Starting phenix.real_space_refine on Wed Feb 4 12:56:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sdx_54793/02_2026/9sdx_54793.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sdx_54793/02_2026/9sdx_54793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9sdx_54793/02_2026/9sdx_54793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sdx_54793/02_2026/9sdx_54793.map" model { file = "/net/cci-nas-00/data/ceres_data/9sdx_54793/02_2026/9sdx_54793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sdx_54793/02_2026/9sdx_54793.cif" } resolution = 2.97 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= 0.001 sd= 0.010 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: 5 Type Number sf(0) Gaussians Zn 7 6.06 5 S 75 5.16 5 C 6711 2.51 5 N 1851 2.21 5 O 1928 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10572 Number of models: 1 Model: "" Number of chains: 9 Chain: "N" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 463 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "R" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 665 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "U" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 519 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASP:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "G" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1022 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 12, 'TRANS': 130} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 2, 'GLU:plan': 7, 'TYR:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "C" Number of atoms: 4456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4456 Classifications: {'peptide': 574} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 16, 'TRANS': 557} Chain breaks: 5 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 291 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 22, 'ARG:plan': 6, 'GLN:plan1': 4, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 152 Chain: "H" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3433 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 16, 'TRANS': 411} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 6, 'ASP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "R" 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: "U" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'SY8': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 645 SG CYS R 50 23.662 85.439 76.469 1.00 54.37 S ATOM 664 SG CYS R 53 26.255 87.166 74.463 1.00 46.73 S ATOM 922 SG CYS R 88 22.603 87.925 74.108 1.00 49.58 S ATOM 725 SG CYS R 61 23.236 93.388 74.836 1.00 61.88 S ATOM 750 SG CYS R 64 21.937 96.725 74.918 1.00 91.61 S ATOM 803 SG CYS R 73 22.044 94.825 78.090 1.00 84.82 S ATOM 916 SG CYS R 87 19.477 93.944 75.121 1.00 84.54 S ATOM 857 SG CYS R 80 14.507 75.616 82.287 1.00 76.50 S ATOM 1012 SG CYS R 99 15.124 76.827 78.960 1.00 72.06 S ATOM 1033 SG CYS R 102 16.421 73.485 79.873 1.00 68.56 S ATOM 8818 SG CYS H 257 46.035 68.159 61.114 1.00 42.49 S ATOM 8844 SG CYS H 260 45.397 66.935 57.818 1.00 64.49 S ATOM 8927 SG CYS H 270 44.013 65.001 60.636 1.00 34.08 S ATOM 7881 SG CYS H 139 75.963 29.914 52.639 1.00 65.52 S ATOM 7897 SG CYS H 142 77.273 29.793 49.300 1.00 29.04 S ATOM 8033 SG CYS H 161 78.923 32.031 51.738 1.00 55.82 S ATOM 8056 SG CYS H 164 75.292 32.805 50.235 1.00 74.16 S ATOM 8589 SG CYS H 228 57.514 72.058 53.769 1.00 49.87 S ATOM 8619 SG CYS H 233 60.639 72.968 52.247 1.00 52.46 S ATOM 8752 SG CYS H 249 59.423 74.972 55.117 1.00 59.76 S ATOM 8777 SG CYS H 252 57.695 75.109 51.507 1.00 52.74 S ATOM 7992 SG CYS H 156 70.196 34.864 63.492 1.00 46.17 S ATOM 8194 SG CYS H 183 68.770 35.027 60.192 1.00 53.08 S ATOM 8230 SG CYS H 188 66.482 34.988 63.102 1.00 21.70 S Time building chain proxies: 2.49, per 1000 atoms: 0.24 Number of scatterers: 10572 At special positions: 0 Unit cell: (94.4832, 144.704, 149.811, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 7 29.99 S 75 16.00 O 1928 8.00 N 1851 7.00 C 6711 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 additional links: simple=1, symmetry=0 Simple link: pdb=" C GLY U 75 " - pdb=" N SY8 U 101 " Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 476.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 501 " pdb="ZN ZN H 501 " - pdb=" SG CYS H 260 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 265 " pdb="ZN ZN H 501 " - pdb=" SG CYS H 270 " pdb="ZN ZN H 501 " - pdb=" SG CYS H 257 " pdb=" ZN H 502 " pdb="ZN ZN H 502 " - pdb=" SG CYS H 161 " pdb="ZN ZN H 502 " - pdb=" SG CYS H 142 " pdb="ZN ZN H 502 " - pdb=" SG CYS H 164 " pdb="ZN ZN H 502 " - pdb=" SG CYS H 139 " pdb=" ZN H 503 " pdb="ZN ZN H 503 " - pdb=" SG CYS H 228 " pdb="ZN ZN H 503 " - pdb=" SG CYS H 252 " pdb="ZN ZN H 503 " - pdb=" SG CYS H 249 " pdb="ZN ZN H 503 " - pdb=" SG CYS H 233 " pdb=" ZN H 504 " pdb="ZN ZN H 504 " - pdb=" SG CYS H 188 " pdb="ZN ZN H 504 " - pdb=" SG CYS H 156 " pdb="ZN ZN H 504 " - pdb=" ND1 HIS H 158 " pdb="ZN ZN H 504 " - pdb=" SG CYS H 183 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 50 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 88 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 53 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 85 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 64 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 61 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 87 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 73 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 102 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 80 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 99 " Number of angles added : 30 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2670 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 12 sheets defined 53.6% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'N' and resid 22 through 34 removed outlier: 3.733A pdb=" N VAL N 30 " --> pdb=" O ILE N 26 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU N 31 " --> pdb=" O LYS N 27 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU N 32 " --> pdb=" O GLU N 28 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS N 33 " --> pdb=" O ARG N 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 67 Processing helix chain 'R' and resid 86 through 93 Processing helix chain 'U' and resid 22 through 34 removed outlier: 3.656A pdb=" N VAL U 26 " --> pdb=" O THR U 22 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 39 No H-bonds generated for 'chain 'U' and resid 37 through 39' Processing helix chain 'U' and resid 56 through 60 Processing helix chain 'G' and resid 2 through 17 removed outlier: 3.560A pdb=" N ARG G 6 " --> pdb=" O ALA G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 64 Processing helix chain 'G' and resid 91 through 95 removed outlier: 3.591A pdb=" N ASN G 94 " --> pdb=" O SER G 91 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TRP G 95 " --> pdb=" O ALA G 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 91 through 95' Processing helix chain 'G' and resid 100 through 114 Processing helix chain 'G' and resid 122 through 132 removed outlier: 3.731A pdb=" N ASP G 132 " --> pdb=" O GLU G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 139 Processing helix chain 'G' and resid 140 through 144 removed outlier: 3.672A pdb=" N PHE G 143 " --> pdb=" O ALA G 140 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR G 144 " --> pdb=" O GLU G 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 140 through 144' Processing helix chain 'C' and resid 159 through 169 removed outlier: 3.753A pdb=" N VAL C 163 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU C 166 " --> pdb=" O LEU C 162 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG C 167 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 168 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 181 removed outlier: 3.686A pdb=" N GLY C 179 " --> pdb=" O GLN C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 248 Proline residue: C 219 - end of helix removed outlier: 7.932A pdb=" N VAL C 227 " --> pdb=" O GLN C 223 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N GLN C 228 " --> pdb=" O GLN C 224 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN C 229 " --> pdb=" O ASN C 225 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 289 through 302 removed outlier: 3.815A pdb=" N LEU C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS C 302 " --> pdb=" O SER C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 328 Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 336 through 360 removed outlier: 3.521A pdb=" N GLN C 360 " --> pdb=" O LYS C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 378 Processing helix chain 'C' and resid 403 through 417 Processing helix chain 'C' and resid 419 through 424 Processing helix chain 'C' and resid 426 through 442 Processing helix chain 'C' and resid 446 through 461 removed outlier: 4.255A pdb=" N PHE C 450 " --> pdb=" O ASN C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 484 removed outlier: 3.559A pdb=" N GLU C 473 " --> pdb=" O ASP C 469 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY C 484 " --> pdb=" O LEU C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 515 removed outlier: 3.653A pdb=" N VAL C 490 " --> pdb=" O PRO C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 524 No H-bonds generated for 'chain 'C' and resid 522 through 524' Processing helix chain 'C' and resid 533 through 537 Processing helix chain 'C' and resid 548 through 553 Processing helix chain 'C' and resid 553 through 566 removed outlier: 4.339A pdb=" N GLU C 557 " --> pdb=" O ASP C 553 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASN C 565 " --> pdb=" O PHE C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 604 Processing helix chain 'C' and resid 605 through 607 No H-bonds generated for 'chain 'C' and resid 605 through 607' Processing helix chain 'C' and resid 615 through 623 Processing helix chain 'C' and resid 626 through 639 Processing helix chain 'C' and resid 700 through 726 removed outlier: 4.219A pdb=" N ASN C 704 " --> pdb=" O ARG C 700 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE C 722 " --> pdb=" O ALA C 718 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET C 723 " --> pdb=" O ILE C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 742 Processing helix chain 'C' and resid 749 through 763 Processing helix chain 'H' and resid 46 through 50 Processing helix chain 'H' and resid 65 through 85 removed outlier: 3.778A pdb=" N MET H 77 " --> pdb=" O LEU H 73 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR H 78 " --> pdb=" O ASN H 74 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER H 79 " --> pdb=" O GLU H 75 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LEU H 80 " --> pdb=" O HIS H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 98 removed outlier: 3.910A pdb=" N ASN H 97 " --> pdb=" O LEU H 93 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE H 98 " --> pdb=" O ILE H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 112 Processing helix chain 'H' and resid 114 through 120 Processing helix chain 'H' and resid 165 through 176 Processing helix chain 'H' and resid 193 through 197 Processing helix chain 'H' and resid 203 through 222 removed outlier: 3.760A pdb=" N ARG H 207 " --> pdb=" O ASN H 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 279 Processing helix chain 'H' and resid 286 through 294 Processing helix chain 'H' and resid 353 through 381 removed outlier: 4.496A pdb=" N GLU H 360 " --> pdb=" O ALA H 356 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA H 361 " --> pdb=" O GLN H 357 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG H 371 " --> pdb=" O PHE H 367 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU H 379 " --> pdb=" O HIS H 375 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN H 380 " --> pdb=" O ASN H 376 " (cutoff:3.500A) Processing helix chain 'H' and resid 382 through 399 Processing helix chain 'H' and resid 403 through 408 removed outlier: 4.266A pdb=" N GLN H 408 " --> pdb=" O ILE H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 409 through 433 removed outlier: 4.060A pdb=" N TYR H 428 " --> pdb=" O LEU H 424 " (cutoff:3.500A) Proline residue: H 429 - end of helix Processing helix chain 'H' and resid 437 through 463 removed outlier: 3.850A pdb=" N GLU H 444 " --> pdb=" O LYS H 440 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TYR H 445 " --> pdb=" O LYS H 441 " (cutoff:3.500A) Processing helix chain 'H' and resid 468 through 488 Processing sheet with id=AA1, first strand: chain 'N' and resid 12 through 16 removed outlier: 3.695A pdb=" N ILE N 15 " --> pdb=" O ILE N 3 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE N 3 " --> pdb=" O ILE N 15 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N LEU N 67 " --> pdb=" O LEU N 2 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS N 4 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU N 69 " --> pdb=" O LYS N 4 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS N 6 " --> pdb=" O LEU N 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 526 through 532 Processing sheet with id=AA3, first strand: chain 'C' and resid 526 through 532 removed outlier: 5.867A pdb=" N LEU R 32 " --> pdb=" O THR C 583 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR C 583 " --> pdb=" O LEU R 32 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN C 579 " --> pdb=" O ASN R 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 83 through 85 removed outlier: 6.597A pdb=" N VAL R 75 " --> pdb=" O ILE R 111 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ILE R 111 " --> pdb=" O VAL R 75 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N TRP R 77 " --> pdb=" O GLN R 109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'U' and resid 12 through 16 removed outlier: 3.716A pdb=" N ILE U 13 " --> pdb=" O VAL U 5 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU U 69 " --> pdb=" O LYS U 6 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'U' and resid 12 through 16 removed outlier: 3.716A pdb=" N ILE U 13 " --> pdb=" O VAL U 5 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU U 69 " --> pdb=" O LYS U 6 " (cutoff:3.500A) removed outlier: 12.542A pdb=" N CYS H 303 " --> pdb=" O LEU U 67 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LEU U 69 " --> pdb=" O CYS H 303 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N GLU H 305 " --> pdb=" O LEU U 69 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU U 71 " --> pdb=" O GLU H 305 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 22 through 25 removed outlier: 3.656A pdb=" N ASN G 24 " --> pdb=" O LEU G 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 648 through 650 Processing sheet with id=AA9, first strand: chain 'C' and resid 728 through 730 removed outlier: 4.017A pdb=" N ILE C 729 " --> pdb=" O PHE C 776 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE C 776 " --> pdb=" O ILE C 729 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 61 through 64 Processing sheet with id=AB2, first strand: chain 'H' and resid 246 through 247 removed outlier: 3.687A pdb=" N VAL H 247 " --> pdb=" O PHE H 256 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE H 256 " --> pdb=" O VAL H 247 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'H' and resid 312 through 314 547 hydrogen bonds defined for protein. 1596 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 1.06 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: 3137 1.34 - 1.46: 2617 1.46 - 1.59: 4898 1.59 - 1.71: 0 1.71 - 1.84: 110 Bond restraints: 10762 Sorted by residual: bond pdb=" N SY8 U 101 " pdb=" C4 SY8 U 101 " ideal model delta sigma weight residual 1.456 1.485 -0.029 2.00e-02 2.50e+03 2.06e+00 bond pdb=" CB PRO G 41 " pdb=" CG PRO G 41 " ideal model delta sigma weight residual 1.492 1.541 -0.049 5.00e-02 4.00e+02 9.61e-01 bond pdb=" CA ILE N 36 " pdb=" C ILE N 36 " ideal model delta sigma weight residual 1.516 1.527 -0.011 1.11e-02 8.12e+03 9.49e-01 bond pdb=" CB CYS H 257 " pdb=" SG CYS H 257 " ideal model delta sigma weight residual 1.808 1.840 -0.032 3.30e-02 9.18e+02 9.38e-01 bond pdb=" C PHE C 640 " pdb=" N PRO C 641 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.74e-01 ... (remaining 10757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 14338 1.99 - 3.99: 210 3.99 - 5.98: 34 5.98 - 7.97: 5 7.97 - 9.96: 3 Bond angle restraints: 14590 Sorted by residual: angle pdb=" C CYS R 50 " pdb=" N ALA R 51 " pdb=" CA ALA R 51 " ideal model delta sigma weight residual 121.54 127.18 -5.64 1.91e+00 2.74e-01 8.71e+00 angle pdb=" C CYS H 164 " pdb=" N TRP H 165 " pdb=" CA TRP H 165 " ideal model delta sigma weight residual 121.54 127.12 -5.58 1.91e+00 2.74e-01 8.53e+00 angle pdb=" CA SER H 113 " pdb=" C SER H 113 " pdb=" N ALA H 114 " ideal model delta sigma weight residual 116.84 121.83 -4.99 1.71e+00 3.42e-01 8.51e+00 angle pdb=" CA LEU H 381 " pdb=" CB LEU H 381 " pdb=" CG LEU H 381 " ideal model delta sigma weight residual 116.30 126.26 -9.96 3.50e+00 8.16e-02 8.10e+00 angle pdb=" C PRO C 641 " pdb=" N LYS C 642 " pdb=" CA LYS C 642 " ideal model delta sigma weight residual 122.44 119.09 3.35 1.19e+00 7.06e-01 7.92e+00 ... (remaining 14585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.99: 6319 29.99 - 59.97: 164 59.97 - 89.96: 30 89.96 - 119.94: 1 119.94 - 149.93: 1 Dihedral angle restraints: 6515 sinusoidal: 2436 harmonic: 4079 Sorted by residual: dihedral pdb=" CA LEU C 462 " pdb=" C LEU C 462 " pdb=" N ILE C 463 " pdb=" CA ILE C 463 " ideal model delta harmonic sigma weight residual 180.00 153.59 26.41 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA GLN H 408 " pdb=" C GLN H 408 " pdb=" N TYR H 409 " pdb=" CA TYR H 409 " ideal model delta harmonic sigma weight residual 180.00 157.39 22.61 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" C1 SY8 U 101 " pdb=" C2 SY8 U 101 " pdb=" C3 SY8 U 101 " pdb=" C4 SY8 U 101 " ideal model delta sinusoidal sigma weight residual 57.79 -92.14 149.93 1 3.00e+01 1.11e-03 1.99e+01 ... (remaining 6512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1102 0.034 - 0.068: 403 0.068 - 0.102: 118 0.102 - 0.135: 39 0.135 - 0.169: 6 Chirality restraints: 1668 Sorted by residual: chirality pdb=" CA PRO C 641 " pdb=" N PRO C 641 " pdb=" C PRO C 641 " pdb=" CB PRO C 641 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CA GLN H 408 " pdb=" N GLN H 408 " pdb=" C GLN H 408 " pdb=" CB GLN H 408 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CA ILE G 55 " pdb=" N ILE G 55 " pdb=" C ILE G 55 " pdb=" CB ILE G 55 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 ... (remaining 1665 not shown) Planarity restraints: 1873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP H 165 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C TRP H 165 " 0.044 2.00e-02 2.50e+03 pdb=" O TRP H 165 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU H 166 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 640 " -0.035 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO C 641 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 641 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 641 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS H 188 " -0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO H 189 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO H 189 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 189 " -0.027 5.00e-02 4.00e+02 ... (remaining 1870 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 3204 2.83 - 3.35: 9864 3.35 - 3.87: 16155 3.87 - 4.38: 17679 4.38 - 4.90: 31206 Nonbonded interactions: 78108 Sorted by model distance: nonbonded pdb=" OD1 ASP C 235 " pdb=" NZ LYS C 239 " model vdw 2.316 3.120 nonbonded pdb=" NE1 TRP H 404 " pdb=" OE1 GLN H 408 " model vdw 2.322 3.120 nonbonded pdb=" N GLN G 26 " pdb=" O GLN G 36 " model vdw 2.330 3.120 nonbonded pdb=" OG1 THR C 426 " pdb=" OE1 GLU C 429 " model vdw 2.338 3.040 nonbonded pdb=" O ILE H 290 " pdb=" OG1 THR H 294 " model vdw 2.342 3.040 ... (remaining 78103 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.690 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.770 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 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 0.239 10793 Z= 0.179 Angle : 0.683 11.158 14622 Z= 0.335 Chirality : 0.040 0.169 1668 Planarity : 0.004 0.054 1872 Dihedral : 14.642 149.931 3844 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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: -0.22 (0.23), residues: 1347 helix: 1.40 (0.21), residues: 664 sheet: -0.59 (0.57), residues: 93 loop : -1.97 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 244 TYR 0.020 0.001 TYR H 223 PHE 0.022 0.001 PHE C 604 TRP 0.020 0.001 TRP H 165 HIS 0.007 0.001 HIS H 265 Details of bonding type rmsd covalent geometry : bond 0.00262 (10762) covalent geometry : angle 0.61906 (14590) hydrogen bonds : bond 0.15178 ( 536) hydrogen bonds : angle 5.58423 ( 1596) metal coordination : bond 0.09006 ( 28) metal coordination : angle 6.31816 ( 30) Misc. bond : bond 0.06553 ( 2) link_TRANS : bond 0.00898 ( 1) link_TRANS : angle 3.82434 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: C 310 MET cc_start: 0.7363 (mmt) cc_final: 0.7140 (mmt) outliers start: 0 outliers final: 1 residues processed: 160 average time/residue: 0.6450 time to fit residues: 110.0051 Evaluate side-chains 105 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 176 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 49 GLN R 81 ASN H 186 GLN H 240 GLN ** H 265 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 = 0.3728 r_free = 0.3728 target = 0.064283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.053376 restraints weight = 48987.557| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.23 r_work: 0.3294 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10793 Z= 0.166 Angle : 0.679 10.244 14622 Z= 0.331 Chirality : 0.042 0.210 1668 Planarity : 0.004 0.049 1872 Dihedral : 5.945 103.329 1477 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.61 % Allowed : 8.73 % Favored : 89.66 % 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: -0.09 (0.23), residues: 1347 helix: 1.44 (0.21), residues: 677 sheet: -0.10 (0.60), residues: 84 loop : -1.96 (0.23), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 768 TYR 0.029 0.002 TYR C 233 PHE 0.021 0.002 PHE C 604 TRP 0.013 0.002 TRP G 35 HIS 0.005 0.001 HIS H 222 Details of bonding type rmsd covalent geometry : bond 0.00392 (10762) covalent geometry : angle 0.64974 (14590) hydrogen bonds : bond 0.05090 ( 536) hydrogen bonds : angle 4.45717 ( 1596) metal coordination : bond 0.01281 ( 28) metal coordination : angle 4.41837 ( 30) Misc. bond : bond 0.00085 ( 2) link_TRANS : bond 0.00172 ( 1) link_TRANS : angle 0.03794 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: N 31 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8213 (mm-30) REVERT: N 46 SER cc_start: 0.8729 (OUTLIER) cc_final: 0.8447 (p) REVERT: R 79 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7893 (mm-30) REVERT: R 107 VAL cc_start: 0.9213 (m) cc_final: 0.8802 (m) REVERT: G 22 PHE cc_start: 0.5986 (t80) cc_final: 0.5590 (t80) REVERT: C 326 MET cc_start: 0.8686 (tpp) cc_final: 0.8427 (mmm) REVERT: C 733 GLN cc_start: 0.8670 (tp-100) cc_final: 0.8405 (tp-100) REVERT: H 121 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8163 (mpt-90) REVERT: H 325 MET cc_start: 0.7342 (OUTLIER) cc_final: 0.6997 (ppp) outliers start: 17 outliers final: 4 residues processed: 123 average time/residue: 0.5803 time to fit residues: 76.9851 Evaluate side-chains 106 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 46 SER Chi-restraints excluded: chain U residue 61 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain H residue 121 ARG Chi-restraints excluded: chain H residue 325 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 25 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 108 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 117 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 49 GLN C 225 ASN C 646 GLN C 731 ASN H 250 ASN ** H 265 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 = 0.3700 r_free = 0.3700 target = 0.063261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.052049 restraints weight = 49082.340| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.31 r_work: 0.3253 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10793 Z= 0.193 Angle : 0.681 10.672 14622 Z= 0.330 Chirality : 0.042 0.196 1668 Planarity : 0.004 0.051 1872 Dihedral : 4.697 57.541 1477 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.09 % Allowed : 11.57 % Favored : 86.34 % 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 (0.23), residues: 1347 helix: 1.51 (0.20), residues: 676 sheet: -0.54 (0.57), residues: 98 loop : -1.90 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 768 TYR 0.035 0.002 TYR C 233 PHE 0.020 0.002 PHE C 604 TRP 0.024 0.002 TRP G 35 HIS 0.008 0.001 HIS H 222 Details of bonding type rmsd covalent geometry : bond 0.00458 (10762) covalent geometry : angle 0.64663 (14590) hydrogen bonds : bond 0.05141 ( 536) hydrogen bonds : angle 4.37738 ( 1596) metal coordination : bond 0.01371 ( 28) metal coordination : angle 4.78236 ( 30) Misc. bond : bond 0.00070 ( 2) link_TRANS : bond 0.00168 ( 1) link_TRANS : angle 0.32431 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: N 46 SER cc_start: 0.8820 (OUTLIER) cc_final: 0.8541 (p) REVERT: R 31 SER cc_start: 0.9081 (m) cc_final: 0.8785 (t) REVERT: R 79 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7912 (mm-30) REVERT: C 733 GLN cc_start: 0.8785 (tp-100) cc_final: 0.8443 (tp-100) REVERT: H 121 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8243 (mpt-90) REVERT: H 325 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6964 (ppp) outliers start: 22 outliers final: 9 residues processed: 114 average time/residue: 0.4896 time to fit residues: 61.1503 Evaluate side-chains 109 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 46 SER Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 61 ILE Chi-restraints excluded: chain G residue 22 PHE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain H residue 121 ARG Chi-restraints excluded: chain H residue 325 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 60 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 49 GLN ** H 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 447 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.062333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.051032 restraints weight = 49672.140| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.29 r_work: 0.3228 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10793 Z= 0.205 Angle : 0.704 11.397 14622 Z= 0.335 Chirality : 0.042 0.181 1668 Planarity : 0.004 0.049 1872 Dihedral : 4.521 40.705 1477 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.56 % Allowed : 12.24 % Favored : 85.20 % 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 (0.23), residues: 1347 helix: 1.48 (0.20), residues: 676 sheet: 0.23 (0.59), residues: 89 loop : -1.98 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 768 TYR 0.030 0.002 TYR C 233 PHE 0.016 0.002 PHE C 604 TRP 0.017 0.002 TRP H 165 HIS 0.009 0.001 HIS H 222 Details of bonding type rmsd covalent geometry : bond 0.00490 (10762) covalent geometry : angle 0.66351 (14590) hydrogen bonds : bond 0.05199 ( 536) hydrogen bonds : angle 4.27697 ( 1596) metal coordination : bond 0.01437 ( 28) metal coordination : angle 5.21375 ( 30) Misc. bond : bond 0.00030 ( 2) link_TRANS : bond 0.00133 ( 1) link_TRANS : angle 0.13405 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: N 46 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8568 (p) REVERT: R 31 SER cc_start: 0.9015 (m) cc_final: 0.8778 (t) REVERT: R 79 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8043 (mm-30) REVERT: G 22 PHE cc_start: 0.6436 (t80) cc_final: 0.6194 (t80) REVERT: C 160 MET cc_start: 0.8345 (mmm) cc_final: 0.8057 (mmm) REVERT: C 733 GLN cc_start: 0.8880 (tp-100) cc_final: 0.8536 (tp-100) REVERT: H 121 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8307 (mpt-90) REVERT: H 325 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.6495 (ppp) outliers start: 27 outliers final: 7 residues processed: 114 average time/residue: 0.4583 time to fit residues: 56.9812 Evaluate side-chains 103 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 46 SER Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 61 ILE Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain H residue 121 ARG Chi-restraints excluded: chain H residue 325 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 40 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 288 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.062407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.051160 restraints weight = 49547.415| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.28 r_work: 0.3229 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10793 Z= 0.178 Angle : 0.678 11.597 14622 Z= 0.322 Chirality : 0.041 0.173 1668 Planarity : 0.004 0.050 1872 Dihedral : 4.351 31.059 1475 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.94 % Allowed : 13.76 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.23), residues: 1347 helix: 1.52 (0.20), residues: 677 sheet: -0.33 (0.56), residues: 103 loop : -1.93 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 244 TYR 0.026 0.002 TYR C 233 PHE 0.014 0.002 PHE C 365 TRP 0.019 0.002 TRP H 165 HIS 0.006 0.001 HIS H 222 Details of bonding type rmsd covalent geometry : bond 0.00425 (10762) covalent geometry : angle 0.64314 (14590) hydrogen bonds : bond 0.04873 ( 536) hydrogen bonds : angle 4.18018 ( 1596) metal coordination : bond 0.01236 ( 28) metal coordination : angle 4.77500 ( 30) Misc. bond : bond 0.00033 ( 2) link_TRANS : bond 0.00080 ( 1) link_TRANS : angle 0.06874 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 96 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 46 SER cc_start: 0.8906 (OUTLIER) cc_final: 0.8644 (p) REVERT: R 31 SER cc_start: 0.9001 (m) cc_final: 0.8754 (t) REVERT: R 104 GLN cc_start: 0.8651 (pm20) cc_final: 0.8388 (pm20) REVERT: C 733 GLN cc_start: 0.8884 (tp-100) cc_final: 0.8543 (tp-100) REVERT: H 121 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8268 (mpt-90) REVERT: H 325 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6510 (pmm) outliers start: 31 outliers final: 11 residues processed: 116 average time/residue: 0.3995 time to fit residues: 50.9690 Evaluate side-chains 107 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 46 SER Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain R residue 101 LEU Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 61 ILE Chi-restraints excluded: chain G residue 70 PHE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain H residue 121 ARG Chi-restraints excluded: chain H residue 270 CYS Chi-restraints excluded: chain H residue 325 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 111 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 18 optimal weight: 0.0170 chunk 108 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 129 optimal weight: 0.0170 chunk 103 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.5260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 491 ASN ** H 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.063250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.052091 restraints weight = 49200.366| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 3.26 r_work: 0.3263 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10793 Z= 0.118 Angle : 0.640 12.143 14622 Z= 0.305 Chirality : 0.039 0.154 1668 Planarity : 0.004 0.048 1872 Dihedral : 4.112 22.498 1475 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.90 % Allowed : 15.65 % Favored : 82.45 % 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: 0.21 (0.23), residues: 1347 helix: 1.76 (0.21), residues: 673 sheet: 0.04 (0.58), residues: 99 loop : -1.93 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 244 TYR 0.024 0.001 TYR C 233 PHE 0.026 0.001 PHE G 22 TRP 0.020 0.001 TRP H 165 HIS 0.003 0.001 HIS H 168 Details of bonding type rmsd covalent geometry : bond 0.00268 (10762) covalent geometry : angle 0.61555 (14590) hydrogen bonds : bond 0.04056 ( 536) hydrogen bonds : angle 3.91682 ( 1596) metal coordination : bond 0.00872 ( 28) metal coordination : angle 3.91724 ( 30) Misc. bond : bond 0.00027 ( 2) link_TRANS : bond 0.00031 ( 1) link_TRANS : angle 0.06761 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: N 46 SER cc_start: 0.8889 (OUTLIER) cc_final: 0.8640 (p) REVERT: R 31 SER cc_start: 0.8929 (m) cc_final: 0.8681 (t) REVERT: C 710 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8299 (tt) REVERT: C 733 GLN cc_start: 0.8871 (tp-100) cc_final: 0.8554 (tp-100) REVERT: H 235 MET cc_start: 0.7846 (mmm) cc_final: 0.7638 (mmm) REVERT: H 325 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6739 (ppp) outliers start: 20 outliers final: 10 residues processed: 108 average time/residue: 0.4121 time to fit residues: 49.0968 Evaluate side-chains 107 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 46 SER Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 61 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain H residue 270 CYS Chi-restraints excluded: chain H residue 325 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 47 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 131 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 85 optimal weight: 0.0670 chunk 117 optimal weight: 3.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 78 ASN ** H 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.062902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.051640 restraints weight = 49739.938| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.29 r_work: 0.3251 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10793 Z= 0.143 Angle : 0.662 12.210 14622 Z= 0.313 Chirality : 0.040 0.156 1668 Planarity : 0.004 0.050 1872 Dihedral : 4.096 20.239 1475 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.09 % Allowed : 16.32 % Favored : 81.59 % 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: 0.21 (0.23), residues: 1347 helix: 1.74 (0.21), residues: 674 sheet: -0.28 (0.54), residues: 113 loop : -1.86 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 244 TYR 0.021 0.001 TYR C 233 PHE 0.023 0.002 PHE G 22 TRP 0.018 0.001 TRP H 165 HIS 0.004 0.001 HIS H 222 Details of bonding type rmsd covalent geometry : bond 0.00336 (10762) covalent geometry : angle 0.63464 (14590) hydrogen bonds : bond 0.04281 ( 536) hydrogen bonds : angle 3.90197 ( 1596) metal coordination : bond 0.01017 ( 28) metal coordination : angle 4.22138 ( 30) Misc. bond : bond 0.00023 ( 2) link_TRANS : bond 0.00078 ( 1) link_TRANS : angle 0.08040 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: N 46 SER cc_start: 0.8788 (OUTLIER) cc_final: 0.8541 (p) REVERT: R 31 SER cc_start: 0.8900 (m) cc_final: 0.8655 (t) REVERT: G 22 PHE cc_start: 0.6597 (t80) cc_final: 0.6294 (t80) REVERT: G 25 ILE cc_start: 0.8249 (pp) cc_final: 0.8008 (mm) REVERT: C 710 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8345 (tt) REVERT: C 733 GLN cc_start: 0.8934 (tp-100) cc_final: 0.8631 (tp-100) REVERT: H 77 MET cc_start: 0.8173 (ttp) cc_final: 0.7967 (tmm) REVERT: H 325 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6629 (ppp) outliers start: 22 outliers final: 12 residues processed: 107 average time/residue: 0.4489 time to fit residues: 53.0148 Evaluate side-chains 106 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 46 SER Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 61 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 270 CYS Chi-restraints excluded: chain H residue 303 CYS Chi-restraints excluded: chain H residue 325 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 105 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.063066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.051776 restraints weight = 49395.630| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.27 r_work: 0.3255 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10793 Z= 0.134 Angle : 0.668 12.788 14622 Z= 0.317 Chirality : 0.040 0.167 1668 Planarity : 0.004 0.048 1872 Dihedral : 4.042 19.212 1475 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.99 % Allowed : 17.08 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.23), residues: 1347 helix: 1.77 (0.21), residues: 673 sheet: -0.29 (0.54), residues: 108 loop : -1.94 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 29 TYR 0.022 0.001 TYR C 233 PHE 0.022 0.001 PHE G 22 TRP 0.018 0.001 TRP H 165 HIS 0.003 0.001 HIS H 222 Details of bonding type rmsd covalent geometry : bond 0.00315 (10762) covalent geometry : angle 0.64350 (14590) hydrogen bonds : bond 0.04114 ( 536) hydrogen bonds : angle 3.85841 ( 1596) metal coordination : bond 0.00924 ( 28) metal coordination : angle 4.00646 ( 30) Misc. bond : bond 0.00018 ( 2) link_TRANS : bond 0.00031 ( 1) link_TRANS : angle 0.04386 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.314 Fit side-chains REVERT: N 46 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8527 (p) REVERT: R 31 SER cc_start: 0.8893 (m) cc_final: 0.8635 (t) REVERT: G 22 PHE cc_start: 0.6448 (t80) cc_final: 0.6040 (t80) REVERT: G 25 ILE cc_start: 0.8329 (pp) cc_final: 0.8017 (mm) REVERT: C 710 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8329 (tt) REVERT: C 733 GLN cc_start: 0.8914 (tp-100) cc_final: 0.8636 (tp-100) REVERT: H 77 MET cc_start: 0.8167 (ttp) cc_final: 0.7967 (tmm) REVERT: H 325 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.6441 (ppp) outliers start: 21 outliers final: 13 residues processed: 107 average time/residue: 0.4398 time to fit residues: 51.8372 Evaluate side-chains 108 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 46 SER Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 58 ASP Chi-restraints excluded: chain U residue 61 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain H residue 143 MET Chi-restraints excluded: chain H residue 270 CYS Chi-restraints excluded: chain H residue 303 CYS Chi-restraints excluded: chain H residue 325 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 102 optimal weight: 5.9990 chunk 108 optimal weight: 0.4980 chunk 95 optimal weight: 0.0670 chunk 133 optimal weight: 5.9990 chunk 94 optimal weight: 0.0770 chunk 36 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 320 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.063878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.052717 restraints weight = 49490.021| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.27 r_work: 0.3287 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10793 Z= 0.111 Angle : 0.653 12.712 14622 Z= 0.310 Chirality : 0.039 0.165 1668 Planarity : 0.004 0.049 1872 Dihedral : 3.931 19.028 1475 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.42 % Allowed : 18.12 % Favored : 80.46 % 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: 0.29 (0.23), residues: 1347 helix: 1.86 (0.21), residues: 674 sheet: -0.31 (0.54), residues: 108 loop : -1.88 (0.23), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 29 TYR 0.023 0.001 TYR U 59 PHE 0.019 0.001 PHE G 22 TRP 0.021 0.001 TRP H 165 HIS 0.004 0.001 HIS H 168 Details of bonding type rmsd covalent geometry : bond 0.00247 (10762) covalent geometry : angle 0.63569 (14590) hydrogen bonds : bond 0.03656 ( 536) hydrogen bonds : angle 3.74376 ( 1596) metal coordination : bond 0.00722 ( 28) metal coordination : angle 3.36328 ( 30) Misc. bond : bond 0.00013 ( 2) link_TRANS : bond 0.00066 ( 1) link_TRANS : angle 0.11615 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.467 Fit side-chains REVERT: N 46 SER cc_start: 0.8762 (OUTLIER) cc_final: 0.8521 (p) REVERT: R 31 SER cc_start: 0.8843 (m) cc_final: 0.8585 (t) REVERT: G 22 PHE cc_start: 0.6254 (t80) cc_final: 0.5799 (t80) REVERT: G 25 ILE cc_start: 0.8218 (pp) cc_final: 0.7841 (mm) REVERT: C 414 MET cc_start: 0.8147 (mtt) cc_final: 0.7893 (mtt) REVERT: C 710 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8322 (tt) REVERT: C 733 GLN cc_start: 0.8936 (tp-100) cc_final: 0.8648 (tp-100) REVERT: H 77 MET cc_start: 0.8126 (ttp) cc_final: 0.7924 (tmm) REVERT: H 325 MET cc_start: 0.7017 (OUTLIER) cc_final: 0.6787 (pmt) outliers start: 15 outliers final: 9 residues processed: 102 average time/residue: 0.4740 time to fit residues: 53.3614 Evaluate side-chains 103 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 46 SER Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 13 ILE Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 61 ILE Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain H residue 270 CYS Chi-restraints excluded: chain H residue 325 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 61 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.061851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.050481 restraints weight = 49478.902| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.27 r_work: 0.3213 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 10793 Z= 0.217 Angle : 0.759 13.702 14622 Z= 0.361 Chirality : 0.043 0.234 1668 Planarity : 0.004 0.048 1872 Dihedral : 4.266 19.858 1475 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.52 % Allowed : 18.79 % Favored : 79.70 % 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: 0.07 (0.23), residues: 1347 helix: 1.63 (0.21), residues: 672 sheet: -0.24 (0.53), residues: 114 loop : -1.98 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 244 TYR 0.024 0.002 TYR C 233 PHE 0.020 0.002 PHE G 22 TRP 0.015 0.002 TRP G 35 HIS 0.007 0.001 HIS H 222 Details of bonding type rmsd covalent geometry : bond 0.00518 (10762) covalent geometry : angle 0.72222 (14590) hydrogen bonds : bond 0.05168 ( 536) hydrogen bonds : angle 4.10546 ( 1596) metal coordination : bond 0.01526 ( 28) metal coordination : angle 5.23150 ( 30) Misc. bond : bond 0.00013 ( 2) link_TRANS : bond 0.00105 ( 1) link_TRANS : angle 0.01906 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2694 Ramachandran restraints generated. 1347 Oldfield, 0 Emsley, 1347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.446 Fit side-chains REVERT: N 46 SER cc_start: 0.8697 (OUTLIER) cc_final: 0.8474 (p) REVERT: R 31 SER cc_start: 0.8883 (m) cc_final: 0.8608 (t) REVERT: G 13 GLU cc_start: 0.7876 (pp20) cc_final: 0.7548 (pm20) REVERT: C 710 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8342 (tt) REVERT: C 733 GLN cc_start: 0.8988 (tp-100) cc_final: 0.8685 (tp-100) REVERT: H 77 MET cc_start: 0.8197 (ttp) cc_final: 0.7973 (tmm) REVERT: H 325 MET cc_start: 0.7165 (OUTLIER) cc_final: 0.6543 (ppp) outliers start: 16 outliers final: 12 residues processed: 100 average time/residue: 0.4662 time to fit residues: 51.3875 Evaluate side-chains 106 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 46 SER Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 61 ILE Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 655 ASN Chi-restraints excluded: chain C residue 710 LEU Chi-restraints excluded: chain H residue 143 MET Chi-restraints excluded: chain H residue 270 CYS Chi-restraints excluded: chain H residue 303 CYS Chi-restraints excluded: chain H residue 313 MET Chi-restraints excluded: chain H residue 325 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 103 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 37 optimal weight: 0.1980 chunk 112 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.062740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.051524 restraints weight = 49475.486| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.25 r_work: 0.3246 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10793 Z= 0.145 Angle : 0.695 13.165 14622 Z= 0.330 Chirality : 0.041 0.269 1668 Planarity : 0.004 0.048 1872 Dihedral : 4.150 20.068 1475 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.52 % Allowed : 18.69 % Favored : 79.79 % 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 (0.23), residues: 1347 helix: 1.75 (0.21), residues: 672 sheet: -0.47 (0.51), residues: 123 loop : -1.90 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 244 TYR 0.023 0.002 TYR C 233 PHE 0.015 0.001 PHE G 70 TRP 0.018 0.001 TRP H 165 HIS 0.004 0.001 HIS H 222 Details of bonding type rmsd covalent geometry : bond 0.00338 (10762) covalent geometry : angle 0.66775 (14590) hydrogen bonds : bond 0.04343 ( 536) hydrogen bonds : angle 3.92849 ( 1596) metal coordination : bond 0.01090 ( 28) metal coordination : angle 4.29955 ( 30) Misc. bond : bond 0.00017 ( 2) link_TRANS : bond 0.00075 ( 1) link_TRANS : angle 0.07293 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3364.80 seconds wall clock time: 58 minutes 1.75 seconds (3481.75 seconds total)