Starting phenix.real_space_refine on Mon Sep 14 19:20:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7x74_33031/09_2026/7x74_33031.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x74_33031/09_2026/7x74_33031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7x74_33031/09_2026/7x74_33031.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7x74_33031/09_2026/7x74_33031.cif" model { file = "/net/cci-nas-00/data/ceres_data/7x74_33031/09_2026/7x74_33031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x74_33031/09_2026/7x74_33031.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x74_33031/09_2026/7x74_33031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x74_33031/09_2026/7x74_33031.map" } 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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32550 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1742 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 13, 'TRANS': 212} Chain: "B" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1792 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 13, 'TRANS': 219} Chain: "C" Number of atoms: 8692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 8692 Classifications: {'peptide': 1116} Link IDs: {'PTRANS': 58, 'TRANS': 1057} Chain: "D" Number of atoms: 9846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1259, 9846 Classifications: {'peptide': 1259} Link IDs: {'PTRANS': 56, 'TRANS': 1202} Chain: "E" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 597 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "F" Number of atoms: 2379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2379 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 285} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "H" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "M" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "N" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 984 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "O" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1714 Classifications: {'DNA': 84} Link IDs: {'rna3p': 83} Chain: "P" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1729 Classifications: {'DNA': 84} Link IDs: {'rna3p': 83} Chain: "Q" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 108 Classifications: {'RNAv2': 5} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: 6.70, per 1000 atoms: 0.21 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: 2.78 Conformation dependent library (CDL) restraints added in 1.4 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: 3.77 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: 8.41 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10044 1.34 - 1.46: 5930 1.46 - 1.58: 16933 1.58 - 1.70: 342 1.70 - 1.82: 189 Bond restraints: 33438 Sorted by residual: bond pdb=" C1' DC O 8 " pdb=" N1 DC O 8 " ideal model delta sigma weight residual 1.468 1.547 -0.079 1.40e-02 5.10e+03 3.20e+01 bond pdb=" C1' DT O 67 " pdb=" N1 DT O 67 " ideal model delta sigma weight residual 1.468 1.536 -0.068 1.40e-02 5.10e+03 2.39e+01 bond pdb=" C1' DC P 67 " pdb=" N1 DC P 67 " ideal model delta sigma weight residual 1.468 1.533 -0.065 1.40e-02 5.10e+03 2.13e+01 bond pdb=" C1' DC O 29 " pdb=" N1 DC O 29 " ideal model delta sigma weight residual 1.468 1.532 -0.064 1.40e-02 5.10e+03 2.11e+01 bond pdb=" C1' DC P 24 " pdb=" N1 DC P 24 " ideal model delta sigma weight residual 1.468 1.530 -0.062 1.40e-02 5.10e+03 1.94e+01 ... (remaining 33433 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 44580 2.22 - 4.44: 1231 4.44 - 6.67: 143 6.67 - 8.89: 23 8.89 - 11.11: 2 Bond angle restraints: 45979 Sorted by residual: angle pdb=" N GLN A 157 " pdb=" CA GLN A 157 " pdb=" C GLN A 157 " ideal model delta sigma weight residual 111.28 118.88 -7.60 1.09e+00 8.42e-01 4.87e+01 angle pdb=" N TYR A 168 " pdb=" CA TYR A 168 " pdb=" C TYR A 168 " ideal model delta sigma weight residual 111.28 118.34 -7.06 1.09e+00 8.42e-01 4.19e+01 angle pdb=" N VAL A 155 " pdb=" CA VAL A 155 " pdb=" C VAL A 155 " ideal model delta sigma weight residual 106.61 117.72 -11.11 1.78e+00 3.16e-01 3.90e+01 angle pdb=" N ASP D 878 " pdb=" CA ASP D 878 " pdb=" C ASP D 878 " ideal model delta sigma weight residual 111.28 117.67 -6.39 1.09e+00 8.42e-01 3.44e+01 angle pdb=" N VAL C 510 " pdb=" CA VAL C 510 " pdb=" C VAL C 510 " ideal model delta sigma weight residual 106.85 114.99 -8.14 1.42e+00 4.96e-01 3.29e+01 ... (remaining 45974 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 18681 35.94 - 71.87: 1156 71.87 - 107.81: 53 107.81 - 143.74: 4 143.74 - 179.68: 13 Dihedral angle restraints: 19907 sinusoidal: 9224 harmonic: 10683 Sorted by residual: dihedral pdb=" O4' G Q 5 " pdb=" C2' G Q 5 " pdb=" C1' G Q 5 " pdb=" C3' G Q 5 " ideal model delta sinusoidal sigma weight residual 25.59 5.55 20.05 3 3.80e+00 6.93e-02 3.71e+01 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 ... (remaining 19904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 4801 0.102 - 0.204: 394 0.204 - 0.306: 25 0.306 - 0.408: 4 0.408 - 0.510: 1 Chirality restraints: 5225 Sorted by residual: chirality pdb=" CA ASP E 24 " pdb=" N ASP E 24 " pdb=" C ASP E 24 " pdb=" CB ASP E 24 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.50e+00 chirality pdb=" CA LYS A 153 " pdb=" N LYS A 153 " pdb=" C LYS A 153 " pdb=" CB LYS A 153 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" C3' DG O 20 " pdb=" C4' DG O 20 " pdb=" O3' DG O 20 " pdb=" C2' DG O 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.37 -0.36 2.00e-01 2.50e+01 3.21e+00 ... (remaining 5222 not shown) Planarity restraints: 5422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 407 " 0.079 5.00e-02 4.00e+02 1.18e-01 2.21e+01 pdb=" N PRO C 408 " -0.203 5.00e-02 4.00e+02 pdb=" CA PRO C 408 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO C 408 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG O 72 " 0.038 2.00e-02 2.50e+03 1.66e-02 8.27e+00 pdb=" N9 DG O 72 " -0.039 2.00e-02 2.50e+03 pdb=" C8 DG O 72 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DG O 72 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG O 72 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG O 72 " 0.012 2.00e-02 2.50e+03 pdb=" O6 DG O 72 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DG O 72 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG O 72 " -0.003 2.00e-02 2.50e+03 pdb=" N2 DG O 72 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DG O 72 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DG O 72 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG P 49 " 0.009 2.00e-02 2.50e+03 1.51e-02 6.80e+00 pdb=" N9 DG P 49 " -0.003 2.00e-02 2.50e+03 pdb=" C8 DG P 49 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG P 49 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DG P 49 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG P 49 " 0.000 2.00e-02 2.50e+03 pdb=" O6 DG P 49 " -0.000 2.00e-02 2.50e+03 pdb=" N1 DG P 49 " 0.015 2.00e-02 2.50e+03 pdb=" C2 DG P 49 " -0.043 2.00e-02 2.50e+03 pdb=" N2 DG P 49 " 0.022 2.00e-02 2.50e+03 pdb=" N3 DG P 49 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG P 49 " 0.003 2.00e-02 2.50e+03 ... (remaining 5419 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 202 2.51 - 3.11: 24973 3.11 - 3.70: 53572 3.70 - 4.30: 70421 4.30 - 4.90: 113458 Nonbonded interactions: 262626 Sorted by model distance: nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D1401 " model vdw 1.912 2.170 nonbonded pdb=" O3' G Q 5 " pdb="MG MG D1401 " model vdw 1.915 2.170 nonbonded pdb=" OE2 GLU N 105 " pdb="ZN ZN N 203 " model vdw 1.975 2.230 nonbonded pdb=" OD2 ASP N 65 " pdb="ZN ZN N 202 " model vdw 1.981 2.230 nonbonded pdb=" OD2 ASP D 535 " pdb="MG MG D1401 " model vdw 2.048 2.170 ... (remaining 262621 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 2 through 227) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 37.640 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.229 33486 Z= 0.353 Angle : 0.852 19.244 46015 Z= 0.531 Chirality : 0.055 0.510 5225 Planarity : 0.005 0.118 5422 Dihedral : 20.681 179.680 13031 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.87 % Allowed : 22.12 % Favored : 77.01 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.14), residues: 3713 helix: 1.24 (0.14), residues: 1452 sheet: -0.88 (0.23), residues: 465 loop : -0.89 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 808 TYR 0.023 0.002 TYR E 32 PHE 0.018 0.002 PHE A 17 TRP 0.021 0.002 TRP C 924 HIS 0.009 0.001 HIS H 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.35 (33438) covalent geometry : angle 0.82674 / 0.53 (45979) hydrogen bonds : bond 0.14875 / 10.23 ( 1510) hydrogen bonds : angle 5.89141 / 4.15 ( 4142) metal coordination : bond 0.04908 / 3.78 ( 48) metal coordination : angle 7.33477 / 4.34 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 434 time to evaluate : 1.235 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: 0.2380 time to fit residues: 166.7889 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 : 1.186 ------------------------------------------------------------------------------- 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... A 152 ASN C 256 GLN C 286 ASN C 424 GLN C 465 HIS ** C 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1040 GLN E 64 HIS F 221 GLN F 305 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.181445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.141090 restraints weight = 63732.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.139123 restraints weight = 92076.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.140844 restraints weight = 80077.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.140678 restraints weight = 53373.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.141380 restraints weight = 49614.942| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 33486 Z= 0.157 Angle : 0.707 10.149 46015 Z= 0.373 Chirality : 0.048 0.364 5225 Planarity : 0.005 0.071 5422 Dihedral : 20.869 178.881 5945 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.64 % Allowed : 20.80 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.13), residues: 3713 helix: 1.21 (0.13), residues: 1491 sheet: -0.53 (0.24), residues: 445 loop : -0.84 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 173 TYR 0.024 0.002 TYR E 32 PHE 0.016 0.002 PHE F 462 TRP 0.011 0.001 TRP C 930 HIS 0.031 0.001 HIS F 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 (33438) covalent geometry : angle 0.69086 / 0.37 (45979) hydrogen bonds : bond 0.05571 / 3.82 ( 1510) hydrogen bonds : angle 4.71998 / 3.31 ( 4142) metal coordination : bond 0.00536 / 0.34 ( 48) metal coordination : angle 5.41714 / 3.65 ( 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 444 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 362 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LEU cc_start: 0.7043 (mm) cc_final: 0.6777 (mm) REVERT: C 27 LYS cc_start: 0.7161 (mmtt) cc_final: 0.6791 (mmtt) REVERT: C 191 LYS cc_start: 0.6677 (pttt) cc_final: 0.6353 (pttt) REVERT: C 382 MET cc_start: 0.7877 (tmm) cc_final: 0.7466 (tmm) REVERT: C 598 MET cc_start: 0.7332 (mtp) cc_final: 0.7071 (ttm) REVERT: C 1109 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8017 (tp) REVERT: D 296 LEU cc_start: 0.7405 (mt) cc_final: 0.7150 (mt) REVERT: D 916 TYR cc_start: 0.7406 (m-10) cc_final: 0.6975 (m-80) REVERT: H 25 GLU cc_start: -0.0025 (OUTLIER) cc_final: -0.0229 (pt0) REVERT: N 38 MET cc_start: -0.0810 (ptt) cc_final: -0.2272 (mmp) REVERT: N 79 CYS cc_start: 0.1963 (OUTLIER) cc_final: 0.1136 (p) outliers start: 82 outliers final: 38 residues processed: 419 average time/residue: 0.2044 time to fit residues: 138.8451 Evaluate side-chains 359 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 318 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1197 SER Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 460 MET Chi-restraints excluded: chain F residue 485 ARG Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain F residue 490 GLU Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 130 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 138 optimal weight: 0.3980 chunk 258 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 195 optimal weight: 0.0370 chunk 237 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 377 optimal weight: 20.0000 overall best weight: 1.4864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN B 185 GLN C 405 ASN ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 916 GLN D 160 GLN ** D 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.178341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.133984 restraints weight = 64045.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.129414 restraints weight = 70162.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.130821 restraints weight = 66652.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.130904 restraints weight = 44361.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.134987 restraints weight = 42776.176| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33486 Z= 0.197 Angle : 0.713 10.593 46015 Z= 0.375 Chirality : 0.048 0.374 5225 Planarity : 0.005 0.068 5422 Dihedral : 20.860 178.492 5939 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.02 % Allowed : 20.83 % Favored : 75.14 % 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: 1.10 (0.13), residues: 1502 sheet: -0.63 (0.24), residues: 465 loop : -0.91 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 161 TYR 0.019 0.002 TYR F 479 PHE 0.019 0.002 PHE B 219 TRP 0.010 0.001 TRP D 718 HIS 0.007 0.001 HIS F 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (33438) covalent geometry : angle 0.69931 / 0.37 (45979) hydrogen bonds : bond 0.05283 / 3.62 ( 1510) hydrogen bonds : angle 4.62846 / 3.22 ( 4142) metal coordination : bond 0.00481 / 0.25 ( 48) metal coordination : angle 5.00915 / 3.30 ( 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 464 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 339 time to evaluate : 1.188 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: A 128 LEU cc_start: 0.7305 (mm) cc_final: 0.7070 (mm) REVERT: B 202 MET cc_start: 0.6660 (ttm) cc_final: 0.6419 (ttp) REVERT: C 27 LYS cc_start: 0.7172 (mmtt) cc_final: 0.6870 (mmtt) REVERT: C 243 TYR cc_start: 0.8267 (m-80) cc_final: 0.7304 (m-10) REVERT: C 382 MET cc_start: 0.8070 (tmm) cc_final: 0.7480 (tmm) REVERT: C 565 MET cc_start: 0.7693 (ppp) cc_final: 0.6766 (ptm) REVERT: C 598 MET cc_start: 0.7252 (mtp) cc_final: 0.6915 (ttp) REVERT: C 1042 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8461 (pp) REVERT: C 1061 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7601 (tp) REVERT: D 296 LEU cc_start: 0.7581 (mt) cc_final: 0.7243 (mt) REVERT: D 745 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7201 (mm-30) REVERT: D 916 TYR cc_start: 0.7576 (m-10) cc_final: 0.7171 (m-80) REVERT: F 398 LYS cc_start: 0.6630 (mptt) cc_final: 0.6406 (mptt) REVERT: F 479 TYR cc_start: 0.7368 (t80) cc_final: 0.7165 (t80) REVERT: H 25 GLU cc_start: 0.0251 (OUTLIER) cc_final: -0.0006 (pt0) REVERT: N 79 CYS cc_start: 0.3336 (OUTLIER) cc_final: 0.2170 (p) outliers start: 125 outliers final: 77 residues processed: 435 average time/residue: 0.2162 time to fit residues: 152.4146 Evaluate side-chains 381 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 300 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 96 TYR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 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 37 SER Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 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 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 1042 LEU Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 40 LYS Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 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 306 SER Chi-restraints excluded: chain D residue 316 CYS Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 702 VAL Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 949 HIS 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 1029 LEU Chi-restraints excluded: chain D residue 1100 ASN Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain D residue 1253 ILE Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 485 ARG Chi-restraints excluded: chain F residue 486 ILE Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 305 optimal weight: 9.9990 chunk 166 optimal weight: 0.0050 chunk 226 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 273 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 320 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 326 optimal weight: 40.0000 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN C 877 ASN D 160 GLN D 669 ASN F 221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.178761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.133759 restraints weight = 63989.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.129494 restraints weight = 65801.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.131323 restraints weight = 68846.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.130629 restraints weight = 49596.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.131818 restraints weight = 45020.695| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2113 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= 0.164 Angle : 0.675 12.278 46015 Z= 0.353 Chirality : 0.046 0.355 5225 Planarity : 0.005 0.072 5422 Dihedral : 20.769 176.704 5936 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.86 % Allowed : 22.44 % Favored : 73.70 % 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: -0.04 (0.13), residues: 3713 helix: 1.16 (0.13), residues: 1502 sheet: -0.56 (0.24), residues: 459 loop : -0.90 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 550 TYR 0.020 0.002 TYR D 106 PHE 0.019 0.002 PHE B 63 TRP 0.010 0.001 TRP C 712 HIS 0.022 0.001 HIS F 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (33438) covalent geometry : angle 0.66285 / 0.35 (45979) hydrogen bonds : bond 0.04868 / 3.33 ( 1510) hydrogen bonds : angle 4.46767 / 3.10 ( 4142) metal coordination : bond 0.00394 / 0.21 ( 48) metal coordination : angle 4.67183 / 3.14 ( 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 447 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 327 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 GLN cc_start: 0.6226 (OUTLIER) cc_final: 0.5879 (tp40) REVERT: B 120 ASN cc_start: 0.6917 (p0) cc_final: 0.6614 (p0) REVERT: B 157 GLN cc_start: 0.7825 (mp10) cc_final: 0.7452 (mp10) REVERT: B 202 MET cc_start: 0.6800 (ttm) cc_final: 0.6567 (ttp) REVERT: C 27 LYS cc_start: 0.7293 (mmtt) cc_final: 0.6959 (mmtt) REVERT: C 243 TYR cc_start: 0.8165 (m-80) cc_final: 0.7371 (m-80) REVERT: C 382 MET cc_start: 0.8237 (tmm) cc_final: 0.7493 (tmm) REVERT: C 565 MET cc_start: 0.7738 (ppp) cc_final: 0.6876 (ptm) REVERT: C 598 MET cc_start: 0.7384 (mtp) cc_final: 0.7132 (ttp) REVERT: C 1042 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8383 (pp) REVERT: D 30 LYS cc_start: 0.8375 (mtmt) cc_final: 0.7958 (mtpt) REVERT: D 129 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7977 (pt) REVERT: D 296 LEU cc_start: 0.7669 (mt) cc_final: 0.7296 (mt) REVERT: D 474 ARG cc_start: 0.7481 (ttp80) cc_final: 0.7221 (tmt170) REVERT: D 745 GLU cc_start: 0.7293 (mm-30) cc_final: 0.7071 (mm-30) REVERT: D 916 TYR cc_start: 0.7522 (m-10) cc_final: 0.7237 (m-80) REVERT: D 1147 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8469 (tpp80) REVERT: F 245 PHE cc_start: 0.8206 (m-80) cc_final: 0.7904 (m-80) REVERT: H 25 GLU cc_start: 0.0284 (OUTLIER) cc_final: 0.0025 (pt0) REVERT: N 79 CYS cc_start: 0.3124 (OUTLIER) cc_final: 0.1889 (p) outliers start: 120 outliers final: 74 residues processed: 417 average time/residue: 0.2190 time to fit residues: 146.9144 Evaluate side-chains 377 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 297 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 96 TYR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 918 LEU Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 214 ARG Chi-restraints excluded: chain D residue 316 CYS Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 971 MET Chi-restraints excluded: chain D residue 987 GLU Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1132 ILE Chi-restraints excluded: chain D residue 1147 ARG Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain D residue 1253 ILE Chi-restraints excluded: chain D residue 1265 MET Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 482 THR 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 66 VAL Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 284 optimal weight: 0.3980 chunk 233 optimal weight: 5.9990 chunk 310 optimal weight: 3.9990 chunk 325 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 69.5892 > 50:) chunk 74 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 230 optimal weight: 7.9990 chunk 286 optimal weight: 0.0070 chunk 99 optimal weight: 7.9990 chunk 320 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 overall best weight: 2.2804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN A 119 HIS A 151 GLN C 358 HIS ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 980 ASN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1122 GLN ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 366 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.175171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.135440 restraints weight = 63391.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.133249 restraints weight = 109130.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.134493 restraints weight = 85651.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.135575 restraints weight = 52904.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.135858 restraints weight = 51345.014| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 33486 Z= 0.264 Angle : 0.773 13.436 46015 Z= 0.401 Chirality : 0.049 0.367 5225 Planarity : 0.006 0.077 5422 Dihedral : 20.731 177.978 5932 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 5.54 % Allowed : 22.22 % Favored : 72.25 % 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: -0.39 (0.13), residues: 3713 helix: 0.85 (0.13), residues: 1505 sheet: -0.70 (0.24), residues: 467 loop : -1.10 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 808 TYR 0.032 0.002 TYR D 106 PHE 0.020 0.002 PHE D 512 TRP 0.013 0.002 TRP D 718 HIS 0.017 0.001 HIS F 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.26 (33438) covalent geometry : angle 0.75951 / 0.40 (45979) hydrogen bonds : bond 0.05598 / 3.83 ( 1510) hydrogen bonds : angle 4.71757 / 3.28 ( 4142) metal coordination : bond 0.00586 / 0.27 ( 48) metal coordination : angle 5.12974 / 3.29 ( 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 492 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 320 time to evaluate : 1.252 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 185 GLN cc_start: 0.6311 (OUTLIER) cc_final: 0.6043 (tp40) REVERT: C 27 LYS cc_start: 0.7246 (mmtt) cc_final: 0.6976 (mmtt) REVERT: C 243 TYR cc_start: 0.7736 (m-80) cc_final: 0.6771 (m-10) REVERT: C 382 MET cc_start: 0.8561 (tmm) cc_final: 0.7798 (tmm) REVERT: C 565 MET cc_start: 0.7850 (ppp) cc_final: 0.7036 (ptm) REVERT: C 598 MET cc_start: 0.7697 (mtp) cc_final: 0.7316 (ttp) REVERT: C 804 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7553 (tm-30) REVERT: C 1048 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.8079 (m-80) REVERT: C 1061 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7425 (tp) REVERT: D 296 LEU cc_start: 0.7595 (mt) cc_final: 0.7261 (mt) REVERT: D 474 ARG cc_start: 0.7483 (ttp80) cc_final: 0.7264 (tmt170) REVERT: D 745 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6898 (mm-30) REVERT: D 916 TYR cc_start: 0.7679 (m-10) cc_final: 0.7450 (m-80) REVERT: D 1006 MET cc_start: 0.2049 (ppp) cc_final: 0.1409 (ppp) REVERT: E 32 TYR cc_start: 0.6037 (OUTLIER) cc_final: 0.4633 (t80) REVERT: F 245 PHE cc_start: 0.7518 (m-80) cc_final: 0.7275 (m-80) REVERT: H 25 GLU cc_start: 0.0130 (OUTLIER) cc_final: -0.0107 (pt0) REVERT: N 79 CYS cc_start: 0.2282 (OUTLIER) cc_final: 0.0999 (p) outliers start: 172 outliers final: 113 residues processed: 460 average time/residue: 0.2076 time to fit residues: 155.5369 Evaluate side-chains 417 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 298 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 110 ILE Chi-restraints excluded: chain A residue 131 LYS 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 150 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 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 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 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 40 LYS 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 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 114 LEU Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 290 THR 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 702 VAL Chi-restraints excluded: chain D residue 724 VAL Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 874 ASP Chi-restraints excluded: chain D residue 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 979 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 1132 ILE Chi-restraints excluded: chain D residue 1168 LYS Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1215 VAL Chi-restraints excluded: chain D residue 1265 MET Chi-restraints excluded: chain E residue 12 ILE 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 472 LEU Chi-restraints excluded: chain F residue 477 LYS Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain M residue 28 GLU Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 239 optimal weight: 0.6980 chunk 254 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 365 optimal weight: 20.0000 chunk 276 optimal weight: 0.5980 chunk 331 optimal weight: 10.0000 chunk 311 optimal weight: 5.9990 chunk 371 optimal weight: 50.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN C 741 HIS ** C 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.177897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.135104 restraints weight = 62752.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.131636 restraints weight = 73812.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.133264 restraints weight = 75808.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.132964 restraints weight = 51722.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.133171 restraints weight = 45017.426| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33486 Z= 0.145 Angle : 0.676 12.471 46015 Z= 0.354 Chirality : 0.046 0.368 5225 Planarity : 0.005 0.064 5422 Dihedral : 20.664 177.770 5932 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.41 % Allowed : 23.79 % 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: -0.14 (0.14), residues: 3713 helix: 1.08 (0.13), residues: 1503 sheet: -0.64 (0.24), residues: 464 loop : -0.96 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG D 211 TYR 0.025 0.002 TYR A 32 PHE 0.017 0.001 PHE B 219 TRP 0.013 0.001 TRP C 930 HIS 0.012 0.001 HIS F 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (33438) covalent geometry : angle 0.66537 / 0.35 (45979) hydrogen bonds : bond 0.04772 / 3.25 ( 1510) hydrogen bonds : angle 4.41074 / 3.06 ( 4142) metal coordination : bond 0.00310 / 0.16 ( 48) metal coordination : angle 4.36073 / 2.93 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7426 Ramachandran restraints generated. 3713 Oldfield, 0 Emsley, 3713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 329 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASN cc_start: 0.7976 (OUTLIER) cc_final: 0.7595 (t0) REVERT: A 185 GLN cc_start: 0.6322 (OUTLIER) cc_final: 0.6013 (tp40) REVERT: B 208 MET cc_start: 0.8366 (mtm) cc_final: 0.8096 (mtm) REVERT: C 27 LYS cc_start: 0.7267 (mmtt) cc_final: 0.6953 (mmtt) REVERT: C 243 TYR cc_start: 0.7963 (m-80) cc_final: 0.7303 (m-80) REVERT: C 382 MET cc_start: 0.8520 (tmm) cc_final: 0.7732 (tmm) REVERT: C 565 MET cc_start: 0.7857 (ppp) cc_final: 0.6921 (ptm) REVERT: C 584 GLU cc_start: 0.8830 (pm20) cc_final: 0.8615 (pm20) REVERT: C 1048 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.8200 (m-80) REVERT: C 1061 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7609 (tp) REVERT: D 9 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6373 (pt0) REVERT: D 30 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8350 (mtpt) REVERT: D 59 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6995 (tt0) REVERT: D 141 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7223 (mm-30) REVERT: D 208 LEU cc_start: 0.8274 (tp) cc_final: 0.7495 (tp) REVERT: D 296 LEU cc_start: 0.7618 (mt) cc_final: 0.7223 (mt) REVERT: D 387 ARG cc_start: 0.6428 (OUTLIER) cc_final: 0.6081 (mtp85) REVERT: D 474 ARG cc_start: 0.7460 (ttp80) cc_final: 0.7260 (tmt170) REVERT: D 916 TYR cc_start: 0.7550 (m-10) cc_final: 0.7292 (m-80) REVERT: D 997 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8564 (mt) REVERT: E 74 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7519 (mm-30) REVERT: F 245 PHE cc_start: 0.7914 (m-80) cc_final: 0.7644 (m-80) REVERT: H 25 GLU cc_start: 0.0200 (OUTLIER) cc_final: -0.0060 (pt0) REVERT: N 79 CYS cc_start: 0.2586 (OUTLIER) cc_final: 0.1273 (p) outliers start: 137 outliers final: 86 residues processed: 436 average time/residue: 0.2143 time to fit residues: 151.4012 Evaluate side-chains 396 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 300 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 602 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 840 ASP Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 387 ARG Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 702 VAL Chi-restraints excluded: chain D residue 762 LYS Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1065 ASP Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1132 ILE Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1265 MET Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 477 LYS Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 90 CYS Chi-restraints excluded: chain H residue 25 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 83 ASP Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 376 optimal weight: 20.0000 chunk 353 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 325 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 330 optimal weight: 0.0170 overall best weight: 2.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 ASN A 151 GLN ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.175135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.135066 restraints weight = 63370.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.132655 restraints weight = 105232.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.133965 restraints weight = 84233.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.135015 restraints weight = 51480.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.135308 restraints weight = 50692.795| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 33486 Z= 0.235 Angle : 0.742 11.831 46015 Z= 0.386 Chirality : 0.048 0.368 5225 Planarity : 0.005 0.090 5422 Dihedral : 20.654 177.749 5932 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 5.09 % Allowed : 24.40 % Favored : 70.51 % 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: -0.37 (0.13), residues: 3713 helix: 0.93 (0.13), residues: 1510 sheet: -0.77 (0.23), residues: 485 loop : -1.12 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 829 TYR 0.034 0.002 TYR A 32 PHE 0.017 0.002 PHE C 892 TRP 0.011 0.002 TRP D 718 HIS 0.010 0.001 HIS F 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.23 (33438) covalent geometry : angle 0.73079 / 0.39 (45979) hydrogen bonds : bond 0.05236 / 3.59 ( 1510) hydrogen bonds : angle 4.59861 / 3.19 ( 4142) metal coordination : bond 0.00511 / 0.24 ( 48) metal coordination : angle 4.67953 / 3.06 ( 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 474 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 316 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASP cc_start: 0.6898 (m-30) cc_final: 0.6599 (m-30) REVERT: A 152 ASN cc_start: 0.7998 (OUTLIER) cc_final: 0.7579 (t0) REVERT: B 157 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.7029 (pm20) REVERT: C 27 LYS cc_start: 0.7294 (mmtt) cc_final: 0.6953 (mmtt) REVERT: C 243 TYR cc_start: 0.7695 (m-80) cc_final: 0.6779 (m-10) REVERT: C 382 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.7786 (tmm) REVERT: C 554 VAL cc_start: 0.8555 (m) cc_final: 0.8221 (p) REVERT: C 565 MET cc_start: 0.7993 (ppp) cc_final: 0.7113 (ptm) REVERT: C 1048 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.8086 (m-80) REVERT: C 1061 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7298 (tp) REVERT: D 30 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8571 (mtpt) REVERT: D 59 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6955 (tt0) REVERT: D 296 LEU cc_start: 0.7680 (mt) cc_final: 0.7388 (mt) REVERT: D 815 MET cc_start: 0.8683 (ppp) cc_final: 0.8243 (ptt) REVERT: D 916 TYR cc_start: 0.7686 (m-10) cc_final: 0.7471 (m-80) REVERT: D 997 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8579 (mt) REVERT: D 1006 MET cc_start: 0.1788 (ppp) cc_final: 0.0902 (ppp) REVERT: E 32 TYR cc_start: 0.6032 (OUTLIER) cc_final: 0.4767 (t80) REVERT: N 79 CYS cc_start: 0.2239 (OUTLIER) cc_final: 0.0969 (p) outliers start: 158 outliers final: 121 residues processed: 444 average time/residue: 0.2093 time to fit residues: 151.1577 Evaluate side-chains 435 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 305 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 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 152 ASN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 195 ASP 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 37 SER Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 350 VAL 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 403 LEU Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 426 MET 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 527 ILE 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 668 THR Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 822 SER Chi-restraints excluded: chain C residue 840 ASP Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 884 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 30 LYS Chi-restraints excluded: chain D residue 32 GLU 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 247 ARG Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain D residue 316 CYS Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 633 THR Chi-restraints excluded: chain D residue 702 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 818 LEU 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 841 VAL Chi-restraints excluded: chain D residue 874 ASP Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain D residue 924 VAL Chi-restraints excluded: chain D residue 956 THR Chi-restraints excluded: chain D residue 958 SER Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 979 THR Chi-restraints excluded: chain D residue 987 GLU Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1065 ASP 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 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 24 ASP Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain 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 348 THR Chi-restraints excluded: chain F residue 387 ASP Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 477 LYS 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: 0.7980 chunk 278 optimal weight: 1.9990 chunk 334 optimal weight: 30.0000 chunk 281 optimal weight: 0.8980 chunk 140 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 327 optimal weight: 40.0000 chunk 2 optimal weight: 0.7980 chunk 352 optimal weight: 40.0000 chunk 51 optimal weight: 0.0870 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN C 157 ASN C 428 GLN ** C 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.176892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.131983 restraints weight = 63957.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.128546 restraints weight = 67773.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.129213 restraints weight = 74822.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.129004 restraints weight = 50739.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.130911 restraints weight = 42792.507| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33486 Z= 0.141 Angle : 0.686 12.167 46015 Z= 0.357 Chirality : 0.046 0.367 5225 Planarity : 0.005 0.072 5422 Dihedral : 20.615 177.908 5932 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.96 % Allowed : 25.85 % Favored : 70.19 % 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: -0.18 (0.14), residues: 3713 helix: 1.12 (0.13), residues: 1501 sheet: -0.66 (0.24), residues: 466 loop : -1.04 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 808 TYR 0.026 0.001 TYR A 32 PHE 0.018 0.001 PHE B 219 TRP 0.018 0.001 TRP C 930 HIS 0.010 0.001 HIS F 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (33438) covalent geometry : angle 0.67632 / 0.36 (45979) hydrogen bonds : bond 0.04626 / 3.15 ( 1510) hydrogen bonds : angle 4.34596 / 3.01 ( 4142) metal coordination : bond 0.00269 / 0.13 ( 48) metal coordination : angle 4.15991 / 2.83 ( 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 446 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 323 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASP cc_start: 0.7072 (m-30) cc_final: 0.6764 (m-30) REVERT: B 136 MET cc_start: 0.8269 (ppp) cc_final: 0.7950 (ppp) REVERT: B 157 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.7121 (pm20) REVERT: C 27 LYS cc_start: 0.7287 (mmtt) cc_final: 0.6969 (mmtt) REVERT: C 243 TYR cc_start: 0.8072 (m-80) cc_final: 0.7406 (m-80) REVERT: C 382 MET cc_start: 0.8523 (tmm) cc_final: 0.7779 (tmm) REVERT: C 565 MET cc_start: 0.7870 (ppp) cc_final: 0.7083 (ptm) REVERT: C 584 GLU cc_start: 0.8787 (pm20) cc_final: 0.8515 (pm20) REVERT: C 1048 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.8142 (m-80) REVERT: C 1061 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7413 (tp) REVERT: D 30 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8357 (mtpt) REVERT: D 59 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6754 (mt-10) REVERT: D 296 LEU cc_start: 0.7572 (mt) cc_final: 0.7221 (mt) REVERT: D 815 MET cc_start: 0.8701 (ppp) cc_final: 0.8318 (ptt) REVERT: D 916 TYR cc_start: 0.7628 (m-10) cc_final: 0.7422 (m-80) REVERT: D 997 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8410 (mt) REVERT: E 32 TYR cc_start: 0.5765 (OUTLIER) cc_final: 0.4522 (t80) REVERT: E 38 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7766 (ttm-80) REVERT: F 382 LEU cc_start: 0.9034 (tt) cc_final: 0.8791 (pp) REVERT: F 487 ARG cc_start: 0.8502 (ttt-90) cc_final: 0.7502 (ttm-80) REVERT: N 79 CYS cc_start: 0.3080 (OUTLIER) cc_final: 0.1797 (p) outliers start: 123 outliers final: 89 residues processed: 425 average time/residue: 0.2184 time to fit residues: 149.2029 Evaluate side-chains 403 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 307 time to evaluate : 1.182 ------------------------------------------------------------------------------- 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 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 227 ILE 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 37 SER Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 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 840 ASP Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 887 ILE Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 702 VAL Chi-restraints excluded: chain D residue 728 ILE Chi-restraints excluded: chain D residue 762 LYS Chi-restraints excluded: chain D residue 819 VAL Chi-restraints excluded: chain D residue 826 THR Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain D residue 841 VAL Chi-restraints excluded: chain D residue 872 LEU 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 997 ILE Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1182 HIS Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1265 MET Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 477 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 323 optimal weight: 9.9990 chunk 209 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 379 optimal weight: 30.0000 chunk 149 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 151 GLN A 152 ASN ** C 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 ASN ** C 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 GLN ** F 354 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 = 0.4385 r_free = 0.4385 target = 0.173564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.130423 restraints weight = 64360.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.128140 restraints weight = 90764.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.129243 restraints weight = 75589.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.130092 restraints weight = 47907.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.130438 restraints weight = 47789.645| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 33486 Z= 0.253 Angle : 0.777 14.545 46015 Z= 0.401 Chirality : 0.049 0.361 5225 Planarity : 0.005 0.070 5422 Dihedral : 20.641 178.058 5930 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.31 % Allowed : 25.50 % Favored : 70.19 % 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: -0.44 (0.14), residues: 3713 helix: 0.89 (0.13), residues: 1493 sheet: -0.82 (0.24), residues: 475 loop : -1.17 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 211 TYR 0.033 0.002 TYR A 32 PHE 0.054 0.002 PHE F 245 TRP 0.016 0.002 TRP C 930 HIS 0.008 0.001 HIS F 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.25 (33438) covalent geometry : angle 0.76473 / 0.40 (45979) hydrogen bonds : bond 0.05351 / 3.66 ( 1510) hydrogen bonds : angle 4.61266 / 3.20 ( 4142) metal coordination : bond 0.00522 / 0.24 ( 48) metal coordination : angle 4.95552 / 3.31 ( 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 443 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 309 time to evaluate : 1.134 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 109 ASP cc_start: 0.7252 (m-30) cc_final: 0.7003 (m-30) REVERT: B 157 GLN cc_start: 0.7337 (OUTLIER) cc_final: 0.7103 (pm20) REVERT: C 27 LYS cc_start: 0.7348 (mmtt) cc_final: 0.7052 (mmtt) REVERT: C 49 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8261 (mp) REVERT: C 142 MET cc_start: 0.6030 (mmp) cc_final: 0.5803 (mmm) REVERT: C 243 TYR cc_start: 0.7848 (m-80) cc_final: 0.6995 (m-10) REVERT: C 382 MET cc_start: 0.8604 (tmm) cc_final: 0.7778 (tmm) REVERT: C 565 MET cc_start: 0.7891 (ppp) cc_final: 0.7134 (ptm) REVERT: C 803 GLU cc_start: 0.8391 (mp0) cc_final: 0.8164 (mp0) REVERT: C 1048 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.8107 (m-80) REVERT: C 1061 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7322 (tp) REVERT: D 9 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6811 (pt0) REVERT: D 30 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8359 (mtpt) REVERT: D 59 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6793 (mt-10) REVERT: D 296 LEU cc_start: 0.7617 (mt) cc_final: 0.7229 (mt) REVERT: D 320 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8487 (mt) REVERT: D 533 ASN cc_start: 0.7766 (t0) cc_final: 0.7176 (m-40) REVERT: D 815 MET cc_start: 0.8779 (ppp) cc_final: 0.8431 (ptt) REVERT: D 910 ASP cc_start: 0.7277 (p0) cc_final: 0.6946 (p0) REVERT: D 916 TYR cc_start: 0.7781 (m-10) cc_final: 0.7566 (m-80) REVERT: D 997 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8749 (mt) REVERT: D 1006 MET cc_start: 0.2078 (ppp) cc_final: 0.1200 (ppp) REVERT: E 32 TYR cc_start: 0.6079 (OUTLIER) cc_final: 0.4800 (t80) REVERT: E 38 ARG cc_start: 0.8194 (ttm-80) cc_final: 0.7831 (ttm-80) REVERT: F 487 ARG cc_start: 0.8201 (ttt-90) cc_final: 0.7362 (ttm-80) REVERT: N 79 CYS cc_start: 0.2391 (OUTLIER) cc_final: 0.1160 (p) outliers start: 134 outliers final: 110 residues processed: 420 average time/residue: 0.2140 time to fit residues: 146.4778 Evaluate side-chains 418 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 298 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 150 VAL Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 476 GLU 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 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 769 ASP Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 793 THR 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 1031 THR Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 9 GLU Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 504 LEU Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 595 ARG Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 702 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 872 LEU Chi-restraints excluded: chain D residue 874 ASP 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 966 VAL Chi-restraints excluded: chain D residue 968 THR Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1105 LEU Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1132 ILE Chi-restraints excluded: chain D residue 1182 HIS Chi-restraints excluded: chain D residue 1190 LEU 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 309 LEU Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 477 LYS 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 97 VAL Chi-restraints excluded: chain M residue 28 GLU Chi-restraints excluded: chain N residue 79 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 134 optimal weight: 0.9990 chunk 194 optimal weight: 0.0870 chunk 283 optimal weight: 0.6980 chunk 154 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 333 optimal weight: 9.9990 chunk 141 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 375 optimal weight: 20.0000 chunk 196 optimal weight: 0.8980 chunk 303 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN C 596 ASN ** C 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 GLN ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.176245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.131564 restraints weight = 64523.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.127237 restraints weight = 69787.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.129081 restraints weight = 69947.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.128312 restraints weight = 49458.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.128549 restraints weight = 44307.914| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33486 Z= 0.148 Angle : 0.721 15.870 46015 Z= 0.371 Chirality : 0.047 0.380 5225 Planarity : 0.005 0.064 5422 Dihedral : 20.607 178.732 5930 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.54 % Allowed : 26.37 % Favored : 70.09 % 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: -0.28 (0.14), residues: 3713 helix: 1.00 (0.13), residues: 1499 sheet: -0.71 (0.24), residues: 463 loop : -1.06 (0.14), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.001 ARG D 211 TYR 0.039 0.002 TYR A 32 PHE 0.017 0.001 PHE B 219 TRP 0.016 0.001 TRP F 333 HIS 0.010 0.001 HIS F 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (33438) covalent geometry : angle 0.71118 / 0.37 (45979) hydrogen bonds : bond 0.04747 / 3.22 ( 1510) hydrogen bonds : angle 4.40521 / 3.05 ( 4142) metal coordination : bond 0.00291 / 0.14 ( 48) metal coordination : angle 4.22067 / 2.85 ( 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 416 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 306 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASP cc_start: 0.7334 (m-30) cc_final: 0.7092 (m-30) REVERT: B 157 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7247 (pm20) REVERT: C 27 LYS cc_start: 0.7320 (mmtt) cc_final: 0.6954 (mmtt) REVERT: C 49 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8185 (mp) REVERT: C 243 TYR cc_start: 0.8075 (m-80) cc_final: 0.7446 (m-80) REVERT: C 382 MET cc_start: 0.8554 (tmm) cc_final: 0.7770 (tmm) REVERT: C 565 MET cc_start: 0.8059 (ppp) cc_final: 0.7275 (ptm) REVERT: C 803 GLU cc_start: 0.8513 (mp0) cc_final: 0.8308 (mp0) REVERT: C 1048 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.8089 (m-80) REVERT: C 1061 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7455 (tp) REVERT: D 30 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8377 (mtpt) REVERT: D 59 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6773 (mt-10) REVERT: D 229 LEU cc_start: 0.7828 (mt) cc_final: 0.7326 (mm) REVERT: D 296 LEU cc_start: 0.7578 (mt) cc_final: 0.7166 (mt) REVERT: D 320 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8351 (mt) REVERT: D 474 ARG cc_start: 0.7699 (tmt170) cc_final: 0.7307 (tpt90) REVERT: D 815 MET cc_start: 0.8725 (ppp) cc_final: 0.8375 (ptt) REVERT: D 916 TYR cc_start: 0.7625 (m-10) cc_final: 0.7409 (m-80) REVERT: D 997 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8504 (mt) REVERT: D 1006 MET cc_start: 0.1750 (ppp) cc_final: 0.1006 (ppp) REVERT: E 32 TYR cc_start: 0.5861 (OUTLIER) cc_final: 0.4555 (t80) REVERT: E 38 ARG cc_start: 0.8133 (ttm-80) cc_final: 0.7807 (ttm-80) REVERT: F 386 LEU cc_start: 0.6902 (mm) cc_final: 0.6591 (mm) REVERT: F 487 ARG cc_start: 0.8570 (ttt-90) cc_final: 0.7668 (ttm-80) REVERT: N 79 CYS cc_start: 0.2862 (OUTLIER) cc_final: 0.1582 (p) outliers start: 110 outliers final: 94 residues processed: 395 average time/residue: 0.2145 time to fit residues: 138.2523 Evaluate side-chains 406 residues out of total 3107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 303 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 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 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 510 VAL 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 602 VAL Chi-restraints excluded: chain C residue 710 MET Chi-restraints excluded: chain C residue 741 HIS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 840 ASP Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain C residue 887 ILE Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 1015 ILE Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 75 CYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 105 TRP Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 475 MET Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 702 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 872 LEU 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 997 ILE Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1130 VAL Chi-restraints excluded: chain D residue 1182 HIS Chi-restraints excluded: chain D residue 1190 LEU Chi-restraints excluded: chain D residue 1202 SER Chi-restraints excluded: chain D residue 1265 MET Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 62 HIS Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 477 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 67 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 384 optimal weight: 50.0000 chunk 55 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 370 optimal weight: 50.0000 chunk 63 optimal weight: 1.9990 chunk 228 optimal weight: 5.9990 chunk 253 optimal weight: 0.0170 chunk 204 optimal weight: 1.9990 chunk 180 optimal weight: 7.9990 overall best weight: 1.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 ASN ** C 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 GLN ** F 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.176159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.132446 restraints weight = 64515.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.129182 restraints weight = 78454.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.130209 restraints weight = 70935.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.131293 restraints weight = 45046.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.131673 restraints weight = 43489.810| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.197 33486 Z= 0.176 Angle : 0.795 59.200 46015 Z= 0.428 Chirality : 0.047 0.544 5225 Planarity : 0.005 0.062 5422 Dihedral : 20.605 178.717 5930 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.61 % Allowed : 26.66 % Favored : 69.74 % 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: -0.27 (0.14), residues: 3713 helix: 1.00 (0.13), residues: 1499 sheet: -0.70 (0.24), residues: 463 loop : -1.06 (0.14), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.000 ARG D 211 TYR 0.035 0.002 TYR A 32 PHE 0.016 0.001 PHE B 219 TRP 0.025 0.002 TRP C 930 HIS 0.008 0.001 HIS F 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (33438) covalent geometry : angle 0.78628 / 0.43 (45979) hydrogen bonds : bond 0.04751 / 3.22 ( 1510) hydrogen bonds : angle 4.40678 / 3.05 ( 4142) metal coordination : bond 0.00311 / 0.15 ( 48) metal coordination : angle 4.22405 / 2.85 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5797.17 seconds wall clock time: 101 minutes 5.98 seconds (6065.98 seconds total)