing sheet with id=AF2, first strand: chain 'M' and resid 96 through 99 removed outlier: 5.146A pdb=" N HIS M 87 " --> pdb=" O VAL M 124 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE M 126 " --> pdb=" O HIS M 87 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE N 127 " --> pdb=" O ALA M 121 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR M 123 " --> pdb=" O GLU N 125 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU N 125 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N HIS N 87 " --> pdb=" O ILE N 126 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 30 through 31 1332 hydrogen bonds defined for protein. 3786 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 180 hydrogen bonds 356 hydrogen bond angles 0 basepair planarities 68 basepair parallelities 116 stacking parallelities Total time for adding SS restraints: 9.67 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10044 1.34 - 1.46: 5930 1.46 - 1.58: 16933 1.58 - 1.70: 342 1.70 - 1.82: 189 Bond restraints: 33438 Sorted by residual: bond pdb=" C1' DC O 8 " pdb=" N1 DC O 8 " ideal model delta sigma weight residual 1.468 1.547 -0.079 1.40e-02 5.10e+03 3.20e+01 bond pdb=" C1' DT O 67 " pdb=" N1 DT O 67 " ideal model delta sigma weight residual 1.468 1.536 -0.068 1.40e-02 5.10e+03 2.39e+01 bond pdb=" C1' DC P 67 " pdb=" N1 DC P 67 " ideal model delta sigma weight residual 1.468 1.533 -0.065 1.40e-02 5.10e+03 2.13e+01 bond pdb=" C1' DC O 29 " pdb=" N1 DC O 29 " ideal model delta sigma weight residual 1.468 1.532 -0.064 1.40e-02 5.10e+03 2.11e+01 bond pdb=" C1' DC P 24 " pdb=" N1 DC P 24 " ideal model delta sigma weight residual 1.468 1.530 -0.062 1.40e-02 5.10e+03 1.94e+01 ... (remaining 33433 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 44589 2.22 - 4.44: 1226 4.44 - 6.67: 139 6.67 - 8.89: 23 8.89 - 11.11: 2 Bond angle restraints: 45979 Sorted by residual: angle pdb=" N GLN A 157 " pdb=" CA GLN A 157 " pdb=" C GLN A 157 " ideal model delta sigma weight residual 111.28 118.88 -7.60 1.09e+00 8.42e-01 4.87e+01 angle pdb=" N TYR A 168 " pdb=" CA TYR A 168 " pdb=" C TYR A 168 " ideal model delta sigma weight residual 111.28 118.34 -7.06 1.09e+00 8.42e-01 4.19e+01 angle pdb=" N VAL A 155 " pdb=" CA VAL A 155 " pdb=" C VAL A 155 " ideal model delta sigma weight residual 106.61 117.72 -11.11 1.78e+00 3.16e-01 3.90e+01 angle pdb=" N ASP D 878 " pdb=" CA ASP D 878 " pdb=" C ASP D 878 " ideal model delta sigma weight residual 111.28 117.67 -6.39 1.09e+00 8.42e-01 3.44e+01 angle pdb=" N VAL C 510 " pdb=" CA VAL C 510 " pdb=" C VAL C 510 " ideal model delta sigma weight residual 106.85 114.99 -8.14 1.42e+00 4.96e-01 3.29e+01 ... (remaining 45974 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 18687 35.94 - 71.87: 1150 71.87 - 107.81: 53 107.81 - 143.74: 4 143.74 - 179.68: 13 Dihedral angle restraints: 19907 sinusoidal: 9224 harmonic: 10683 Sorted by residual: dihedral pdb=" C ASP E 24 " pdb=" N ASP E 24 " pdb=" CA ASP E 24 " pdb=" CB ASP E 24 " ideal model delta harmonic sigma weight residual -122.60 -137.22 14.62 0 2.50e+00 1.60e-01 3.42e+01 dihedral pdb=" N ASP E 24 " pdb=" C ASP E 24 " pdb=" CA ASP E 24 " pdb=" CB ASP E 24 " ideal model delta harmonic sigma weight residual 122.80 136.86 -14.06 0 2.50e+00 1.60e-01 3.17e+01 dihedral pdb=" CA ASP D 537 " pdb=" C ASP D 537 " pdb=" N GLY D 538 " pdb=" CA GLY D 538 " ideal model delta harmonic sigma weight residual 180.00 158.02 21.98 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 19904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 4805 0.102 - 0.204: 391 0.204 - 0.306: 24 0.306 - 0.408: 4 0.408 - 0.510: 1 Chirality restraints: 5225 Sorted by residual: chirality pdb=" CA ASP E 24 " pdb=" N ASP E 24 " pdb=" C ASP E 24 " pdb=" CB ASP E 24 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.50e+00 chirality pdb=" CA LYS A 153 " pdb=" N LYS A 153 " pdb=" C LYS A 153 " pdb=" CB LYS A 153 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" C3' DG O 20 " pdb=" C4' DG O 20 " pdb=" O3' DG O 20 " pdb=" C2' DG O 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.37 -0.36 2.00e-01 2.50e+01 3.21e+00 ... (remaining 5222 not shown) Planarity restraints: 5422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 407 " 0.079 5.00e-02 4.00e+02 1.18e-01 2.21e+01 pdb=" N PRO C 408 " -0.203 5.00e-02 4.00e+02 pdb=" CA PRO C 408 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO C 408 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG O 72 " 0.038 2.00e-02 2.50e+03 1.66e-02 8.27e+00 pdb=" N9 DG O 72 " -0.039 2.00e-02 2.50e+03 pdb=" C8 DG O 72 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DG O 72 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG O 72 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG O 72 " 0.012 2.00e-02 2.50e+03 pdb=" O6 DG O 72 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DG O 72 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG O 72 " -0.003 2.00e-02 2.50e+03 pdb=" N2 DG O 72 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DG O 72 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DG O 72 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG P 49 " 0.009 2.00e-02 2.50e+03 1.51e-02 6.80e+00 pdb=" N9 DG P 49 " -0.003 2.00e-02 2.50e+03 pdb=" C8 DG P 49 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG P 49 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DG P 49 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG P 49 " 0.000 2.00e-02 2.50e+03 pdb=" O6 DG P 49 " -0.000 2.00e-02 2.50e+03 pdb=" N1 DG P 49 " 0.015 2.00e-02 2.50e+03 pdb=" C2 DG P 49 " -0.043 2.00e-02 2.50e+03 pdb=" N2 DG P 49 " 0.022 2.00e-02 2.50e+03 pdb=" N3 DG P 49 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG P 49 " 0.003 2.00e-02 2.50e+03 ... (remaining 5419 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 202 2.51 - 3.11: 24973 3.11 - 3.70: 53572 3.70 - 4.30: 70421 4.30 - 4.90: 113458 Nonbonded interactions: 262626 Sorted by model distance: nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D1401 " model vdw 1.912 2.170 nonbonded pdb=" O3' G Q 5 " pdb="MG MG D1401 " model vdw 1.915 2.170 nonbonded pdb=" OE2 GLU N 105 " pdb="ZN ZN N 203 " model vdw 1.975 2.230 nonbonded pdb=" OD2 ASP N 65 " pdb="ZN ZN N 202 " model vdw 1.981 2.230 nonbonded pdb=" OD2 ASP D 535 " pdb="MG MG D1401 " model vdw 2.048 2.170 ... (remaining 262621 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 'A' selection = (chain 'B' and resid 2 through 227) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 41.580 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 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 : 0.005 0.229 33486 Z= 0.351 Angle : 0.848 19.244 46015 Z= 0.528 Chirality : 0.055 0.510 5225 Planarity : 0.005 0.118 5422 Dihedral : 20.659 179.680 13031 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.87 % Allowed : 22.12 % Favored : 77.01 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.08 (0.14), residues: 3713 helix: 1.24 (0.14), residues: 1452 sheet: -0.88 (0.23), residues: 465 loop : -0.89 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 808 TYR 0.023 0.002 TYR E 32 PHE 0.018 0.002 PHE A 17 TRP 0.021 0.002 TRP C 924 HIS 0.009 0.001 HIS H 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.35 (33438) covalent geometry : angle 0.82358 / 0.53 (45979) hydrogen bonds : bond 0.14875 / 10.23 ( 1510) hydrogen bonds : angle 5.89141 / 4.15 ( 4142) metal coordination : bond 0.04908 / 3.78 ( 48) metal coordination : angle 7.33477 / 4.34 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 434 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 LYS cc_start: 0.7205 (mmtt) cc_final: 0.6939 (mmtt) REVERT: C 142 MET cc_start: 0.6608 (mmm) cc_final: 0.6094 (mmm) REVERT: C 550 ARG cc_start: 0.6347 (ttm110) cc_final: 0.5875 (mtp85) REVERT: C 821 THR cc_start: 0.8503 (OUTLIER) cc_final: 0.8050 (t) REVERT: D 59 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6659 (mt-10) REVERT: D 296 LEU cc_start: 0.7434 (mt) cc_final: 0.7096 (mt) REVERT: D 861 ARG cc_start: 0.6222 (OUTLIER) cc_final: 0.6001 (mmt-90) REVERT: D 888 THR cc_start: 0.7640 (t) cc_final: 0.7413 (t) REVERT: D 916 TYR cc_start: 0.7374 (m-10) cc_final: 0.6848 (m-80) REVERT: E 74 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7760 (mt-10) REVERT: F 245 PHE cc_start: 0.8157 (m-10) cc_final: 0.7941 (m-80) REVERT: F 282 ASN cc_start: 0.6488 (m110) cc_final: 0.6105 (t0) outliers start: 27 outliers final: 8 residues processed: 449 average time/residue: 0.2407 time to fit residues: 167.5234 Evaluate side-chains 337 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 327 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 793 THR Chi-restraints excluded: chain C residue 821 THR Chi-restraints excluded: chain D residue 861 ARG Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain F residue 460 MET Chi-restraints excluded: chain F residue 485 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.0040 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.1980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 6.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 256 GLN C 286 ASN C 424 GLN C 465 HIS ** C 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1040 GLN E 64 HIS F 305 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.181510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.141078 restraints weight = 63698.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.139077 restraints weight = 92065.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.140881 restraints weight = 79268.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.140552 restraints weight = 53113.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.141360 restraints weight = 49101.622| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 33486 Z= 0.158 Angle : 0.705 9.999 46015 Z= 0.374 Chirality : 0.047 0.341 5225 Planarity : 0.005 0.070 5422 Dihedral : 20.873 178.607 5945 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.61 % Allowed : 20.90 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.02 (0.13), residues: 3713 helix: 1.19 (0.13), residues: 1491 sheet: -0.55 (0.24), residues: 451 loop : -0.82 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 173 TYR 0.024 0.002 TYR E 32 PHE 0.019 0.002 PHE B 63 TRP 0.012 0.001 TRP C 930 HIS 0.031 0.001 HIS F 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (33438) covalent geometry : angle 0.68839 / 0.37 (45979) hydrogen bonds : bond 0.05461 / 3.75 ( 1510) hydrogen bonds : angle 4.71857 / 3.31 ( 4142) metal coordination : bond 0.00486 / 0.29 ( 48) metal coordination : angle 5.42114 / 3.68 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 362 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LEU cc_start: 0.7038 (mm) cc_final: 0.6775 (mm) REVERT: C 27 LYS cc_start: 0.7166 (mmtt) cc_final: 0.6798 (mmtt) REVERT: C 191 LYS cc_start: 0.6737 (pttt) cc_final: 0.6473 (pttt) REVERT: C 382 MET cc_start: 0.7871 (tmm) cc_final: 0.7457 (tmm) REVERT: C 598 MET cc_start: 0.7324 (mtp) cc_final: 0.7065 (ttm) REVERT: C 1109 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8015 (tp) REVERT: D 296 LEU cc_start: 0.7406 (mt) cc_final: 0.7152 (mt) REVERT: D 916 TYR cc_start: 0.7411 (m-10) cc_final: 0.6979 (m-80) REVERT: H 25 GLU cc_start: -0.0022 (OUTLIER) cc_final: -0.0226 (pt0) REVERT: N 38 MET cc_start: -0.0774 (ptt) cc_final: -0.2185 (mmp) REVERT: N 79 CYS cc_start: 0.2554 (OUTLIER) cc_final: 0.1534 (p) outliers start: 81 outliers final: 40 residues processed: 418 average time/residue: 0.2161 time to fit residues: 145.7815 Evaluate side-chains 361 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 318 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 1039 GLN Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 460 MET Chi-restraints excluded: chain F residue 485 ARG Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 490 GLU Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 130 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 258 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 0.0470 chunk 195 optimal weight: 0.8980 chunk 237 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 377 optimal weight: 20.0000 overall best weight: 1.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN A 152 ASN B 185 GLN ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN ** D 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 GLN ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.179666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.135517 restraints weight = 64132.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.130629 restraints weight = 70616.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.132077 restraints weight = 66604.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.132610 restraints weight = 44520.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.133081 restraints weight = 45985.789| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33486 Z= 0.170 Angle : 0.678 10.371 46015 Z= 0.360 Chirality : 0.046 0.335 5225 Planarity : 0.005 0.069 5422 Dihedral : 20.848 178.451 5939 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.57 % Allowed : 21.15 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.00 (0.13), residues: 3713 helix: 1.21 (0.13), residues: 1496 sheet: -0.61 (0.23), residues: 473 loop : -0.86 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 453 TYR 0.016 0.002 TYR E 32 PHE 0.018 0.002 PHE B 219 TRP 0.009 0.001 TRP D 718 HIS 0.007 0.001 HIS F 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (33438) covalent geometry : angle 0.66478 / 0.36 (45979) hydrogen bonds : bond 0.05150 / 3.52 ( 1510) hydrogen bonds : angle 4.57051 / 3.19 ( 4142) metal coordination : bond 0.00431 / 0.23 ( 48) metal coordination : angle 4.89268 / 3.28 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 336 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LEU cc_start: 0.7193 (mm) cc_final: 0.6974 (mm) REVERT: A 152 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7953 (t0) REVERT: B 202 MET cc_start: 0.6565 (ttm) cc_final: 0.6343 (ttp) REVERT: C 243 TYR cc_start: 0.8269 (m-80) cc_final: 0.7561 (m-80) REVERT: C 246 MET cc_start: 0.8796 (mmm) cc_final: 0.8444 (mmm) REVERT: C 382 MET cc_start: 0.8050 (tmm) cc_final: 0.7490 (tmm) REVERT: C 404 ILE cc_start: 0.8176 (pp) cc_final: 0.7964 (pt) REVERT: C 598 MET cc_start: 0.7210 (mtp) cc_final: 0.6889 (ttp) REVERT: C 1042 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8370 (pp) REVERT: C 1061 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7820 (tp) REVERT: D 70 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7752 (p90) REVERT: D 296 LEU cc_start: 0.7598 (mt) cc_final: 0.7256 (mt) REVERT: D 474 ARG cc_start: 0.7615 (ttp80) cc_final: 0.7287 (tmt170) REVERT: D 815 MET cc_start: 0.8456 (ppp) cc_final: 0.8197 (ptt) REVERT: D 916 TYR cc_start: 0.7438 (m-10) cc_final: 0.7102 (m-80) REVERT: F 245 PHE cc_start: 0.7978 (m-80) cc_final: 0.7682 (m-80) REVERT: H 25 GLU cc_start: 0.0198 (OUTLIER) cc_final: -0.0054 (pt0) REVERT: N 38 MET cc_start: -0.0971 (ptt) cc_final: -0.2051 (mmp) REVERT: N 79 CYS cc_start: 0.3063 (OUTLIER) cc_final: 0.1912 (p) outliers start: 111 outliers final: 70 residues processed: 419 average time/residue: 0.2157 time to fit residues: 145.6598 Evaluate side-chains 376 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 300 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 912 MET Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 316 CYS Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 949 HIS Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 1029 LEU Chi-restraints excluded: chain D residue 1100 ASN Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain D residue 1253 ILE Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 485 ARG Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 305 optimal weight: 6.9990 chunk 166 optimal weight: 0.4980 chunk 226 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 273 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 121 optimal weight: 0.0020 chunk 320 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 326 optimal weight: 40.0000 overall best weight: 1.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN A 119 HIS A 151 GLN ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 ASN H 86 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.177637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.135997 restraints weight = 63856.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.134240 restraints weight = 87541.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.136070 restraints weight = 73631.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.135427 restraints weight = 51249.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.136480 restraints weight = 46260.074| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.369 33486 Z= 0.219 Angle : 0.703 12.212 46015 Z= 0.368 Chirality : 0.046 0.319 5225 Planarity : 0.005 0.073 5422 Dihedral : 20.800 176.372 5936 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.48 % Allowed : 21.51 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.11 (0.13), residues: 3713 helix: 1.12 (0.13), residues: 1497 sheet: -0.58 (0.24), residues: 460 loop : -0.95 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 550 TYR 0.019 0.002 TYR D 106 PHE 0.019 0.002 PHE B 219 TRP 0.011 0.002 TRP C 712 HIS 0.024 0.001 HIS F 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 (33438) covalent geometry : angle 0.68986 / 0.37 (45979) hydrogen bonds : bond 0.05144 / 3.53 ( 1510) hydrogen bonds : angle 4.56161 / 3.17 ( 4142) metal coordination : bond 0.05356 / 4.38 ( 48) metal coordination : angle 4.92305 / 3.25 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 321 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 GLN cc_start: 0.6080 (OUTLIER) cc_final: 0.5851 (tp40) REVERT: B 157 GLN cc_start: 0.7705 (mp10) cc_final: 0.7448 (mp10) REVERT: B 202 MET cc_start: 0.6884 (ttm) cc_final: 0.6667 (ttp) REVERT: C 196 ARG cc_start: 0.6420 (ptp-170) cc_final: 0.6208 (ptp-170) REVERT: C 243 TYR cc_start: 0.7854 (m-80) cc_final: 0.6920 (m-10) REVERT: C 382 MET cc_start: 0.8255 (tmm) cc_final: 0.7514 (tmm) REVERT: C 565 MET cc_start: 0.7750 (ppp) cc_final: 0.6866 (ptm) REVERT: C 598 MET cc_start: 0.7371 (mtp) cc_final: 0.7121 (ttp) REVERT: C 1061 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7714 (tp) REVERT: D 30 LYS cc_start: 0.8411 (mtmt) cc_final: 0.7959 (mtpt) REVERT: D 296 LEU cc_start: 0.7699 (mt) cc_final: 0.7306 (mt) REVERT: D 320 ILE cc_start: 0.8298 (mm) cc_final: 0.7999 (mm) REVERT: D 474 ARG cc_start: 0.7604 (ttp80) cc_final: 0.7275 (tmt170) REVERT: D 815 MET cc_start: 0.8557 (ppp) cc_final: 0.8350 (ptt) REVERT: D 916 TYR cc_start: 0.7569 (m-10) cc_final: 0.7282 (m-80) REVERT: D 1147 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8395 (tpp80) REVERT: F 245 PHE cc_start: 0.7598 (m-80) cc_final: 0.7394 (m-80) REVERT: H 25 GLU cc_start: 0.0180 (OUTLIER) cc_final: -0.0043 (pt0) REVERT: N 79 CYS cc_start: 0.2708 (OUTLIER) cc_final: 0.1485 (p) outliers start: 139 outliers final: 90 residues processed: 431 average time/residue: 0.2151 time to fit residues: 149.2860 Evaluate side-chains 392 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 297 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 96 TYR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 857 VAL Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 316 CYS Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 702 VAL Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 971 MET Chi-restraints excluded: chain D residue 987 GLU Chi-restraints excluded: chain D residue 1100 ASN Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1132 ILE Chi-restraints excluded: chain D residue 1147 ARG Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain D residue 1253 ILE Chi-restraints excluded: chain D residue 1265 MET Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 326 PHE Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 485 ARG Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 284 optimal weight: 0.2980 chunk 233 optimal weight: 4.9990 chunk 310 optimal weight: 1.9990 chunk 325 optimal weight: 0.0970 chunk 74 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 230 optimal weight: 7.9990 chunk 286 optimal weight: 0.5980 chunk 99 optimal weight: 7.9990 chunk 320 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN C 877 ASN ** C 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN F 221 GLN ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 366 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.179579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.136795 restraints weight = 63840.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.134842 restraints weight = 81550.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.136006 restraints weight = 70981.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.136057 restraints weight = 45751.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.139200 restraints weight = 43423.293| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33486 Z= 0.134 Angle : 0.649 11.252 46015 Z= 0.342 Chirality : 0.044 0.331 5225 Planarity : 0.004 0.071 5422 Dihedral : 20.735 176.686 5936 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.57 % Allowed : 22.92 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.05 (0.14), residues: 3713 helix: 1.23 (0.13), residues: 1503 sheet: -0.44 (0.24), residues: 454 loop : -0.87 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 211 TYR 0.021 0.001 TYR E 32 PHE 0.021 0.001 PHE B 63 TRP 0.010 0.001 TRP D 773 HIS 0.018 0.001 HIS F 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (33438) covalent geometry : angle 0.63752 / 0.34 (45979) hydrogen bonds : bond 0.04643 / 3.16 ( 1510) hydrogen bonds : angle 4.34451 / 3.02 ( 4142) metal coordination : bond 0.00410 / 0.29 ( 48) metal coordination : angle 4.40471 / 3.00 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 327 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 GLN cc_start: 0.6111 (OUTLIER) cc_final: 0.5889 (tp40) REVERT: B 208 MET cc_start: 0.7926 (mtm) cc_final: 0.7524 (mtm) REVERT: B 225 LEU cc_start: 0.7328 (mm) cc_final: 0.6940 (tp) REVERT: C 243 TYR cc_start: 0.7782 (m-80) cc_final: 0.7179 (m-80) REVERT: C 382 MET cc_start: 0.8301 (tmm) cc_final: 0.7534 (tmm) REVERT: C 565 MET cc_start: 0.7692 (ppp) cc_final: 0.6887 (ptm) REVERT: C 598 MET cc_start: 0.7350 (mtp) cc_final: 0.7112 (ttp) REVERT: D 9 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6191 (pt0) REVERT: D 141 GLU cc_start: 0.7235 (mm-30) cc_final: 0.7016 (mm-30) REVERT: D 296 LEU cc_start: 0.7614 (mt) cc_final: 0.7252 (mt) REVERT: D 474 ARG cc_start: 0.7514 (ttp80) cc_final: 0.7212 (tmt170) REVERT: D 493 GLU cc_start: 0.7759 (pm20) cc_final: 0.7310 (pm20) REVERT: D 815 MET cc_start: 0.8554 (ppp) cc_final: 0.8317 (ptt) REVERT: D 916 TYR cc_start: 0.7376 (m-10) cc_final: 0.7049 (m-80) REVERT: E 70 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7312 (mt) REVERT: F 245 PHE cc_start: 0.7595 (m-80) cc_final: 0.7360 (m-80) REVERT: F 479 TYR cc_start: 0.6791 (t80) cc_final: 0.6558 (t80) REVERT: H 25 GLU cc_start: 0.0238 (OUTLIER) cc_final: 0.0007 (pt0) REVERT: N 79 CYS cc_start: 0.2665 (OUTLIER) cc_final: 0.1364 (p) outliers start: 111 outliers final: 66 residues processed: 412 average time/residue: 0.2181 time to fit residues: 144.2995 Evaluate side-chains 374 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 303 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 537 ASP Chi-restraints excluded: chain D residue 702 VAL Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 971 MET Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1253 ILE Chi-restraints excluded: chain D residue 1265 MET Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 485 ARG Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 239 optimal weight: 0.8980 chunk 254 optimal weight: 0.5980 chunk 145 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 365 optimal weight: 4.9990 chunk 276 optimal weight: 2.9990 chunk 331 optimal weight: 10.0000 chunk 311 optimal weight: 3.9990 chunk 371 optimal weight: 50.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN C 358 HIS ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 980 ASN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.177459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.134506 restraints weight = 63649.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.132365 restraints weight = 83069.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.134173 restraints weight = 74324.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.133419 restraints weight = 52779.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.134664 restraints weight = 46852.136| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 33486 Z= 0.185 Angle : 0.684 12.015 46015 Z= 0.358 Chirality : 0.046 0.334 5225 Planarity : 0.005 0.073 5422 Dihedral : 20.686 176.907 5936 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.57 % Allowed : 22.76 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.06 (0.13), residues: 3713 helix: 1.13 (0.13), residues: 1503 sheet: -0.51 (0.24), residues: 464 loop : -0.92 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 808 TYR 0.018 0.002 TYR A 32 PHE 0.020 0.002 PHE B 63 TRP 0.009 0.001 TRP D 718 HIS 0.016 0.001 HIS F 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (33438) covalent geometry : angle 0.67229 / 0.36 (45979) hydrogen bonds : bond 0.04866 / 3.32 ( 1510) hydrogen bonds : angle 4.42888 / 3.08 ( 4142) metal coordination : bond 0.00412 / 0.20 ( 48) metal coordination : angle 4.51068 / 2.99 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 324 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.6616 (ptmt) cc_final: 0.6132 (ptmm) REVERT: A 185 GLN cc_start: 0.6278 (OUTLIER) cc_final: 0.6009 (tp40) REVERT: B 120 ASN cc_start: 0.6638 (p0) cc_final: 0.6407 (p0) REVERT: B 208 MET cc_start: 0.8272 (mtm) cc_final: 0.7898 (mtm) REVERT: C 27 LYS cc_start: 0.7208 (mmtt) cc_final: 0.6993 (mmtt) REVERT: C 243 TYR cc_start: 0.7862 (m-80) cc_final: 0.6940 (m-10) REVERT: C 382 MET cc_start: 0.8456 (tmm) cc_final: 0.7670 (tmm) REVERT: C 565 MET cc_start: 0.7840 (ppp) cc_final: 0.7008 (ptm) REVERT: C 598 MET cc_start: 0.7586 (mtp) cc_final: 0.7350 (ttp) REVERT: C 1048 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.8141 (m-80) REVERT: D 30 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8168 (mtpp) REVERT: D 59 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6705 (mt-10) REVERT: D 296 LEU cc_start: 0.7686 (mt) cc_final: 0.7325 (mt) REVERT: D 387 ARG cc_start: 0.6486 (OUTLIER) cc_final: 0.6226 (mtp85) REVERT: D 493 GLU cc_start: 0.7891 (pm20) cc_final: 0.7423 (pm20) REVERT: D 815 MET cc_start: 0.8644 (ppp) cc_final: 0.8386 (ptt) REVERT: D 916 TYR cc_start: 0.7618 (m-10) cc_final: 0.7356 (m-80) REVERT: D 997 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8670 (mt) REVERT: D 1006 MET cc_start: 0.1382 (ppp) cc_final: 0.0722 (ppp) REVERT: E 74 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7893 (mt-10) REVERT: F 245 PHE cc_start: 0.7644 (m-80) cc_final: 0.7385 (m-80) REVERT: F 490 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7930 (tp30) REVERT: H 25 GLU cc_start: 0.0147 (OUTLIER) cc_final: -0.0093 (pt0) REVERT: N 79 CYS cc_start: 0.2433 (OUTLIER) cc_final: 0.1149 (p) outliers start: 142 outliers final: 104 residues processed: 435 average time/residue: 0.2079 time to fit residues: 145.8663 Evaluate side-chains 414 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 303 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 96 TYR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 305 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 822 SER Chi-restraints excluded: chain C residue 840 ASP Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 918 LEU Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 316 CYS Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 702 VAL Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 874 ASP Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 971 MET Chi-restraints excluded: chain D residue 979 THR Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain D residue 1253 ILE Chi-restraints excluded: chain D residue 1265 MET Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 485 ARG Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain M residue 28 GLU Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 376 optimal weight: 20.0000 chunk 353 optimal weight: 50.0000 chunk 150 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 178 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 325 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 330 optimal weight: 20.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 HIS ** 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 = 0.4418 r_free = 0.4418 target = 0.176410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.135374 restraints weight = 63248.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.133966 restraints weight = 92956.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.135649 restraints weight = 76717.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.135339 restraints weight = 51998.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.136160 restraints weight = 47112.424| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 33486 Z= 0.212 Angle : 0.711 11.400 46015 Z= 0.372 Chirality : 0.046 0.336 5225 Planarity : 0.005 0.075 5422 Dihedral : 20.678 178.158 5936 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.80 % Allowed : 23.15 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.19 (0.14), residues: 3713 helix: 1.04 (0.13), residues: 1505 sheet: -0.58 (0.24), residues: 474 loop : -1.01 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG D 211 TYR 0.022 0.002 TYR D 106 PHE 0.022 0.002 PHE B 219 TRP 0.013 0.002 TRP C 712 HIS 0.009 0.001 HIS F 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (33438) covalent geometry : angle 0.69921 / 0.37 (45979) hydrogen bonds : bond 0.05034 / 3.44 ( 1510) hydrogen bonds : angle 4.50042 / 3.12 ( 4142) metal coordination : bond 0.00478 / 0.22 ( 48) metal coordination : angle 4.60396 / 3.01 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 314 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 GLN cc_start: 0.6345 (OUTLIER) cc_final: 0.6104 (tp40) REVERT: B 157 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.7069 (pm20) REVERT: B 225 LEU cc_start: 0.7166 (mm) cc_final: 0.6722 (tp) REVERT: C 202 MET cc_start: 0.6002 (mtp) cc_final: 0.5770 (mtm) REVERT: C 243 TYR cc_start: 0.7715 (m-80) cc_final: 0.6830 (m-10) REVERT: C 382 MET cc_start: 0.8550 (tmm) cc_final: 0.7788 (tmm) REVERT: C 565 MET cc_start: 0.7885 (ppp) cc_final: 0.7003 (ptm) REVERT: C 598 MET cc_start: 0.7647 (mtp) cc_final: 0.7236 (ttp) REVERT: C 1036 MET cc_start: 0.7691 (mpp) cc_final: 0.7468 (mpt) REVERT: C 1048 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8127 (m-80) REVERT: C 1061 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7338 (tp) REVERT: D 9 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6483 (pt0) REVERT: D 30 LYS cc_start: 0.8580 (mtpt) cc_final: 0.8007 (mtpp) REVERT: D 296 LEU cc_start: 0.7639 (mt) cc_final: 0.7253 (mt) REVERT: D 374 LEU cc_start: 0.6432 (OUTLIER) cc_final: 0.6054 (tp) REVERT: D 387 ARG cc_start: 0.6488 (OUTLIER) cc_final: 0.6130 (mtp85) REVERT: D 474 ARG cc_start: 0.7595 (ttp80) cc_final: 0.7218 (tmt170) REVERT: D 493 GLU cc_start: 0.7908 (pm20) cc_final: 0.7568 (pm20) REVERT: D 815 MET cc_start: 0.8696 (ppp) cc_final: 0.8409 (ptt) REVERT: D 916 TYR cc_start: 0.7680 (m-10) cc_final: 0.7455 (m-80) REVERT: D 997 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8661 (mt) REVERT: D 1006 MET cc_start: 0.2096 (ppp) cc_final: 0.1502 (ppp) REVERT: E 32 TYR cc_start: 0.5775 (OUTLIER) cc_final: 0.4557 (t80) REVERT: F 461 ARG cc_start: 0.8153 (tpt170) cc_final: 0.7851 (tpt170) REVERT: H 25 GLU cc_start: 0.0148 (OUTLIER) cc_final: -0.0070 (pt0) REVERT: N 38 MET cc_start: 0.0554 (pmm) cc_final: 0.0211 (mpp) REVERT: N 79 CYS cc_start: 0.2293 (OUTLIER) cc_final: 0.1015 (p) outliers start: 149 outliers final: 105 residues processed: 432 average time/residue: 0.2055 time to fit residues: 142.5010 Evaluate side-chains 413 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 297 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 96 TYR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 305 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 840 ASP Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 316 CYS Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 702 VAL Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 874 ASP Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 971 MET Chi-restraints excluded: chain D residue 979 THR Chi-restraints excluded: chain D residue 987 GLU Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1132 ILE Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain D residue 1265 MET Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain F residue 485 ARG Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain M residue 28 GLU Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 215 optimal weight: 0.0060 chunk 278 optimal weight: 0.9980 chunk 334 optimal weight: 7.9990 chunk 281 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 327 optimal weight: 40.0000 chunk 2 optimal weight: 1.9990 chunk 352 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 ASN A 151 GLN C 157 ASN C 405 ASN C 741 HIS F 252 ASN ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.177153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.133303 restraints weight = 64198.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.129458 restraints weight = 77414.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.130733 restraints weight = 67635.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.131715 restraints weight = 44035.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.132048 restraints weight = 43481.470| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33486 Z= 0.143 Angle : 0.676 14.034 46015 Z= 0.353 Chirality : 0.045 0.335 5225 Planarity : 0.005 0.086 5422 Dihedral : 20.634 177.237 5936 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.83 % Allowed : 24.57 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.05 (0.14), residues: 3713 helix: 1.20 (0.13), residues: 1497 sheet: -0.57 (0.24), residues: 472 loop : -0.95 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 829 TYR 0.027 0.002 TYR A 32 PHE 0.059 0.002 PHE F 245 TRP 0.014 0.001 TRP C 930 HIS 0.011 0.001 HIS F 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (33438) covalent geometry : angle 0.66601 / 0.35 (45979) hydrogen bonds : bond 0.04617 / 3.15 ( 1510) hydrogen bonds : angle 4.33233 / 3.01 ( 4142) metal coordination : bond 0.00268 / 0.13 ( 48) metal coordination : angle 4.15356 / 2.82 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 329 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLN cc_start: 0.7407 (mm110) cc_final: 0.7150 (mm110) REVERT: A 185 GLN cc_start: 0.6514 (OUTLIER) cc_final: 0.6204 (tp40) REVERT: B 120 ASN cc_start: 0.7052 (p0) cc_final: 0.6619 (p0) REVERT: B 136 MET cc_start: 0.7913 (ppp) cc_final: 0.7613 (ppp) REVERT: B 157 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.7121 (pm20) REVERT: B 225 LEU cc_start: 0.7457 (mm) cc_final: 0.7041 (tp) REVERT: C 142 MET cc_start: 0.6128 (mmm) cc_final: 0.5916 (mmm) REVERT: C 243 TYR cc_start: 0.7928 (m-80) cc_final: 0.7269 (m-80) REVERT: C 382 MET cc_start: 0.8515 (tmm) cc_final: 0.7784 (tmm) REVERT: C 565 MET cc_start: 0.7952 (ppp) cc_final: 0.7193 (ptm) REVERT: C 584 GLU cc_start: 0.8681 (pm20) cc_final: 0.8458 (pm20) REVERT: C 1036 MET cc_start: 0.7630 (mpp) cc_final: 0.7402 (mpt) REVERT: C 1048 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.8112 (m-80) REVERT: C 1061 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7514 (tp) REVERT: D 9 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6425 (pt0) REVERT: D 30 LYS cc_start: 0.8628 (mtpt) cc_final: 0.8046 (mtpp) REVERT: D 229 LEU cc_start: 0.7919 (mt) cc_final: 0.7477 (mm) REVERT: D 296 LEU cc_start: 0.7634 (mt) cc_final: 0.7228 (mt) REVERT: D 474 ARG cc_start: 0.7687 (ttp80) cc_final: 0.7279 (tmt170) REVERT: D 493 GLU cc_start: 0.7844 (pm20) cc_final: 0.7526 (pm20) REVERT: D 815 MET cc_start: 0.8730 (ppp) cc_final: 0.8435 (ptt) REVERT: D 916 TYR cc_start: 0.7615 (m-10) cc_final: 0.7380 (m-80) REVERT: D 997 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8484 (mt) REVERT: E 32 TYR cc_start: 0.5769 (OUTLIER) cc_final: 0.4586 (t80) REVERT: E 74 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7618 (mm-30) REVERT: F 382 LEU cc_start: 0.8921 (tt) cc_final: 0.8408 (mp) REVERT: H 25 GLU cc_start: 0.0226 (OUTLIER) cc_final: -0.0022 (pt0) REVERT: N 38 MET cc_start: 0.0403 (pmm) cc_final: 0.0177 (mpp) REVERT: N 79 CYS cc_start: 0.2726 (OUTLIER) cc_final: 0.1430 (p) outliers start: 119 outliers final: 90 residues processed: 424 average time/residue: 0.1966 time to fit residues: 135.2763 Evaluate side-chains 402 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 303 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 305 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 840 ASP Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 887 ILE Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 702 VAL Chi-restraints excluded: chain D residue 728 ILE Chi-restraints excluded: chain D residue 762 LYS Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 841 VAL Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 971 MET Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1182 HIS Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1265 MET Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain M residue 28 GLU Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 197 optimal weight: 2.9990 chunk 323 optimal weight: 50.0000 chunk 209 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 167 optimal weight: 2.9990 chunk 379 optimal weight: 30.0000 chunk 149 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.175838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.133046 restraints weight = 64238.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.130276 restraints weight = 91690.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.131969 restraints weight = 71861.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.131994 restraints weight = 46673.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.135120 restraints weight = 44358.129| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33486 Z= 0.181 Angle : 0.702 12.407 46015 Z= 0.366 Chirality : 0.046 0.332 5225 Planarity : 0.005 0.106 5422 Dihedral : 20.600 177.553 5930 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.99 % Allowed : 24.66 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.13 (0.14), residues: 3713 helix: 1.13 (0.13), residues: 1502 sheet: -0.62 (0.24), residues: 471 loop : -0.99 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 211 TYR 0.037 0.002 TYR A 32 PHE 0.018 0.002 PHE B 219 TRP 0.016 0.001 TRP C 930 HIS 0.011 0.001 HIS F 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (33438) covalent geometry : angle 0.69069 / 0.37 (45979) hydrogen bonds : bond 0.04795 / 3.28 ( 1510) hydrogen bonds : angle 4.40372 / 3.05 ( 4142) metal coordination : bond 0.00364 / 0.17 ( 48) metal coordination : angle 4.49782 / 3.06 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 307 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASP cc_start: 0.7051 (m-30) cc_final: 0.6697 (m-30) REVERT: B 157 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.7161 (pm20) REVERT: B 225 LEU cc_start: 0.7479 (mm) cc_final: 0.7076 (tp) REVERT: C 243 TYR cc_start: 0.7775 (m-80) cc_final: 0.6857 (m-10) REVERT: C 382 MET cc_start: 0.8597 (tmm) cc_final: 0.7845 (tmm) REVERT: C 565 MET cc_start: 0.7832 (ppp) cc_final: 0.7096 (ptm) REVERT: C 1036 MET cc_start: 0.7606 (mpp) cc_final: 0.7397 (mpt) REVERT: C 1048 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.8116 (m-80) REVERT: C 1061 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7411 (tp) REVERT: D 9 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6445 (pt0) REVERT: D 30 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8006 (mtpp) REVERT: D 296 LEU cc_start: 0.7672 (mt) cc_final: 0.7329 (mt) REVERT: D 474 ARG cc_start: 0.7634 (ttp80) cc_final: 0.7245 (tmt170) REVERT: D 493 GLU cc_start: 0.7812 (pm20) cc_final: 0.7529 (pm20) REVERT: D 815 MET cc_start: 0.8746 (ppp) cc_final: 0.8450 (ptt) REVERT: D 916 TYR cc_start: 0.7634 (m-10) cc_final: 0.7412 (m-80) REVERT: D 997 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8536 (mt) REVERT: D 1006 MET cc_start: 0.1786 (ppp) cc_final: 0.0915 (ppp) REVERT: E 32 TYR cc_start: 0.5803 (OUTLIER) cc_final: 0.4583 (t80) REVERT: N 79 CYS cc_start: 0.2634 (OUTLIER) cc_final: 0.1396 (p) outliers start: 124 outliers final: 99 residues processed: 406 average time/residue: 0.2071 time to fit residues: 136.6023 Evaluate side-chains 408 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 301 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 305 ASN Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 597 MET Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 840 ASP Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 887 ILE Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 316 CYS Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 702 VAL Chi-restraints excluded: chain D residue 728 ILE Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 841 VAL Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 971 MET Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1105 LEU Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1182 HIS Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1265 MET Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 482 THR Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain M residue 28 GLU Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 134 optimal weight: 0.3980 chunk 194 optimal weight: 0.8980 chunk 283 optimal weight: 0.6980 chunk 154 optimal weight: 0.5980 chunk 248 optimal weight: 0.6980 chunk 333 optimal weight: 9.9990 chunk 141 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 375 optimal weight: 20.0000 chunk 196 optimal weight: 1.9990 chunk 303 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.177491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.135259 restraints weight = 64446.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.133429 restraints weight = 88139.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.135313 restraints weight = 72809.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.134803 restraints weight = 50497.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.135755 restraints weight = 45882.122| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33486 Z= 0.138 Angle : 0.687 14.918 46015 Z= 0.357 Chirality : 0.045 0.328 5225 Planarity : 0.005 0.069 5422 Dihedral : 20.572 177.787 5930 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.38 % Allowed : 25.43 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.03 (0.14), residues: 3713 helix: 1.20 (0.13), residues: 1499 sheet: -0.52 (0.24), residues: 476 loop : -0.93 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG D 211 TYR 0.035 0.001 TYR A 32 PHE 0.015 0.001 PHE B 219 TRP 0.025 0.001 TRP C 930 HIS 0.011 0.001 HIS F 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (33438) covalent geometry : angle 0.67781 / 0.36 (45979) hydrogen bonds : bond 0.04487 / 3.06 ( 1510) hydrogen bonds : angle 4.30514 / 2.99 ( 4142) metal coordination : bond 0.00264 / 0.13 ( 48) metal coordination : angle 4.02605 / 2.76 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 321 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASP cc_start: 0.7127 (m-30) cc_final: 0.6905 (m-30) REVERT: B 157 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.7063 (pm20) REVERT: B 225 LEU cc_start: 0.7522 (mm) cc_final: 0.7118 (tp) REVERT: C 243 TYR cc_start: 0.7634 (m-80) cc_final: 0.7090 (m-80) REVERT: C 382 MET cc_start: 0.8598 (tmm) cc_final: 0.7825 (tmm) REVERT: C 565 MET cc_start: 0.7883 (ppp) cc_final: 0.7057 (ptm) REVERT: C 584 GLU cc_start: 0.8731 (pm20) cc_final: 0.8514 (pm20) REVERT: C 1048 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.8116 (m-80) REVERT: C 1061 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7483 (tp) REVERT: D 9 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6308 (pt0) REVERT: D 30 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7963 (mtpp) REVERT: D 296 LEU cc_start: 0.7648 (mt) cc_final: 0.7305 (mt) REVERT: D 405 MET cc_start: 0.8032 (ptp) cc_final: 0.7687 (ptm) REVERT: D 474 ARG cc_start: 0.7622 (ttp80) cc_final: 0.7228 (tmt170) REVERT: D 493 GLU cc_start: 0.7808 (pm20) cc_final: 0.7529 (pm20) REVERT: D 815 MET cc_start: 0.8700 (ppp) cc_final: 0.8338 (ptt) REVERT: D 997 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8281 (mt) REVERT: D 1006 MET cc_start: 0.1424 (ppp) cc_final: 0.0800 (ppp) REVERT: E 32 TYR cc_start: 0.5805 (OUTLIER) cc_final: 0.4583 (t80) REVERT: E 38 ARG cc_start: 0.8084 (ttm-80) cc_final: 0.7728 (ttm-80) REVERT: E 74 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7694 (mm-30) REVERT: N 79 CYS cc_start: 0.2293 (OUTLIER) cc_final: 0.1092 (p) outliers start: 105 outliers final: 90 residues processed: 402 average time/residue: 0.2018 time to fit residues: 131.8046 Evaluate side-chains 402 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 304 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 305 ASN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 597 MET Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 840 ASP Chi-restraints excluded: chain C residue 887 ILE Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 702 VAL Chi-restraints excluded: chain D residue 728 ILE Chi-restraints excluded: chain D residue 762 LYS Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 971 MET Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1105 LEU Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1182 HIS Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1265 MET Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain M residue 28 GLU Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 67 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 384 optimal weight: 60.0000 chunk 55 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 370 optimal weight: 50.0000 chunk 63 optimal weight: 5.9990 chunk 228 optimal weight: 3.9990 chunk 253 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.173937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.132391 restraints weight = 64620.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.129850 restraints weight = 102501.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.131409 restraints weight = 77280.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.131511 restraints weight = 48834.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.135125 restraints weight = 46275.116| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 33486 Z= 0.248 Angle : 0.770 16.937 46015 Z= 0.398 Chirality : 0.048 0.395 5225 Planarity : 0.006 0.075 5422 Dihedral : 20.613 178.058 5930 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.70 % Allowed : 25.43 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.30 (0.14), residues: 3713 helix: 0.95 (0.13), residues: 1501 sheet: -0.71 (0.24), residues: 472 loop : -1.04 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 211 TYR 0.046 0.002 TYR A 32 PHE 0.027 0.002 PHE C 892 TRP 0.026 0.002 TRP C 930 HIS 0.009 0.001 HIS F 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.25 (33438) covalent geometry : angle 0.75954 / 0.40 (45979) hydrogen bonds : bond 0.05215 / 3.58 ( 1510) hydrogen bonds : angle 4.58379 / 3.18 ( 4142) metal coordination : bond 0.00586 / 0.27 ( 48) metal coordination : angle 4.62853 / 3.01 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5504.41 seconds wall clock time: 96 minutes 11.09 seconds (5771.09 seconds total)