Starting phenix.real_space_refine on Wed Apr 8 00:35:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x74_33031/04_2026/7x74_33031.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x74_33031/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7x74_33031/04_2026/7x74_33031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x74_33031/04_2026/7x74_33031.map" model { file = "/net/cci-nas-00/data/ceres_data/7x74_33031/04_2026/7x74_33031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x74_33031/04_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/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: 7.14, per 1000 atoms: 0.22 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: 2.88 Conformation dependent library (CDL) restraints added in 1.2 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: 4.44 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: 9.03 Time building geometry restraints manager: 3.77 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=" O3' DC O 29 " pdb=" P DG O 30 " ideal model delta sigma weight residual 1.607 1.653 -0.046 1.50e-02 4.44e+03 9.32e+00 bond pdb=" C ALA A 111 " pdb=" N PRO A 112 " ideal model delta sigma weight residual 1.329 1.362 -0.033 1.18e-02 7.18e+03 7.76e+00 bond pdb=" O3' DA P 63 " pdb=" P DA P 64 " ideal model delta sigma weight residual 1.607 1.645 -0.038 1.50e-02 4.44e+03 6.28e+00 bond pdb=" CA ILE B 46 " pdb=" C ILE B 46 " ideal model delta sigma weight residual 1.524 1.554 -0.029 1.20e-02 6.94e+03 5.99e+00 bond pdb=" O3' DT O 22 " pdb=" P DC O 23 " ideal model delta sigma weight residual 1.607 1.642 -0.035 1.50e-02 4.44e+03 5.53e+00 ... (remaining 33433 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 44722 2.22 - 4.44: 1101 4.44 - 6.67: 132 6.67 - 8.89: 22 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: 18694 35.94 - 71.87: 1163 71.87 - 107.81: 53 107.81 - 143.74: 4 143.74 - 179.68: 13 Dihedral angle restraints: 19927 sinusoidal: 9244 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 19924 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 4938 0.102 - 0.204: 261 0.204 - 0.306: 22 0.306 - 0.408: 3 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=" CA GLU C 473 " pdb=" N GLU C 473 " pdb=" C GLU C 473 " pdb=" CB GLU C 473 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.83e+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: 4.490 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: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 38.910 Find NCS groups from input model: 0.330 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 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= 0.231 Angle : 0.823 19.244 46015 Z= 0.462 Chirality : 0.051 0.510 5225 Planarity : 0.005 0.118 5422 Dihedral : 20.730 179.680 13051 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 covalent geometry : bond 0.00462 (33438) covalent geometry : angle 0.79714 (45979) hydrogen bonds : bond 0.14875 ( 1510) hydrogen bonds : angle 5.89141 ( 4142) metal coordination : bond 0.04908 ( 48) metal coordination : angle 7.33477 ( 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 : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.2379 time to fit residues: 164.6785 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 : 1.124 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.181558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.138369 restraints weight = 63396.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.134419 restraints weight = 71564.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.135598 restraints weight = 69001.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.135721 restraints weight = 44966.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.137391 restraints weight = 43329.273| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33486 Z= 0.152 Angle : 0.656 10.272 46015 Z= 0.343 Chirality : 0.043 0.199 5225 Planarity : 0.005 0.074 5422 Dihedral : 20.899 179.046 5965 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.58 % Allowed : 21.15 % Favored : 76.27 % 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: 0.10 (0.13), residues: 3713 helix: 1.33 (0.13), residues: 1493 sheet: -0.66 (0.23), residues: 464 loop : -0.80 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 478 TYR 0.021 0.001 TYR E 32 PHE 0.020 0.001 PHE B 63 TRP 0.009 0.001 TRP C 930 HIS 0.022 0.001 HIS F 354 Details of bonding type rmsd covalent geometry : bond 0.00341 (33438) covalent geometry : angle 0.64185 (45979) hydrogen bonds : bond 0.04962 ( 1510) hydrogen bonds : angle 4.56996 ( 4142) metal coordination : bond 0.00466 ( 48) metal coordination : angle 4.96502 ( 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 449 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 369 time to evaluate : 1.646 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 128 LEU cc_start: 0.7204 (mm) cc_final: 0.6955 (mm) REVERT: C 27 LYS cc_start: 0.7179 (mmtt) cc_final: 0.6903 (mmtt) REVERT: C 382 MET cc_start: 0.7998 (tmm) cc_final: 0.7485 (tmm) REVERT: C 565 MET cc_start: 0.7658 (ppp) cc_final: 0.6592 (ptm) REVERT: D 261 LEU cc_start: 0.8013 (mt) cc_final: 0.7798 (mp) REVERT: D 296 LEU cc_start: 0.7450 (mt) cc_final: 0.7134 (mt) REVERT: D 916 TYR cc_start: 0.7433 (m-10) cc_final: 0.7022 (m-80) REVERT: F 245 PHE cc_start: 0.7831 (m-10) cc_final: 0.7599 (m-80) REVERT: F 282 ASN cc_start: 0.6461 (m110) cc_final: 0.6246 (t0) REVERT: H 25 GLU cc_start: 0.0143 (OUTLIER) cc_final: -0.0087 (pt0) REVERT: N 38 MET cc_start: -0.1116 (ptt) cc_final: -0.2048 (mmp) REVERT: N 79 CYS cc_start: 0.2890 (OUTLIER) cc_final: 0.1780 (p) outliers start: 80 outliers final: 37 residues processed: 423 average time/residue: 0.2089 time to fit residues: 142.0180 Evaluate side-chains 353 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 314 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 74 THR 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 22 VAL 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 C residue 49 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 403 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 741 HIS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 762 LYS 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 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 H residue 83 ASP 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: 0.0980 chunk 138 optimal weight: 0.8980 chunk 258 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 195 optimal weight: 0.7980 chunk 237 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 377 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN B 185 GLN C 358 HIS C 424 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 F 282 ASN ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.178106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.133419 restraints weight = 63950.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.128847 restraints weight = 70249.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.130282 restraints weight = 64814.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.130327 restraints weight = 43903.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.133419 restraints weight = 42226.858| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.345 33486 Z= 0.198 Angle : 0.667 10.447 46015 Z= 0.348 Chirality : 0.043 0.179 5225 Planarity : 0.005 0.073 5422 Dihedral : 20.787 179.353 5956 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.31 % Allowed : 20.44 % Favored : 75.24 % 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 (0.14), residues: 3713 helix: 1.19 (0.13), residues: 1505 sheet: -0.49 (0.24), residues: 441 loop : -0.85 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 871 TYR 0.017 0.002 TYR D 106 PHE 0.018 0.002 PHE B 219 TRP 0.010 0.001 TRP D 718 HIS 0.009 0.001 HIS F 354 Details of bonding type rmsd covalent geometry : bond 0.00438 (33438) covalent geometry : angle 0.65352 (45979) hydrogen bonds : bond 0.04892 ( 1510) hydrogen bonds : angle 4.44704 ( 4142) metal coordination : bond 0.04997 ( 48) metal coordination : angle 4.81038 ( 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 471 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 337 time to evaluate : 1.119 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: B 202 MET cc_start: 0.6861 (ttm) cc_final: 0.6640 (ttp) REVERT: C 27 LYS cc_start: 0.7319 (mmtt) cc_final: 0.6999 (mmtt) REVERT: C 243 TYR cc_start: 0.8163 (m-80) cc_final: 0.7440 (m-80) REVERT: C 382 MET cc_start: 0.8237 (tmm) cc_final: 0.7506 (tmm) REVERT: C 1042 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8389 (pp) REVERT: C 1061 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7625 (tp) REVERT: C 1112 GLU cc_start: 0.7102 (tt0) cc_final: 0.6791 (tt0) REVERT: D 30 LYS cc_start: 0.8360 (mtmt) cc_final: 0.7909 (mtpp) REVERT: D 296 LEU cc_start: 0.7621 (mt) cc_final: 0.7301 (mt) REVERT: D 491 ILE cc_start: 0.8407 (pt) cc_final: 0.8191 (pt) REVERT: D 916 TYR cc_start: 0.7645 (m-10) cc_final: 0.7293 (m-80) REVERT: F 245 PHE cc_start: 0.8203 (m-10) cc_final: 0.7767 (m-80) REVERT: F 282 ASN cc_start: 0.7002 (m-40) cc_final: 0.6553 (t0) REVERT: H 25 GLU cc_start: 0.0320 (OUTLIER) cc_final: 0.0043 (pt0) REVERT: N 79 CYS cc_start: 0.3366 (OUTLIER) cc_final: 0.2139 (p) outliers start: 134 outliers final: 83 residues processed: 441 average time/residue: 0.2167 time to fit residues: 153.3268 Evaluate side-chains 387 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 300 time to evaluate : 1.189 ------------------------------------------------------------------------------- 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 146 TYR 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 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 C residue 28 ILE 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 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 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 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 857 VAL Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 1015 ILE 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 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 214 ARG Chi-restraints excluded: chain D residue 316 CYS 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 762 LYS Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 841 VAL Chi-restraints excluded: chain D residue 876 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 1100 ASN Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1132 ILE 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 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 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: 10.0000 chunk 166 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 273 optimal weight: 5.9990 chunk 142 optimal weight: 0.0000 chunk 216 optimal weight: 2.9990 chunk 121 optimal weight: 0.3980 chunk 320 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 326 optimal weight: 40.0000 overall best weight: 1.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 119 HIS A 151 GLN C 358 HIS C 428 GLN ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 665 ASN C 877 ASN ** C 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 980 ASN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 366 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.176062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.136141 restraints weight = 63095.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.133999 restraints weight = 103305.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.136011 restraints weight = 84382.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.135457 restraints weight = 57394.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.136558 restraints weight = 50684.343| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 33486 Z= 0.225 Angle : 0.700 13.310 46015 Z= 0.363 Chirality : 0.044 0.191 5225 Planarity : 0.005 0.067 5422 Dihedral : 20.730 179.882 5956 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.99 % Allowed : 21.54 % Favored : 73.47 % 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: -0.16 (0.14), residues: 3713 helix: 1.06 (0.13), residues: 1511 sheet: -0.58 (0.24), residues: 456 loop : -0.99 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 928 TYR 0.029 0.002 TYR D 106 PHE 0.020 0.002 PHE F 462 TRP 0.013 0.001 TRP C 712 HIS 0.009 0.001 HIS F 354 Details of bonding type rmsd covalent geometry : bond 0.00534 (33438) covalent geometry : angle 0.68701 (45979) hydrogen bonds : bond 0.05074 ( 1510) hydrogen bonds : angle 4.48405 ( 4142) metal coordination : bond 0.00594 ( 48) metal coordination : angle 4.89979 ( 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 486 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 331 time to evaluate : 1.057 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: C 243 TYR cc_start: 0.7609 (m-80) cc_final: 0.7041 (m-80) REVERT: C 382 MET cc_start: 0.8504 (tmm) cc_final: 0.7771 (tmm) REVERT: C 565 MET cc_start: 0.8075 (ppp) cc_final: 0.7734 (ppp) REVERT: C 718 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7670 (mm-30) REVERT: C 806 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8533 (tt) REVERT: C 1048 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.8102 (m-80) REVERT: C 1061 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7488 (tp) REVERT: C 1113 MET cc_start: 0.8663 (mtp) cc_final: 0.8370 (mtm) REVERT: D 30 LYS cc_start: 0.8185 (mtmt) cc_final: 0.7882 (mtpt) REVERT: D 59 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6569 (mt-10) REVERT: D 296 LEU cc_start: 0.7507 (mt) cc_final: 0.7149 (mt) REVERT: D 474 ARG cc_start: 0.7348 (ttp80) cc_final: 0.7132 (tmt170) REVERT: D 557 ILE cc_start: 0.7246 (OUTLIER) cc_final: 0.7039 (mt) REVERT: D 916 TYR cc_start: 0.7624 (m-10) cc_final: 0.7380 (m-80) REVERT: E 32 TYR cc_start: 0.6006 (OUTLIER) cc_final: 0.4836 (t80) REVERT: N 79 CYS cc_start: 0.2177 (OUTLIER) cc_final: 0.0942 (p) outliers start: 155 outliers final: 95 residues processed: 457 average time/residue: 0.2040 time to fit residues: 148.5779 Evaluate side-chains 395 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 293 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 41 THR 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 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 191 LYS Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 14 VAL 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 116 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 367 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 403 LEU 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 593 MET Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 718 GLU 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 D residue 7 PHE 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 114 LEU Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 316 CYS Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 702 VAL Chi-restraints excluded: chain D residue 724 VAL 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 876 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 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 1113 VAL Chi-restraints excluded: chain D residue 1132 ILE 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 62 HIS Chi-restraints excluded: chain E residue 70 ILE 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 485 ARG Chi-restraints excluded: chain F residue 486 ILE 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: 4.9990 chunk 233 optimal weight: 4.9990 chunk 310 optimal weight: 0.6980 chunk 325 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 230 optimal weight: 0.9980 chunk 286 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 320 optimal weight: 40.0000 chunk 5 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 157 ASN C 428 GLN C 665 ASN C 741 HIS D 160 GLN D 213 GLN ** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.177361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.135844 restraints weight = 63082.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.133657 restraints weight = 90426.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.135589 restraints weight = 79483.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.134940 restraints weight = 56171.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.136099 restraints weight = 49917.897| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 33486 Z= 0.165 Angle : 0.653 14.223 46015 Z= 0.339 Chirality : 0.043 0.287 5225 Planarity : 0.005 0.057 5422 Dihedral : 20.661 179.803 5956 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.09 % Allowed : 23.15 % Favored : 72.76 % 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 (0.14), residues: 3713 helix: 1.14 (0.13), residues: 1505 sheet: -0.48 (0.24), residues: 453 loop : -0.94 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 211 TYR 0.021 0.002 TYR A 32 PHE 0.022 0.002 PHE B 63 TRP 0.008 0.001 TRP C 712 HIS 0.007 0.001 HIS F 354 Details of bonding type rmsd covalent geometry : bond 0.00386 (33438) covalent geometry : angle 0.64225 (45979) hydrogen bonds : bond 0.04541 ( 1510) hydrogen bonds : angle 4.30587 ( 4142) metal coordination : bond 0.00349 ( 48) metal coordination : angle 4.26200 ( 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 453 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 326 time to evaluate : 0.894 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: B 157 GLN cc_start: 0.8025 (pm20) cc_final: 0.7642 (pm20) REVERT: C 243 TYR cc_start: 0.7561 (m-80) cc_final: 0.7036 (m-80) REVERT: C 382 MET cc_start: 0.8571 (tmm) cc_final: 0.7843 (tmm) REVERT: C 1036 MET cc_start: 0.7637 (mpp) cc_final: 0.7427 (mpt) REVERT: C 1048 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.8053 (m-80) REVERT: D 30 LYS cc_start: 0.8198 (mtmt) cc_final: 0.7874 (mtpt) REVERT: D 59 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6523 (mt-10) REVERT: D 296 LEU cc_start: 0.7609 (mt) cc_final: 0.7348 (mt) REVERT: D 474 ARG cc_start: 0.7319 (ttp80) cc_final: 0.7118 (tmt170) REVERT: D 997 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8584 (mt) REVERT: F 245 PHE cc_start: 0.7344 (m-80) cc_final: 0.7026 (m-80) REVERT: N 79 CYS cc_start: 0.2215 (OUTLIER) cc_final: 0.1006 (p) outliers start: 127 outliers final: 91 residues processed: 425 average time/residue: 0.1999 time to fit residues: 136.6146 Evaluate side-chains 389 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 295 time to evaluate : 1.161 ------------------------------------------------------------------------------- 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 155 VAL Chi-restraints excluded: chain A residue 175 THR 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 10 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 52 THR 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 165 SER Chi-restraints excluded: chain C residue 192 ILE 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 426 MET Chi-restraints excluded: chain C residue 460 ASP 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 572 MET Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 642 ASP 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 963 ASP Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain D residue 7 PHE 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 83 THR Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 293 LEU 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 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 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 997 ILE Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1055 LYS Chi-restraints excluded: chain D residue 1100 ASN 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 1202 SER 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 309 LEU Chi-restraints excluded: chain F residue 434 VAL 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 66 VAL Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain N residue 36 HIS 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: 1.9990 chunk 254 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 365 optimal weight: 9.9990 chunk 276 optimal weight: 2.9990 chunk 331 optimal weight: 6.9990 chunk 311 optimal weight: 4.9990 chunk 371 optimal weight: 30.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 151 GLN C 405 ASN C 424 GLN D 213 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.176355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.136467 restraints weight = 62831.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.134109 restraints weight = 107279.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.135509 restraints weight = 84444.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.136462 restraints weight = 52171.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.136760 restraints weight = 52701.396| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33486 Z= 0.185 Angle : 0.669 12.786 46015 Z= 0.348 Chirality : 0.043 0.278 5225 Planarity : 0.005 0.059 5422 Dihedral : 20.639 179.807 5956 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.70 % Allowed : 23.50 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.14), residues: 3713 helix: 1.11 (0.13), residues: 1509 sheet: -0.61 (0.24), residues: 477 loop : -0.95 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 211 TYR 0.024 0.002 TYR A 32 PHE 0.022 0.002 PHE C 425 TRP 0.016 0.001 TRP C 930 HIS 0.006 0.001 HIS F 354 Details of bonding type rmsd covalent geometry : bond 0.00437 (33438) covalent geometry : angle 0.65846 (45979) hydrogen bonds : bond 0.04707 ( 1510) hydrogen bonds : angle 4.34512 ( 4142) metal coordination : bond 0.00428 ( 48) metal coordination : angle 4.19697 ( 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 458 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 312 time to evaluate : 1.067 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: B 1 MET cc_start: 0.4279 (mmt) cc_final: 0.3945 (mmt) REVERT: B 157 GLN cc_start: 0.7946 (pt0) cc_final: 0.7731 (pm20) REVERT: B 225 LEU cc_start: 0.7341 (mm) cc_final: 0.6972 (tp) REVERT: C 243 TYR cc_start: 0.7676 (m-80) cc_final: 0.7144 (m-80) REVERT: C 246 MET cc_start: 0.8631 (mmm) cc_final: 0.8352 (mmm) REVERT: C 382 MET cc_start: 0.8578 (tmm) cc_final: 0.7794 (tmm) REVERT: C 565 MET cc_start: 0.8123 (ppp) cc_final: 0.7742 (tmm) REVERT: C 1048 PHE cc_start: 0.8457 (OUTLIER) cc_final: 0.8056 (m-80) REVERT: C 1061 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7325 (tp) REVERT: D 30 LYS cc_start: 0.8364 (mtmt) cc_final: 0.7973 (mtpt) REVERT: D 59 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6582 (mt-10) REVERT: D 296 LEU cc_start: 0.7596 (mt) cc_final: 0.7270 (mt) REVERT: D 474 ARG cc_start: 0.7437 (ttp80) cc_final: 0.7214 (tmt170) REVERT: D 557 ILE cc_start: 0.7236 (OUTLIER) cc_final: 0.6974 (mt) REVERT: D 997 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8668 (mt) REVERT: D 1006 MET cc_start: 0.1677 (ppp) cc_final: 0.1308 (ppp) REVERT: E 32 TYR cc_start: 0.5968 (OUTLIER) cc_final: 0.4834 (t80) REVERT: E 38 ARG cc_start: 0.8169 (ttm-80) cc_final: 0.7813 (ttm-80) REVERT: F 245 PHE cc_start: 0.7335 (m-80) cc_final: 0.7109 (m-80) REVERT: N 79 CYS cc_start: 0.2181 (OUTLIER) cc_final: 0.1011 (p) outliers start: 146 outliers final: 107 residues processed: 423 average time/residue: 0.1991 time to fit residues: 136.6118 Evaluate side-chains 404 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 291 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 96 TYR Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 133 LYS 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 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 116 VAL Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 192 ILE 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 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 514 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 556 TYR Chi-restraints excluded: chain C residue 572 MET 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 642 ASP 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 906 LEU Chi-restraints excluded: chain C residue 963 ASP 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 55 THR Chi-restraints excluded: chain D residue 60 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 290 THR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 316 CYS 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 557 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 846 ILE Chi-restraints excluded: chain D residue 876 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 966 VAL 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 1055 LYS 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 1215 VAL 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 485 ARG Chi-restraints excluded: chain F residue 486 ILE 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 N residue 36 HIS 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: 4.9990 chunk 353 optimal weight: 10.0000 chunk 150 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 325 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 chunk 330 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS A 152 ASN C 885 ASN D 416 ASN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.172892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.117362 restraints weight = 63264.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.114545 restraints weight = 51529.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.115537 restraints weight = 46050.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.115590 restraints weight = 41753.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.115594 restraints weight = 40482.527| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 33486 Z= 0.310 Angle : 0.795 12.519 46015 Z= 0.411 Chirality : 0.047 0.293 5225 Planarity : 0.006 0.084 5422 Dihedral : 20.698 179.922 5954 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 5.70 % Allowed : 23.63 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.49 (0.14), residues: 3713 helix: 0.82 (0.13), residues: 1506 sheet: -0.86 (0.24), residues: 471 loop : -1.17 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 211 TYR 0.032 0.002 TYR A 32 PHE 0.030 0.002 PHE C 425 TRP 0.019 0.002 TRP C 712 HIS 0.008 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00735 (33438) covalent geometry : angle 0.78318 (45979) hydrogen bonds : bond 0.05692 ( 1510) hydrogen bonds : angle 4.74269 ( 4142) metal coordination : bond 0.00755 ( 48) metal coordination : angle 4.99698 ( 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 489 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 312 time to evaluate : 1.094 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: B 157 GLN cc_start: 0.8283 (pt0) cc_final: 0.8046 (pm20) REVERT: C 49 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8298 (mp) REVERT: C 243 TYR cc_start: 0.8328 (m-80) cc_final: 0.7446 (m-10) REVERT: C 246 MET cc_start: 0.9222 (mmm) cc_final: 0.8866 (mmm) REVERT: C 382 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.7954 (tmm) REVERT: C 565 MET cc_start: 0.8066 (ppp) cc_final: 0.7647 (tmm) REVERT: C 1048 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.8348 (m-80) REVERT: C 1061 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7804 (tp) REVERT: D 30 LYS cc_start: 0.8404 (mtmt) cc_final: 0.8022 (mtpt) REVERT: D 59 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7126 (tt0) REVERT: D 217 ASP cc_start: 0.9120 (t0) cc_final: 0.8565 (t0) REVERT: D 296 LEU cc_start: 0.7606 (mt) cc_final: 0.7057 (mt) REVERT: D 320 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8680 (mt) REVERT: D 506 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8684 (ptt180) REVERT: D 533 ASN cc_start: 0.7613 (t0) cc_final: 0.7390 (m110) REVERT: D 557 ILE cc_start: 0.7350 (OUTLIER) cc_final: 0.7087 (mt) REVERT: D 745 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7080 (mm-30) REVERT: D 832 LYS cc_start: 0.8990 (mptt) cc_final: 0.8656 (mttt) REVERT: D 910 ASP cc_start: 0.7468 (p0) cc_final: 0.7078 (p0) REVERT: D 1006 MET cc_start: 0.2285 (ppp) cc_final: 0.1793 (ppp) REVERT: D 1120 GLU cc_start: 0.6388 (tp30) cc_final: 0.6053 (tp30) REVERT: E 32 TYR cc_start: 0.6122 (OUTLIER) cc_final: 0.5723 (t80) REVERT: E 38 ARG cc_start: 0.8100 (ttm-80) cc_final: 0.7719 (ttm-80) REVERT: N 79 CYS cc_start: 0.3586 (OUTLIER) cc_final: 0.2366 (p) outliers start: 177 outliers final: 131 residues processed: 454 average time/residue: 0.2073 time to fit residues: 151.2570 Evaluate side-chains 433 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 293 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 41 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 138 LEU Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 THR 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 14 VAL 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 34 LEU 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 116 VAL 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 110 CYS Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 177 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 350 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 450 SER 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 556 TYR Chi-restraints excluded: chain C residue 572 MET 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 642 ASP 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 769 ASP 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 963 ASP 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 48 CYS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 74 ILE 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 150 SER Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 316 CYS Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 506 ARG Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 595 ARG Chi-restraints excluded: chain D residue 702 VAL Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 728 ILE Chi-restraints excluded: chain D residue 741 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 846 ILE Chi-restraints excluded: chain D residue 876 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 966 VAL 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 1002 THR Chi-restraints excluded: chain D residue 1055 LYS Chi-restraints excluded: chain D residue 1074 ILE 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 1132 ILE 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 1212 THR Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain D residue 1265 MET Chi-restraints excluded: chain E residue 11 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 387 ASP Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 485 ARG Chi-restraints excluded: chain F residue 486 ILE 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 H residue 97 VAL 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: 1.9990 chunk 278 optimal weight: 0.9980 chunk 334 optimal weight: 7.9990 chunk 281 optimal weight: 0.0070 chunk 140 optimal weight: 0.7980 chunk 147 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 327 optimal weight: 50.0000 chunk 2 optimal weight: 2.9990 chunk 352 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 428 GLN C 596 ASN C 885 ASN D1136 HIS ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.177557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.137448 restraints weight = 62441.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.135980 restraints weight = 94757.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.137700 restraints weight = 78868.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.137180 restraints weight = 55087.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.138224 restraints weight = 48662.686| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33486 Z= 0.140 Angle : 0.670 13.943 46015 Z= 0.347 Chirality : 0.043 0.308 5225 Planarity : 0.005 0.058 5422 Dihedral : 20.569 179.461 5954 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.61 % Allowed : 26.14 % Favored : 70.25 % 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: -0.15 (0.14), residues: 3713 helix: 1.16 (0.13), residues: 1495 sheet: -0.64 (0.24), residues: 464 loop : -1.04 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 211 TYR 0.026 0.001 TYR E 32 PHE 0.051 0.002 PHE F 245 TRP 0.012 0.001 TRP F 333 HIS 0.007 0.001 HIS G 36 Details of bonding type rmsd covalent geometry : bond 0.00317 (33438) covalent geometry : angle 0.66185 (45979) hydrogen bonds : bond 0.04420 ( 1510) hydrogen bonds : angle 4.27973 ( 4142) metal coordination : bond 0.00274 ( 48) metal coordination : angle 3.67052 ( 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 436 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 324 time to evaluate : 1.142 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: B 157 GLN cc_start: 0.8059 (pt0) cc_final: 0.7834 (pm20) REVERT: C 243 TYR cc_start: 0.7499 (m-80) cc_final: 0.7007 (m-80) REVERT: C 246 MET cc_start: 0.8603 (mmm) cc_final: 0.8340 (mmm) REVERT: C 382 MET cc_start: 0.8552 (tmm) cc_final: 0.8012 (tmm) REVERT: C 565 MET cc_start: 0.7998 (ppp) cc_final: 0.7622 (tmm) REVERT: C 608 GLU cc_start: 0.7729 (tp30) cc_final: 0.6562 (tt0) REVERT: C 1048 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.8062 (m-80) REVERT: D 59 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6757 (tt0) REVERT: D 90 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7366 (tm-30) REVERT: D 229 LEU cc_start: 0.7398 (mt) cc_final: 0.6993 (mp) REVERT: D 296 LEU cc_start: 0.7502 (mt) cc_final: 0.7161 (mt) REVERT: D 557 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6828 (mt) REVERT: D 971 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6830 (mmm) REVERT: D 1169 PHE cc_start: 0.7846 (t80) cc_final: 0.7562 (t80) REVERT: E 32 TYR cc_start: 0.5896 (OUTLIER) cc_final: 0.4785 (t80) REVERT: E 38 ARG cc_start: 0.8076 (ttm-80) cc_final: 0.7816 (ttm-80) REVERT: F 386 LEU cc_start: 0.6749 (mm) cc_final: 0.6375 (mm) outliers start: 112 outliers final: 89 residues processed: 410 average time/residue: 0.2064 time to fit residues: 136.0638 Evaluate side-chains 387 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 294 time to evaluate : 1.109 ------------------------------------------------------------------------------- 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 44 SER 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 138 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 THR 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 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 116 VAL 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 110 CYS Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 173 VAL 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 450 SER 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 642 ASP Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 743 VAL 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 D residue 7 PHE 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 113 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 567 LYS Chi-restraints excluded: chain D residue 595 ARG Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 741 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 966 VAL Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 971 MET 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 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 485 ARG 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 H residue 97 VAL Chi-restraints excluded: chain M residue 28 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 0.0040 chunk 197 optimal weight: 1.9990 chunk 323 optimal weight: 50.0000 chunk 209 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 167 optimal weight: 3.9990 chunk 379 optimal weight: 10.0000 chunk 149 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN D 213 GLN D1116 HIS E 46 GLN ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.175010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.133297 restraints weight = 64469.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.130970 restraints weight = 98163.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.132263 restraints weight = 78685.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.133534 restraints weight = 48931.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.133805 restraints weight = 46708.775| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33486 Z= 0.168 Angle : 0.691 14.275 46015 Z= 0.357 Chirality : 0.043 0.342 5225 Planarity : 0.005 0.093 5422 Dihedral : 20.501 179.710 5952 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.80 % Allowed : 26.27 % Favored : 69.93 % 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: -0.16 (0.14), residues: 3713 helix: 1.13 (0.13), residues: 1496 sheet: -0.63 (0.24), residues: 474 loop : -1.03 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 218 TYR 0.028 0.002 TYR C1034 PHE 0.025 0.002 PHE C 425 TRP 0.009 0.001 TRP D 718 HIS 0.008 0.001 HIS F 499 Details of bonding type rmsd covalent geometry : bond 0.00395 (33438) covalent geometry : angle 0.68339 (45979) hydrogen bonds : bond 0.04577 ( 1510) hydrogen bonds : angle 4.33040 ( 4142) metal coordination : bond 0.00400 ( 48) metal coordination : angle 3.79777 ( 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 414 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 296 time to evaluate : 1.224 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: A 25 PRO cc_start: 0.7430 (Cg_endo) cc_final: 0.7189 (Cg_exo) REVERT: B 157 GLN cc_start: 0.8100 (pt0) cc_final: 0.7858 (pm20) REVERT: C 243 TYR cc_start: 0.7785 (m-80) cc_final: 0.7290 (m-80) REVERT: C 246 MET cc_start: 0.8758 (mmm) cc_final: 0.8476 (mmm) REVERT: C 382 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.7955 (tmm) REVERT: C 565 MET cc_start: 0.7986 (ppp) cc_final: 0.7609 (tmm) REVERT: C 584 GLU cc_start: 0.8836 (pm20) cc_final: 0.8613 (pm20) REVERT: C 1048 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.8045 (m-80) REVERT: D 59 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6883 (tt0) REVERT: D 127 LYS cc_start: 0.6940 (mmtt) cc_final: 0.6234 (mttm) REVERT: D 296 LEU cc_start: 0.7566 (mt) cc_final: 0.7178 (mt) REVERT: D 474 ARG cc_start: 0.7670 (ttp80) cc_final: 0.7457 (ttp80) REVERT: D 557 ILE cc_start: 0.7148 (OUTLIER) cc_final: 0.6879 (mt) REVERT: D 1006 MET cc_start: 0.1694 (ppp) cc_final: 0.1128 (ppp) REVERT: E 32 TYR cc_start: 0.5940 (OUTLIER) cc_final: 0.5714 (t80) REVERT: E 38 ARG cc_start: 0.8174 (ttm-80) cc_final: 0.7896 (ttm-80) outliers start: 118 outliers final: 93 residues processed: 385 average time/residue: 0.2076 time to fit residues: 128.7664 Evaluate side-chains 388 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 291 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 44 SER 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 138 LEU Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 147 VAL 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 52 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 173 VAL 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 367 VAL Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 597 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 642 ASP Chi-restraints excluded: chain C residue 668 THR Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 743 VAL 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 D residue 7 PHE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 74 ILE 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 113 ARG Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 567 LYS Chi-restraints excluded: chain D residue 595 ARG Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 728 ILE Chi-restraints excluded: chain D residue 741 VAL 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 846 ILE 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 966 VAL 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 1002 THR Chi-restraints excluded: chain D residue 1074 ILE 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 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 485 ARG Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain M residue 28 GLU 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: 0.5980 chunk 283 optimal weight: 0.9980 chunk 154 optimal weight: 0.6980 chunk 248 optimal weight: 0.0980 chunk 333 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 115 optimal weight: 0.0050 chunk 375 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 chunk 303 optimal weight: 0.7980 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.177268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.133022 restraints weight = 64902.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.130107 restraints weight = 73713.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.131822 restraints weight = 69969.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.131060 restraints weight = 50895.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.132421 restraints weight = 44728.151| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33486 Z= 0.133 Angle : 0.672 16.265 46015 Z= 0.346 Chirality : 0.043 0.345 5225 Planarity : 0.005 0.073 5422 Dihedral : 20.437 179.379 5952 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.99 % Allowed : 26.98 % Favored : 70.03 % 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: -0.01 (0.14), residues: 3713 helix: 1.26 (0.13), residues: 1490 sheet: -0.38 (0.25), residues: 443 loop : -1.00 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 211 TYR 0.025 0.001 TYR E 32 PHE 0.054 0.001 PHE F 245 TRP 0.010 0.001 TRP F 333 HIS 0.007 0.001 HIS F 499 Details of bonding type rmsd covalent geometry : bond 0.00298 (33438) covalent geometry : angle 0.66555 (45979) hydrogen bonds : bond 0.04164 ( 1510) hydrogen bonds : angle 4.22081 ( 4142) metal coordination : bond 0.00224 ( 48) metal coordination : angle 3.40369 ( 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 408 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 315 time to evaluate : 1.169 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: A 25 PRO cc_start: 0.7374 (Cg_endo) cc_final: 0.7123 (Cg_exo) REVERT: A 202 MET cc_start: 0.6914 (ptt) cc_final: 0.6326 (pmm) REVERT: B 136 MET cc_start: 0.7916 (ppp) cc_final: 0.7507 (ppp) REVERT: B 157 GLN cc_start: 0.8185 (pt0) cc_final: 0.7925 (pm20) REVERT: C 202 MET cc_start: 0.7102 (mtp) cc_final: 0.6864 (mtp) REVERT: C 243 TYR cc_start: 0.7908 (m-80) cc_final: 0.7408 (m-80) REVERT: C 246 MET cc_start: 0.8948 (mmm) cc_final: 0.8631 (mmm) REVERT: C 382 MET cc_start: 0.8608 (tmm) cc_final: 0.7948 (tmm) REVERT: C 565 MET cc_start: 0.7864 (ppp) cc_final: 0.7402 (ppp) REVERT: C 608 GLU cc_start: 0.7680 (tp30) cc_final: 0.6554 (tt0) REVERT: C 690 ASP cc_start: 0.7979 (m-30) cc_final: 0.7777 (m-30) REVERT: C 1048 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.8114 (m-80) REVERT: D 90 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7360 (tm-30) REVERT: D 127 LYS cc_start: 0.6880 (mmtt) cc_final: 0.6207 (mttm) REVERT: D 296 LEU cc_start: 0.7560 (mt) cc_final: 0.7134 (mt) REVERT: D 474 ARG cc_start: 0.7621 (ttp80) cc_final: 0.7398 (ttp80) REVERT: D 1006 MET cc_start: 0.1799 (ppp) cc_final: 0.1254 (ppp) REVERT: D 1182 HIS cc_start: 0.7197 (OUTLIER) cc_final: 0.6985 (p-80) REVERT: E 32 TYR cc_start: 0.5744 (OUTLIER) cc_final: 0.5394 (t80) REVERT: E 38 ARG cc_start: 0.8119 (ttm-80) cc_final: 0.7876 (ttm-80) REVERT: E 83 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7585 (tm-30) REVERT: F 398 LYS cc_start: 0.6912 (mptt) cc_final: 0.6598 (mptt) outliers start: 93 outliers final: 81 residues processed: 387 average time/residue: 0.2125 time to fit residues: 131.6051 Evaluate side-chains 383 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 299 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 44 SER 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 140 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 155 VAL 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 52 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 173 VAL 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 350 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 450 SER 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 652 THR Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 743 VAL 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 D residue 7 PHE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 74 ILE 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 113 ARG Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 567 LYS Chi-restraints excluded: chain D residue 595 ARG Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 762 LYS Chi-restraints excluded: chain D residue 807 MET Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 966 VAL 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 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 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 F residue 225 VAL 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 83 ASP Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain M residue 28 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 67 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 384 optimal weight: 60.0000 chunk 55 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 370 optimal weight: 70.0000 chunk 63 optimal weight: 8.9990 chunk 228 optimal weight: 1.9990 chunk 253 optimal weight: 0.4980 chunk 204 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN C 596 ASN C 741 HIS ** H 85 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 = 0.4406 r_free = 0.4406 target = 0.175374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.133023 restraints weight = 64785.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.131079 restraints weight = 91461.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.132177 restraints weight = 74205.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.133340 restraints weight = 46643.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.133594 restraints weight = 45098.309| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 33486 Z= 0.164 Angle : 0.689 15.605 46015 Z= 0.355 Chirality : 0.043 0.346 5225 Planarity : 0.005 0.068 5422 Dihedral : 20.427 179.453 5950 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.09 % Allowed : 27.33 % Favored : 69.58 % 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: -0.07 (0.14), residues: 3713 helix: 1.19 (0.13), residues: 1497 sheet: -0.52 (0.25), residues: 462 loop : -0.98 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 293 TYR 0.021 0.001 TYR E 32 PHE 0.027 0.002 PHE B 63 TRP 0.014 0.001 TRP C 924 HIS 0.006 0.001 HIS F 499 Details of bonding type rmsd covalent geometry : bond 0.00386 (33438) covalent geometry : angle 0.68101 (45979) hydrogen bonds : bond 0.04424 ( 1510) hydrogen bonds : angle 4.33041 ( 4142) metal coordination : bond 0.00349 ( 48) metal coordination : angle 3.72481 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5482.04 seconds wall clock time: 95 minutes 38.82 seconds (5738.82 seconds total)