Starting phenix.real_space_refine on Sun Jul 5 03:37:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7phk_13418/07_2026/7phk_13418.cif Found real_map, /net/cci-nas-00/data/ceres_data/7phk_13418/07_2026/7phk_13418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7phk_13418/07_2026/7phk_13418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7phk_13418/07_2026/7phk_13418.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7phk_13418/07_2026/7phk_13418.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7phk_13418/07_2026/7phk_13418.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7phk_13418/07_2026/7phk_13418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7phk_13418/07_2026/7phk_13418.map" } resolution = 3.1 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= 0.006 sd= 0.057 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 K 8 8.98 5 Zn 8 6.06 5 P 16 5.49 5 S 136 5.16 5 C 16648 2.51 5 N 4216 2.21 5 O 4372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25404 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3095 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 21, 'TRANS': 370} Chain breaks: 3 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3095 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 21, 'TRANS': 370} Chain breaks: 3 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3095 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 21, 'TRANS': 370} Chain breaks: 3 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 75 Chain: "D" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3095 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 21, 'TRANS': 370} Chain breaks: 3 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 75 Chain: "E" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3098 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 22, 'TRANS': 370} Chain breaks: 3 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 75 Chain: "G" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3098 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 22, 'TRANS': 370} Chain breaks: 3 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 75 Chain: "F" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3098 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 22, 'TRANS': 370} Chain breaks: 3 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 75 Chain: "H" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3098 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 22, 'TRANS': 370} Chain breaks: 3 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 75 Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 82 Unusual residues: {' K': 4, ' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "B" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "D" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "E" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 82 Unusual residues: {' K': 4, ' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "G" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "F" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "H" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 798 SG CYS A 104 77.866 68.367 155.359 1.00107.92 S ATOM 804 SG CYS A 105 77.166 65.043 154.127 1.00105.62 S ATOM 6819 SG CYS B 83 74.366 66.914 153.257 1.00103.76 S ATOM 3893 SG CYS C 104 49.706 59.250 155.299 1.00107.92 S ATOM 3899 SG CYS C 105 50.414 62.572 154.065 1.00105.62 S ATOM 9914 SG CYS D 83 53.218 60.823 153.289 1.00103.76 S ATOM 3724 SG CYS C 83 60.743 74.324 153.224 1.00103.76 S ATOM 6988 SG CYS B 104 59.224 77.865 155.286 1.00107.92 S ATOM 6994 SG CYS B 105 62.552 77.175 154.059 1.00105.62 S ATOM 629 SG CYS A 83 66.867 53.263 153.309 1.00103.76 S ATOM 10083 SG CYS D 104 68.302 49.795 155.335 1.00107.92 S ATOM 10089 SG CYS D 105 64.978 50.501 154.105 1.00105.62 S ATOM 13178 SG CYS E 104 77.957 68.173 76.846 1.00107.92 S ATOM 13184 SG CYS E 105 75.487 70.505 78.080 1.00105.62 S ATOM 19205 SG CYS F 83 74.184 67.403 78.945 1.00103.76 S ATOM 16276 SG CYS G 104 49.742 59.485 76.913 1.00107.92 S ATOM 16282 SG CYS G 105 52.231 57.172 78.143 1.00105.62 S ATOM 22303 SG CYS H 83 53.576 60.290 78.918 1.00103.76 S ATOM 16107 SG CYS G 83 67.439 53.487 78.956 1.00103.76 S ATOM 19374 SG CYS F 104 68.180 49.708 76.898 1.00107.92 S ATOM 19380 SG CYS F 105 70.495 52.197 78.127 1.00105.62 S ATOM 13009 SG CYS E 83 60.309 74.305 78.915 1.00103.76 S ATOM 22472 SG CYS H 104 59.488 78.014 76.865 1.00107.92 S ATOM 22478 SG CYS H 105 57.187 75.514 78.096 1.00105.62 S Time building chain proxies: 5.62, per 1000 atoms: 0.22 Number of scatterers: 25404 At special positions: 0 Unit cell: (128.52, 128.52, 233.52, 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 8 29.99 K 8 19.00 S 136 16.00 P 16 15.00 O 4372 8.00 N 4216 7.00 C 16648 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: 2.25 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 603 " pdb="ZN ZN A 603 " - pdb=" ND1 HIS A 77 " pdb="ZN ZN A 603 " - pdb=" SG CYS B 83 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 104 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 105 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" ND1 HIS B 77 " pdb="ZN ZN B 601 " - pdb=" SG CYS C 83 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 104 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 105 " pdb=" ZN C 603 " pdb="ZN ZN C 603 " - pdb=" ND1 HIS C 77 " pdb="ZN ZN C 603 " - pdb=" SG CYS D 83 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 104 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 105 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" ND1 HIS D 77 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 104 " pdb="ZN ZN D 601 " - pdb=" SG CYS A 83 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 105 " pdb=" ZN E 603 " pdb="ZN ZN E 603 " - pdb=" ND1 HIS E 77 " pdb="ZN ZN E 603 " - pdb=" SG CYS F 83 " pdb="ZN ZN E 603 " - pdb=" SG CYS E 104 " pdb="ZN ZN E 603 " - pdb=" SG CYS E 105 " pdb=" ZN F 601 " pdb="ZN ZN F 601 " - pdb=" ND1 HIS F 77 " pdb="ZN ZN F 601 " - pdb=" SG CYS G 83 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 104 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 105 " pdb=" ZN G 603 " pdb="ZN ZN G 603 " - pdb=" ND1 HIS G 77 " pdb="ZN ZN G 603 " - pdb=" SG CYS H 83 " pdb="ZN ZN G 603 " - pdb=" SG CYS G 104 " pdb="ZN ZN G 603 " - pdb=" SG CYS G 105 " pdb=" ZN H 601 " pdb="ZN ZN H 601 " - pdb=" ND1 HIS H 77 " pdb="ZN ZN H 601 " - pdb=" SG CYS E 83 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 104 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 105 " Number of angles added : 24 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5944 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 16 sheets defined 71.1% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 32 through 39 removed outlier: 3.580A pdb=" N GLU A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 74 removed outlier: 3.597A pdb=" N PHE A 64 " --> pdb=" O HIS A 60 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N HIS A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 95 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.622A pdb=" N ASP A 100 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 101 " --> pdb=" O GLU A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.662A pdb=" N TYR A 109 " --> pdb=" O CYS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 119 Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 182 through 185 Processing helix chain 'A' and resid 186 through 211 removed outlier: 3.840A pdb=" N ARG A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 266 removed outlier: 3.724A pdb=" N THR A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE A 266 " --> pdb=" O MET A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 276 Processing helix chain 'A' and resid 276 through 295 Proline residue: A 288 - end of helix removed outlier: 3.812A pdb=" N GLU A 292 " --> pdb=" O PRO A 288 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL A 293 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLY A 294 " --> pdb=" O TYR A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 315 removed outlier: 3.885A pdb=" N ASP A 305 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 319 Processing helix chain 'A' and resid 320 through 326 removed outlier: 3.990A pdb=" N LEU A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 341 removed outlier: 3.676A pdb=" N ARG A 332 " --> pdb=" O PHE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 367 Processing helix chain 'A' and resid 386 through 399 removed outlier: 3.580A pdb=" N GLY A 390 " --> pdb=" O ASN A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 430 Processing helix chain 'A' and resid 431 through 452 Processing helix chain 'C' and resid 23 through 28 Processing helix chain 'C' and resid 32 through 39 removed outlier: 3.580A pdb=" N GLU C 39 " --> pdb=" O ALA C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 74 removed outlier: 3.598A pdb=" N PHE C 64 " --> pdb=" O HIS C 60 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HIS C 66 " --> pdb=" O GLY C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 95 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.621A pdb=" N ASP C 100 " --> pdb=" O ASP C 97 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL C 101 " --> pdb=" O GLU C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 105 through 110 removed outlier: 3.660A pdb=" N TYR C 109 " --> pdb=" O CYS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 119 Processing helix chain 'C' and resid 172 through 178 Processing helix chain 'C' and resid 182 through 185 Processing helix chain 'C' and resid 186 through 211 removed outlier: 3.840A pdb=" N ARG C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 266 removed outlier: 3.724A pdb=" N THR C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE C 266 " --> pdb=" O MET C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 276 Processing helix chain 'C' and resid 276 through 295 Proline residue: C 288 - end of helix removed outlier: 3.812A pdb=" N GLU C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL C 293 " --> pdb=" O PHE C 289 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY C 294 " --> pdb=" O TYR C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 315 removed outlier: 3.885A pdb=" N ASP C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 319 Processing helix chain 'C' and resid 320 through 326 removed outlier: 3.990A pdb=" N LEU C 324 " --> pdb=" O ARG C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 341 removed outlier: 3.676A pdb=" N ARG C 332 " --> pdb=" O PHE C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 367 Processing helix chain 'C' and resid 386 through 399 removed outlier: 3.581A pdb=" N GLY C 390 " --> pdb=" O ASN C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 430 Processing helix chain 'C' and resid 431 through 452 Processing helix chain 'B' and resid 23 through 28 Processing helix chain 'B' and resid 32 through 39 removed outlier: 3.580A pdb=" N GLU B 39 " --> pdb=" O ALA B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 74 removed outlier: 3.597A pdb=" N PHE B 64 " --> pdb=" O HIS B 60 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HIS B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 95 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.621A pdb=" N ASP B 100 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL B 101 " --> pdb=" O GLU B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 105 through 110 removed outlier: 3.661A pdb=" N TYR B 109 " --> pdb=" O CYS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 119 Processing helix chain 'B' and resid 172 through 178 Processing helix chain 'B' and resid 182 through 185 Processing helix chain 'B' and resid 186 through 211 removed outlier: 3.839A pdb=" N ARG B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 266 removed outlier: 3.724A pdb=" N THR B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE B 266 " --> pdb=" O MET B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 276 through 295 Proline residue: B 288 - end of helix removed outlier: 3.811A pdb=" N GLU B 292 " --> pdb=" O PRO B 288 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY B 294 " --> pdb=" O TYR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 315 removed outlier: 3.885A pdb=" N ASP B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 319 Processing helix chain 'B' and resid 320 through 326 removed outlier: 3.991A pdb=" N LEU B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 341 removed outlier: 3.675A pdb=" N ARG B 332 " --> pdb=" O PHE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 367 Processing helix chain 'B' and resid 386 through 399 removed outlier: 3.580A pdb=" N GLY B 390 " --> pdb=" O ASN B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 430 Processing helix chain 'B' and resid 431 through 452 Processing helix chain 'D' and resid 23 through 28 Processing helix chain 'D' and resid 32 through 39 removed outlier: 3.579A pdb=" N GLU D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 74 removed outlier: 3.597A pdb=" N PHE D 64 " --> pdb=" O HIS D 60 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HIS D 66 " --> pdb=" O GLY D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 95 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.621A pdb=" N ASP D 100 " --> pdb=" O ASP D 97 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL D 101 " --> pdb=" O GLU D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 102 through 104 No H-bonds generated for 'chain 'D' and resid 102 through 104' Processing helix chain 'D' and resid 105 through 110 removed outlier: 3.661A pdb=" N TYR D 109 " --> pdb=" O CYS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 172 through 178 Processing helix chain 'D' and resid 182 through 185 Processing helix chain 'D' and resid 186 through 211 removed outlier: 3.839A pdb=" N ARG D 190 " --> pdb=" O SER D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 266 removed outlier: 3.724A pdb=" N THR D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE D 266 " --> pdb=" O MET D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 276 Processing helix chain 'D' and resid 276 through 295 Proline residue: D 288 - end of helix removed outlier: 3.811A pdb=" N GLU D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL D 293 " --> pdb=" O PHE D 289 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY D 294 " --> pdb=" O TYR D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 315 removed outlier: 3.885A pdb=" N ASP D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 319 Processing helix chain 'D' and resid 320 through 326 removed outlier: 3.991A pdb=" N LEU D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 341 removed outlier: 3.676A pdb=" N ARG D 332 " --> pdb=" O PHE D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 367 Processing helix chain 'D' and resid 386 through 399 removed outlier: 3.581A pdb=" N GLY D 390 " --> pdb=" O ASN D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 430 Processing helix chain 'D' and resid 431 through 452 Processing helix chain 'E' and resid 23 through 28 Processing helix chain 'E' and resid 32 through 39 removed outlier: 3.579A pdb=" N GLU E 39 " --> pdb=" O ALA E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 74 removed outlier: 3.598A pdb=" N PHE E 64 " --> pdb=" O HIS E 60 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HIS E 66 " --> pdb=" O GLY E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 95 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.622A pdb=" N ASP E 100 " --> pdb=" O ASP E 97 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL E 101 " --> pdb=" O GLU E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 102 through 104 No H-bonds generated for 'chain 'E' and resid 102 through 104' Processing helix chain 'E' and resid 105 through 110 removed outlier: 3.662A pdb=" N TYR E 109 " --> pdb=" O CYS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 119 Processing helix chain 'E' and resid 172 through 178 Processing helix chain 'E' and resid 182 through 185 Processing helix chain 'E' and resid 186 through 211 removed outlier: 3.841A pdb=" N ARG E 190 " --> pdb=" O SER E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 266 removed outlier: 3.724A pdb=" N THR E 246 " --> pdb=" O GLU E 242 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE E 266 " --> pdb=" O MET E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 276 Processing helix chain 'E' and resid 276 through 295 Proline residue: E 288 - end of helix removed outlier: 3.812A pdb=" N GLU E 292 " --> pdb=" O PRO E 288 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL E 293 " --> pdb=" O PHE E 289 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY E 294 " --> pdb=" O TYR E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 315 removed outlier: 3.884A pdb=" N ASP E 305 " --> pdb=" O LYS E 301 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL E 312 " --> pdb=" O GLY E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 319 Processing helix chain 'E' and resid 320 through 326 removed outlier: 3.991A pdb=" N LEU E 324 " --> pdb=" O ARG E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 341 removed outlier: 3.675A pdb=" N ARG E 332 " --> pdb=" O PHE E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 367 Processing helix chain 'E' and resid 386 through 399 removed outlier: 3.581A pdb=" N GLY E 390 " --> pdb=" O ASN E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 430 Processing helix chain 'E' and resid 431 through 452 Processing helix chain 'G' and resid 23 through 28 Processing helix chain 'G' and resid 32 through 39 removed outlier: 3.579A pdb=" N GLU G 39 " --> pdb=" O ALA G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 74 removed outlier: 3.598A pdb=" N PHE G 64 " --> pdb=" O HIS G 60 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HIS G 66 " --> pdb=" O GLY G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 95 Processing helix chain 'G' and resid 97 through 101 removed outlier: 3.621A pdb=" N ASP G 100 " --> pdb=" O ASP G 97 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL G 101 " --> pdb=" O GLU G 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 97 through 101' Processing helix chain 'G' and resid 102 through 104 No H-bonds generated for 'chain 'G' and resid 102 through 104' Processing helix chain 'G' and resid 105 through 110 removed outlier: 3.661A pdb=" N TYR G 109 " --> pdb=" O CYS G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 119 Processing helix chain 'G' and resid 172 through 178 Processing helix chain 'G' and resid 182 through 185 Processing helix chain 'G' and resid 186 through 211 removed outlier: 3.840A pdb=" N ARG G 190 " --> pdb=" O SER G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 242 through 266 removed outlier: 3.724A pdb=" N THR G 246 " --> pdb=" O GLU G 242 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE G 266 " --> pdb=" O MET G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 276 Processing helix chain 'G' and resid 276 through 295 Proline residue: G 288 - end of helix removed outlier: 3.811A pdb=" N GLU G 292 " --> pdb=" O PRO G 288 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL G 293 " --> pdb=" O PHE G 289 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLY G 294 " --> pdb=" O TYR G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 315 removed outlier: 3.884A pdb=" N ASP G 305 " --> pdb=" O LYS G 301 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL G 312 " --> pdb=" O GLY G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 316 through 319 Processing helix chain 'G' and resid 320 through 326 removed outlier: 3.991A pdb=" N LEU G 324 " --> pdb=" O ARG G 320 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 341 removed outlier: 3.676A pdb=" N ARG G 332 " --> pdb=" O PHE G 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 341 through 367 Processing helix chain 'G' and resid 386 through 399 removed outlier: 3.581A pdb=" N GLY G 390 " --> pdb=" O ASN G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 410 through 430 Processing helix chain 'G' and resid 431 through 452 Processing helix chain 'F' and resid 23 through 28 Processing helix chain 'F' and resid 32 through 39 removed outlier: 3.580A pdb=" N GLU F 39 " --> pdb=" O ALA F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 74 removed outlier: 3.598A pdb=" N PHE F 64 " --> pdb=" O HIS F 60 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HIS F 66 " --> pdb=" O GLY F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 95 Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.622A pdb=" N ASP F 100 " --> pdb=" O ASP F 97 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL F 101 " --> pdb=" O GLU F 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 97 through 101' Processing helix chain 'F' and resid 102 through 104 No H-bonds generated for 'chain 'F' and resid 102 through 104' Processing helix chain 'F' and resid 105 through 110 removed outlier: 3.661A pdb=" N TYR F 109 " --> pdb=" O CYS F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 119 Processing helix chain 'F' and resid 172 through 178 Processing helix chain 'F' and resid 182 through 185 Processing helix chain 'F' and resid 186 through 211 removed outlier: 3.840A pdb=" N ARG F 190 " --> pdb=" O SER F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 266 removed outlier: 3.725A pdb=" N THR F 246 " --> pdb=" O GLU F 242 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE F 266 " --> pdb=" O MET F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 276 Processing helix chain 'F' and resid 276 through 295 Proline residue: F 288 - end of helix removed outlier: 3.812A pdb=" N GLU F 292 " --> pdb=" O PRO F 288 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL F 293 " --> pdb=" O PHE F 289 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY F 294 " --> pdb=" O TYR F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 315 removed outlier: 3.885A pdb=" N ASP F 305 " --> pdb=" O LYS F 301 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL F 312 " --> pdb=" O GLY F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 319 Processing helix chain 'F' and resid 320 through 326 removed outlier: 3.990A pdb=" N LEU F 324 " --> pdb=" O ARG F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 341 removed outlier: 3.676A pdb=" N ARG F 332 " --> pdb=" O PHE F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 367 Processing helix chain 'F' and resid 386 through 399 removed outlier: 3.581A pdb=" N GLY F 390 " --> pdb=" O ASN F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 430 Processing helix chain 'F' and resid 431 through 452 Processing helix chain 'H' and resid 23 through 28 Processing helix chain 'H' and resid 32 through 39 removed outlier: 3.579A pdb=" N GLU H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 74 removed outlier: 3.598A pdb=" N PHE H 64 " --> pdb=" O HIS H 60 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N HIS H 66 " --> pdb=" O GLY H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 95 Processing helix chain 'H' and resid 97 through 101 removed outlier: 3.621A pdb=" N ASP H 100 " --> pdb=" O ASP H 97 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL H 101 " --> pdb=" O GLU H 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 97 through 101' Processing helix chain 'H' and resid 102 through 104 No H-bonds generated for 'chain 'H' and resid 102 through 104' Processing helix chain 'H' and resid 105 through 110 removed outlier: 3.662A pdb=" N TYR H 109 " --> pdb=" O CYS H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 119 Processing helix chain 'H' and resid 172 through 178 Processing helix chain 'H' and resid 182 through 185 Processing helix chain 'H' and resid 186 through 211 removed outlier: 3.840A pdb=" N ARG H 190 " --> pdb=" O SER H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 242 through 266 removed outlier: 3.724A pdb=" N THR H 246 " --> pdb=" O GLU H 242 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE H 266 " --> pdb=" O MET H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 276 Processing helix chain 'H' and resid 276 through 295 Proline residue: H 288 - end of helix removed outlier: 3.811A pdb=" N GLU H 292 " --> pdb=" O PRO H 288 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL H 293 " --> pdb=" O PHE H 289 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY H 294 " --> pdb=" O TYR H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 315 removed outlier: 3.885A pdb=" N ASP H 305 " --> pdb=" O LYS H 301 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL H 312 " --> pdb=" O GLY H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 316 through 319 Processing helix chain 'H' and resid 320 through 326 removed outlier: 3.990A pdb=" N LEU H 324 " --> pdb=" O ARG H 320 " (cutoff:3.500A) Processing helix chain 'H' and resid 328 through 341 removed outlier: 3.675A pdb=" N ARG H 332 " --> pdb=" O PHE H 328 " (cutoff:3.500A) Processing helix chain 'H' and resid 341 through 367 Processing helix chain 'H' and resid 386 through 399 removed outlier: 3.581A pdb=" N GLY H 390 " --> pdb=" O ASN H 386 " (cutoff:3.500A) Processing helix chain 'H' and resid 410 through 430 Processing helix chain 'H' and resid 431 through 452 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 22 removed outlier: 3.690A pdb=" N GLU A 54 " --> pdb=" O ASP A 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 218 through 221 removed outlier: 3.754A pdb=" N GLU A 238 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 17 through 22 removed outlier: 3.689A pdb=" N GLU C 54 " --> pdb=" O ASP C 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 218 through 221 removed outlier: 3.754A pdb=" N GLU C 238 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 17 through 22 removed outlier: 3.690A pdb=" N GLU B 54 " --> pdb=" O ASP B 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 218 through 221 removed outlier: 3.753A pdb=" N GLU B 238 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 17 through 22 removed outlier: 3.690A pdb=" N GLU D 54 " --> pdb=" O ASP D 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 218 through 221 removed outlier: 3.754A pdb=" N GLU D 238 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 17 through 22 removed outlier: 3.690A pdb=" N GLU E 54 " --> pdb=" O ASP E 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 218 through 221 removed outlier: 3.753A pdb=" N GLU E 238 " --> pdb=" O VAL E 219 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 17 through 22 removed outlier: 3.689A pdb=" N GLU G 54 " --> pdb=" O ASP G 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 218 through 221 removed outlier: 3.754A pdb=" N GLU G 238 " --> pdb=" O VAL G 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 17 through 22 removed outlier: 3.690A pdb=" N GLU F 54 " --> pdb=" O ASP F 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 218 through 221 removed outlier: 3.754A pdb=" N GLU F 238 " --> pdb=" O VAL F 219 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 17 through 22 removed outlier: 3.691A pdb=" N GLU H 54 " --> pdb=" O ASP H 49 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 218 through 221 removed outlier: 3.754A pdb=" N GLU H 238 " --> pdb=" O VAL H 219 " (cutoff:3.500A) 1504 hydrogen bonds defined for protein. 4416 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: 4.77 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3860 1.31 - 1.43: 7607 1.43 - 1.56: 14381 1.56 - 1.68: 48 1.68 - 1.81: 208 Bond restraints: 26104 Sorted by residual: bond pdb=" C21 PCF F 603 " pdb=" O21 PCF F 603 " ideal model delta sigma weight residual 1.334 1.435 -0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C21 PCF D 603 " pdb=" O21 PCF D 603 " ideal model delta sigma weight residual 1.334 1.435 -0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" C21 PCF B 603 " pdb=" O21 PCF B 603 " ideal model delta sigma weight residual 1.334 1.435 -0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" C21 PCF E 602 " pdb=" O21 PCF E 602 " ideal model delta sigma weight residual 1.334 1.435 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" C21 PCF G 602 " pdb=" O21 PCF G 602 " ideal model delta sigma weight residual 1.334 1.435 -0.101 2.00e-02 2.50e+03 2.53e+01 ... (remaining 26099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 34913 2.87 - 5.74: 498 5.74 - 8.61: 54 8.61 - 11.48: 23 11.48 - 14.35: 16 Bond angle restraints: 35504 Sorted by residual: angle pdb=" O12 PCF E 602 " pdb=" P PCF E 602 " pdb=" O14 PCF E 602 " ideal model delta sigma weight residual 123.69 109.34 14.35 3.00e+00 1.11e-01 2.29e+01 angle pdb=" O12 PCF F 603 " pdb=" P PCF F 603 " pdb=" O14 PCF F 603 " ideal model delta sigma weight residual 123.69 109.38 14.31 3.00e+00 1.11e-01 2.28e+01 angle pdb=" O12 PCF D 603 " pdb=" P PCF D 603 " pdb=" O14 PCF D 603 " ideal model delta sigma weight residual 123.69 109.38 14.31 3.00e+00 1.11e-01 2.27e+01 angle pdb=" O12 PCF A 602 " pdb=" P PCF A 602 " pdb=" O14 PCF A 602 " ideal model delta sigma weight residual 123.69 109.39 14.30 3.00e+00 1.11e-01 2.27e+01 angle pdb=" O12 PCF C 602 " pdb=" P PCF C 602 " pdb=" O14 PCF C 602 " ideal model delta sigma weight residual 123.69 109.39 14.30 3.00e+00 1.11e-01 2.27e+01 ... (remaining 35499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.19: 14812 29.19 - 58.39: 563 58.39 - 87.58: 49 87.58 - 116.77: 0 116.77 - 145.97: 8 Dihedral angle restraints: 15432 sinusoidal: 6268 harmonic: 9164 Sorted by residual: dihedral pdb=" O21 PCF F 602 " pdb=" C2 PCF F 602 " pdb=" C3 PCF F 602 " pdb=" O31 PCF F 602 " ideal model delta sinusoidal sigma weight residual 59.47 -86.50 145.97 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" O21 PCF C 601 " pdb=" C2 PCF C 601 " pdb=" C3 PCF C 601 " pdb=" O31 PCF C 601 " ideal model delta sinusoidal sigma weight residual 59.47 -86.48 145.95 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" O21 PCF E 601 " pdb=" C2 PCF E 601 " pdb=" C3 PCF E 601 " pdb=" O31 PCF E 601 " ideal model delta sinusoidal sigma weight residual 59.47 -86.48 145.95 1 3.00e+01 1.11e-03 1.95e+01 ... (remaining 15429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3105 0.050 - 0.100: 717 0.100 - 0.149: 70 0.149 - 0.199: 0 0.199 - 0.249: 8 Chirality restraints: 3900 Sorted by residual: chirality pdb=" C2 PCF G 602 " pdb=" C1 PCF G 602 " pdb=" C3 PCF G 602 " pdb=" O21 PCF G 602 " both_signs ideal model delta sigma weight residual False -2.60 -2.35 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C2 PCF A 602 " pdb=" C1 PCF A 602 " pdb=" C3 PCF A 602 " pdb=" O21 PCF A 602 " both_signs ideal model delta sigma weight residual False -2.60 -2.35 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" C2 PCF E 602 " pdb=" C1 PCF E 602 " pdb=" C3 PCF E 602 " pdb=" O21 PCF E 602 " both_signs ideal model delta sigma weight residual False -2.60 -2.35 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 3897 not shown) Planarity restraints: 4432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H 432 " -0.031 5.00e-02 4.00e+02 4.61e-02 3.39e+00 pdb=" N PRO H 433 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO H 433 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 433 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 432 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO C 433 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 433 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 433 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 432 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO E 433 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO E 433 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 433 " -0.026 5.00e-02 4.00e+02 ... (remaining 4429 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.84: 8348 2.84 - 3.42: 28359 3.42 - 3.99: 45255 3.99 - 4.57: 66799 4.57 - 5.14: 95246 Nonbonded interactions: 244007 Sorted by model distance: nonbonded pdb=" OH TYR A 48 " pdb=" OD1 ASP A 53 " model vdw 2.269 3.040 nonbonded pdb=" OH TYR F 48 " pdb=" OD1 ASP F 53 " model vdw 2.269 3.040 nonbonded pdb=" OH TYR C 48 " pdb=" OD1 ASP C 53 " model vdw 2.269 3.040 nonbonded pdb=" OH TYR E 48 " pdb=" OD1 ASP E 53 " model vdw 2.270 3.040 nonbonded pdb=" OH TYR B 48 " pdb=" OD1 ASP B 53 " model vdw 2.270 3.040 ... (remaining 244002 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' and (resid 7 through 455 or (resid 456 and (name N or name CA or name \ C or name O or name CB )) or resid 457 through 463)) selection = (chain 'B' and (resid 7 through 455 or (resid 456 and (name N or name CA or name \ C or name O or name CB )) or resid 457 through 463)) selection = (chain 'C' and (resid 7 through 455 or (resid 456 and (name N or name CA or name \ C or name O or name CB )) or resid 457 through 463)) selection = (chain 'D' and (resid 7 through 455 or (resid 456 and (name N or name CA or name \ C or name O or name CB )) or resid 457 through 463)) selection = (chain 'E' and resid 7 through 463) selection = (chain 'F' and resid 7 through 463) selection = (chain 'G' and resid 7 through 463) selection = (chain 'H' and resid 7 through 463) } 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: 6.270 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: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 25.940 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.560 26136 Z= 0.435 Angle : 1.062 29.833 35528 Z= 0.399 Chirality : 0.041 0.249 3900 Planarity : 0.005 0.046 4432 Dihedral : 15.164 145.965 9488 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.53 % Allowed : 6.76 % Favored : 90.70 % 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: -0.88 (0.13), residues: 3076 helix: -0.05 (0.11), residues: 1928 sheet: None (None), residues: 0 loop : -1.38 (0.15), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 320 TYR 0.010 0.001 TYR C 70 PHE 0.009 0.001 PHE E 64 TRP 0.010 0.001 TRP G 94 HIS 0.005 0.001 HIS G 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.29 (26104) covalent geometry : angle 0.81213 / 0.36 (35504) hydrogen bonds : bond 0.11484 / 7.61 ( 1504) hydrogen bonds : angle 5.59354 / 4.10 ( 4416) metal coordination : bond 0.24928 / 17.16 ( 32) metal coordination : angle 26.33114 / 15.33 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 523 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7350 (t70) cc_final: 0.6961 (t0) REVERT: A 190 ARG cc_start: 0.5286 (ttt90) cc_final: 0.4708 (tmm160) REVERT: A 194 PHE cc_start: 0.7027 (m-80) cc_final: 0.6769 (m-10) REVERT: A 238 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.6182 (pm20) REVERT: A 276 ASN cc_start: 0.7636 (t0) cc_final: 0.7430 (t0) REVERT: A 442 TYR cc_start: 0.7715 (m-10) cc_final: 0.7356 (m-80) REVERT: A 447 MET cc_start: 0.7411 (mmt) cc_final: 0.7118 (mmm) REVERT: A 458 LYS cc_start: 0.6688 (mmtp) cc_final: 0.6341 (mtpt) REVERT: C 53 ASP cc_start: 0.7335 (t70) cc_final: 0.6988 (t0) REVERT: C 190 ARG cc_start: 0.5149 (ttt90) cc_final: 0.4439 (tmm160) REVERT: C 199 PHE cc_start: 0.7693 (m-80) cc_final: 0.7101 (m-80) REVERT: C 238 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6247 (pm20) REVERT: C 406 MET cc_start: 0.8331 (ptp) cc_final: 0.8076 (ptp) REVERT: C 458 LYS cc_start: 0.6717 (mmtp) cc_final: 0.6364 (mtpt) REVERT: B 40 PRO cc_start: 0.7668 (Cg_endo) cc_final: 0.7449 (Cg_exo) REVERT: B 53 ASP cc_start: 0.7420 (t70) cc_final: 0.7052 (t0) REVERT: B 190 ARG cc_start: 0.5128 (ttt90) cc_final: 0.4648 (tmm160) REVERT: B 194 PHE cc_start: 0.7024 (m-80) cc_final: 0.6711 (m-10) REVERT: B 199 PHE cc_start: 0.7592 (m-80) cc_final: 0.6892 (m-80) REVERT: B 238 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6307 (pm20) REVERT: B 406 MET cc_start: 0.8361 (ptp) cc_final: 0.8112 (ptp) REVERT: B 442 TYR cc_start: 0.7645 (m-10) cc_final: 0.7304 (m-80) REVERT: B 461 PRO cc_start: 0.8866 (Cg_endo) cc_final: 0.8652 (Cg_exo) REVERT: D 40 PRO cc_start: 0.7553 (Cg_endo) cc_final: 0.7290 (Cg_exo) REVERT: D 53 ASP cc_start: 0.7344 (t70) cc_final: 0.6923 (t0) REVERT: D 190 ARG cc_start: 0.5377 (ttt90) cc_final: 0.4692 (tmm160) REVERT: D 194 PHE cc_start: 0.6935 (m-80) cc_final: 0.6704 (m-10) REVERT: D 238 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6296 (pm20) REVERT: D 447 MET cc_start: 0.7397 (mmt) cc_final: 0.7183 (mmm) REVERT: D 458 LYS cc_start: 0.6667 (mmtp) cc_final: 0.6044 (mmtt) REVERT: E 89 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.6203 (tm-30) REVERT: G 53 ASP cc_start: 0.6759 (t70) cc_final: 0.6450 (t0) REVERT: G 89 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.6199 (tm-30) REVERT: G 278 LEU cc_start: 0.5547 (mp) cc_final: 0.5185 (tt) REVERT: G 321 ILE cc_start: 0.7493 (tp) cc_final: 0.7276 (tt) REVERT: F 89 GLU cc_start: 0.6525 (OUTLIER) cc_final: 0.6217 (tm-30) REVERT: H 41 ASP cc_start: 0.6397 (m-30) cc_final: 0.6189 (t0) REVERT: H 45 HIS cc_start: 0.6252 (m170) cc_final: 0.5874 (m170) REVERT: H 89 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.6156 (tm-30) outliers start: 64 outliers final: 12 residues processed: 574 average time/residue: 0.1953 time to fit residues: 168.2476 Evaluate side-chains 332 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 312 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain G residue 89 GLU Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 329 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.2980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 HIS C 279 ASN C 327 HIS D 383 HIS E 19 HIS E 279 ASN G 19 HIS G 279 ASN F 19 HIS F 279 ASN H 19 HIS H 279 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.200889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.161520 restraints weight = 35890.855| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 1.65 r_work: 0.3719 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 26136 Z= 0.203 Angle : 0.600 9.979 35528 Z= 0.302 Chirality : 0.044 0.183 3900 Planarity : 0.005 0.042 4432 Dihedral : 12.717 135.021 4106 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.45 % Allowed : 10.84 % Favored : 86.71 % 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: 0.52 (0.15), residues: 3076 helix: 0.93 (0.12), residues: 1912 sheet: -0.90 (0.48), residues: 112 loop : -0.45 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 326 TYR 0.011 0.001 TYR C 70 PHE 0.017 0.001 PHE G 283 TRP 0.022 0.001 TRP A 255 HIS 0.008 0.001 HIS H 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (26104) covalent geometry : angle 0.59549 / 0.30 (35504) hydrogen bonds : bond 0.06003 / 3.98 ( 1504) hydrogen bonds : angle 4.68762 / 3.41 ( 4416) metal coordination : bond 0.01180 / 0.77 ( 32) metal coordination : angle 2.79338 / 1.64 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 332 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 238 GLU cc_start: 0.4811 (OUTLIER) cc_final: 0.4603 (pm20) REVERT: C 451 LYS cc_start: 0.6411 (ttmm) cc_final: 0.6195 (mtpp) REVERT: B 199 PHE cc_start: 0.6526 (m-80) cc_final: 0.6088 (m-80) REVERT: B 323 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8441 (ttpp) REVERT: E 197 LEU cc_start: 0.5205 (OUTLIER) cc_final: 0.4733 (tt) REVERT: G 197 LEU cc_start: 0.4639 (OUTLIER) cc_final: 0.4023 (tt) REVERT: G 331 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7800 (mm) REVERT: F 197 LEU cc_start: 0.4625 (OUTLIER) cc_final: 0.4078 (tt) REVERT: F 321 ILE cc_start: 0.6601 (tp) cc_final: 0.6383 (tt) REVERT: F 331 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7728 (mm) REVERT: F 445 LEU cc_start: 0.8522 (tp) cc_final: 0.8256 (tt) REVERT: H 197 LEU cc_start: 0.4324 (OUTLIER) cc_final: 0.3777 (tt) outliers start: 62 outliers final: 35 residues processed: 379 average time/residue: 0.1771 time to fit residues: 104.3777 Evaluate side-chains 314 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 271 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain B residue 45 HIS Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 441 MET Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 441 MET Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 389 ILE Chi-restraints excluded: chain H residue 441 MET Chi-restraints excluded: chain H residue 451 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 93 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 166 optimal weight: 1.9990 chunk 170 optimal weight: 30.0000 chunk 105 optimal weight: 0.6980 chunk 135 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 161 optimal weight: 0.3980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.199417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.158482 restraints weight = 35845.862| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 1.73 r_work: 0.3527 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 26136 Z= 0.203 Angle : 0.598 12.067 35528 Z= 0.299 Chirality : 0.044 0.344 3900 Planarity : 0.005 0.042 4432 Dihedral : 11.755 133.542 4074 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.77 % Allowed : 12.94 % Favored : 84.30 % 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: 0.86 (0.15), residues: 3076 helix: 1.07 (0.12), residues: 1940 sheet: -0.15 (0.80), residues: 56 loop : -0.15 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 326 TYR 0.010 0.001 TYR D 70 PHE 0.025 0.001 PHE F 351 TRP 0.017 0.001 TRP B 255 HIS 0.005 0.001 HIS G 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 (26104) covalent geometry : angle 0.59240 / 0.30 (35504) hydrogen bonds : bond 0.05888 / 3.90 ( 1504) hydrogen bonds : angle 4.57907 / 3.32 ( 4416) metal coordination : bond 0.00764 / 0.48 ( 32) metal coordination : angle 3.21074 / 1.83 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 311 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 PHE cc_start: 0.7383 (m-80) cc_final: 0.7113 (m-80) REVERT: C 9 ARG cc_start: 0.8321 (ptt180) cc_final: 0.7990 (mtt180) REVERT: C 199 PHE cc_start: 0.7504 (m-10) cc_final: 0.7223 (m-10) REVERT: C 451 LYS cc_start: 0.6854 (ttmm) cc_final: 0.6605 (mtpp) REVERT: B 199 PHE cc_start: 0.7491 (m-80) cc_final: 0.7211 (m-10) REVERT: E 207 PHE cc_start: 0.6845 (t80) cc_final: 0.6617 (t80) REVERT: E 321 ILE cc_start: 0.7816 (tp) cc_final: 0.7534 (tt) REVERT: G 197 LEU cc_start: 0.6005 (OUTLIER) cc_final: 0.5636 (tt) REVERT: F 197 LEU cc_start: 0.5918 (OUTLIER) cc_final: 0.5590 (tt) REVERT: F 321 ILE cc_start: 0.7653 (tp) cc_final: 0.7397 (tt) REVERT: F 331 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8003 (mm) REVERT: F 338 LEU cc_start: 0.8299 (mm) cc_final: 0.7927 (mt) outliers start: 70 outliers final: 41 residues processed: 366 average time/residue: 0.1684 time to fit residues: 96.2769 Evaluate side-chains 311 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 267 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 338 LEU Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 441 MET Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 441 MET Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 389 ILE Chi-restraints excluded: chain H residue 441 MET Chi-restraints excluded: chain H residue 460 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 18 optimal weight: 9.9990 chunk 301 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 166 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 chunk 238 optimal weight: 2.9990 chunk 148 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN ** E 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 381 HIS H 381 HIS H 383 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.201217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.160979 restraints weight = 35685.439| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 1.68 r_work: 0.3581 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26136 Z= 0.138 Angle : 0.551 12.833 35528 Z= 0.272 Chirality : 0.041 0.318 3900 Planarity : 0.005 0.042 4432 Dihedral : 11.466 131.279 4068 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.61 % Allowed : 14.28 % Favored : 83.11 % 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: 1.29 (0.15), residues: 3076 helix: 1.35 (0.12), residues: 1924 sheet: 0.08 (0.82), residues: 56 loop : 0.17 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 326 TYR 0.008 0.001 TYR H 365 PHE 0.022 0.001 PHE F 351 TRP 0.012 0.001 TRP E 392 HIS 0.003 0.001 HIS C 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (26104) covalent geometry : angle 0.54900 / 0.27 (35504) hydrogen bonds : bond 0.05067 / 3.37 ( 1504) hydrogen bonds : angle 4.35090 / 3.16 ( 4416) metal coordination : bond 0.00418 / 0.26 ( 32) metal coordination : angle 2.03411 / 1.17 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 301 time to evaluate : 0.963 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: A 199 PHE cc_start: 0.7354 (m-80) cc_final: 0.7092 (m-10) REVERT: C 451 LYS cc_start: 0.6855 (ttmm) cc_final: 0.6598 (mtpp) REVERT: B 199 PHE cc_start: 0.7324 (m-80) cc_final: 0.7038 (m-10) REVERT: D 255 TRP cc_start: 0.7473 (t60) cc_final: 0.7018 (t60) REVERT: E 321 ILE cc_start: 0.7831 (tp) cc_final: 0.7557 (tt) REVERT: E 449 LYS cc_start: 0.7398 (mmtt) cc_final: 0.6913 (ttpp) REVERT: E 462 ARG cc_start: 0.6268 (ptt180) cc_final: 0.5909 (mtm180) REVERT: G 315 PHE cc_start: 0.6802 (OUTLIER) cc_final: 0.5944 (t80) REVERT: F 315 PHE cc_start: 0.6877 (OUTLIER) cc_final: 0.6105 (t80) REVERT: F 321 ILE cc_start: 0.7685 (tp) cc_final: 0.7438 (tt) REVERT: F 323 LYS cc_start: 0.7018 (mmtt) cc_final: 0.6735 (mmtm) REVERT: F 338 LEU cc_start: 0.8342 (mm) cc_final: 0.8020 (mt) REVERT: F 445 LEU cc_start: 0.8214 (tp) cc_final: 0.7993 (tt) REVERT: H 331 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7939 (mm) outliers start: 66 outliers final: 36 residues processed: 351 average time/residue: 0.1750 time to fit residues: 95.9164 Evaluate side-chains 310 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 271 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 365 TYR Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 315 PHE Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 441 MET Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 389 ILE Chi-restraints excluded: chain H residue 441 MET Chi-restraints excluded: chain H residue 460 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 99 optimal weight: 9.9990 chunk 273 optimal weight: 1.9990 chunk 311 optimal weight: 9.9990 chunk 250 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 chunk 263 optimal weight: 20.0000 chunk 78 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 HIS A 450 GLN C 383 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 HIS ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN E 336 HIS ** E 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 383 HIS ** G 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.198917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.157977 restraints weight = 35533.266| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 1.67 r_work: 0.3559 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26136 Z= 0.191 Angle : 0.591 12.404 35528 Z= 0.293 Chirality : 0.044 0.429 3900 Planarity : 0.005 0.043 4432 Dihedral : 11.482 130.730 4068 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.81 % Allowed : 15.23 % Favored : 81.96 % 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: 1.23 (0.15), residues: 3076 helix: 1.32 (0.12), residues: 1920 sheet: -0.20 (0.80), residues: 56 loop : 0.13 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 326 TYR 0.017 0.001 TYR G 365 PHE 0.017 0.001 PHE G 199 TRP 0.009 0.001 TRP C 94 HIS 0.004 0.001 HIS F 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (26104) covalent geometry : angle 0.58798 / 0.29 (35504) hydrogen bonds : bond 0.05663 / 3.75 ( 1504) hydrogen bonds : angle 4.46469 / 3.23 ( 4416) metal coordination : bond 0.00627 / 0.41 ( 32) metal coordination : angle 2.25479 / 1.28 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 292 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 PHE cc_start: 0.7242 (m-80) cc_final: 0.7007 (m-10) REVERT: C 327 HIS cc_start: 0.8122 (m-70) cc_final: 0.7921 (m-70) REVERT: C 451 LYS cc_start: 0.6742 (ttmm) cc_final: 0.6511 (mtpp) REVERT: B 199 PHE cc_start: 0.7277 (m-80) cc_final: 0.6991 (m-10) REVERT: B 323 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8773 (ttpp) REVERT: E 321 ILE cc_start: 0.7761 (tp) cc_final: 0.7487 (tt) REVERT: E 449 LYS cc_start: 0.7416 (mmtt) cc_final: 0.6966 (ttpp) REVERT: G 315 PHE cc_start: 0.6790 (OUTLIER) cc_final: 0.5973 (t80) REVERT: F 315 PHE cc_start: 0.6778 (OUTLIER) cc_final: 0.6074 (t80) REVERT: F 321 ILE cc_start: 0.7640 (tp) cc_final: 0.7372 (tt) REVERT: F 338 LEU cc_start: 0.8196 (mm) cc_final: 0.7928 (mt) REVERT: F 445 LEU cc_start: 0.8254 (tp) cc_final: 0.8053 (tt) REVERT: H 331 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8062 (mm) REVERT: H 454 LYS cc_start: 0.6487 (mmtt) cc_final: 0.6191 (tppt) outliers start: 71 outliers final: 45 residues processed: 350 average time/residue: 0.1715 time to fit residues: 94.6602 Evaluate side-chains 314 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 265 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 365 TYR Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 441 MET Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 252 CYS Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 315 PHE Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 441 MET Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 252 CYS Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 389 ILE Chi-restraints excluded: chain H residue 441 MET Chi-restraints excluded: chain H residue 460 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 75 optimal weight: 0.7980 chunk 168 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 126 optimal weight: 0.4980 chunk 213 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 253 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 12 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 HIS C 20 GLN ** C 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 GLN E 220 ASN E 381 HIS ** G 381 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 = 0.4563 r_free = 0.4563 target = 0.202401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.165061 restraints weight = 35809.080| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 1.63 r_work: 0.3643 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26136 Z= 0.120 Angle : 0.528 10.795 35528 Z= 0.260 Chirality : 0.041 0.427 3900 Planarity : 0.005 0.043 4432 Dihedral : 11.269 127.982 4068 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.25 % Allowed : 15.55 % Favored : 82.20 % 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: 1.51 (0.15), residues: 3076 helix: 1.53 (0.12), residues: 1912 sheet: -0.10 (0.79), residues: 56 loop : 0.26 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 326 TYR 0.016 0.001 TYR G 365 PHE 0.022 0.001 PHE C 199 TRP 0.049 0.001 TRP C 255 HIS 0.006 0.001 HIS E 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (26104) covalent geometry : angle 0.52623 / 0.26 (35504) hydrogen bonds : bond 0.04600 / 3.06 ( 1504) hydrogen bonds : angle 4.18534 / 3.04 ( 4416) metal coordination : bond 0.00330 / 0.21 ( 32) metal coordination : angle 1.64816 / 0.94 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 297 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 451 LYS cc_start: 0.6854 (ttmm) cc_final: 0.6638 (mtpp) REVERT: B 199 PHE cc_start: 0.7175 (m-80) cc_final: 0.6915 (m-10) REVERT: E 321 ILE cc_start: 0.7762 (tp) cc_final: 0.7501 (tt) REVERT: E 445 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7592 (tt) REVERT: E 449 LYS cc_start: 0.7391 (mmtt) cc_final: 0.6923 (ttpp) REVERT: E 462 ARG cc_start: 0.6149 (ptt180) cc_final: 0.5826 (mtm180) REVERT: G 315 PHE cc_start: 0.6820 (OUTLIER) cc_final: 0.6044 (t80) REVERT: F 315 PHE cc_start: 0.6864 (OUTLIER) cc_final: 0.6199 (t80) REVERT: F 323 LYS cc_start: 0.7567 (mmtm) cc_final: 0.7085 (mmtt) REVERT: F 331 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7870 (mm) REVERT: F 338 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7896 (mt) REVERT: F 445 LEU cc_start: 0.8235 (tp) cc_final: 0.8007 (tt) REVERT: H 454 LYS cc_start: 0.6486 (mmtt) cc_final: 0.6262 (tppt) outliers start: 57 outliers final: 40 residues processed: 342 average time/residue: 0.1591 time to fit residues: 86.5494 Evaluate side-chains 311 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 266 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 252 CYS Chi-restraints excluded: chain E residue 365 TYR Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain E residue 445 LEU Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 252 CYS Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 252 CYS Chi-restraints excluded: chain F residue 315 PHE Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 441 MET Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 252 CYS Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 441 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 230 optimal weight: 0.9990 chunk 305 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 105 optimal weight: 0.3980 chunk 69 optimal weight: 10.0000 chunk 177 optimal weight: 20.0000 chunk 227 optimal weight: 3.9990 chunk 170 optimal weight: 30.0000 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 HIS ** C 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 GLN E 220 ASN G 220 ASN ** G 381 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 = 0.4522 r_free = 0.4522 target = 0.198388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.159638 restraints weight = 35586.636| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 1.61 r_work: 0.3556 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 26136 Z= 0.205 Angle : 0.595 10.744 35528 Z= 0.296 Chirality : 0.044 0.417 3900 Planarity : 0.005 0.045 4432 Dihedral : 11.420 128.714 4068 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.77 % Allowed : 16.06 % Favored : 81.17 % 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: 1.33 (0.15), residues: 3076 helix: 1.36 (0.12), residues: 1948 sheet: -0.64 (0.43), residues: 136 loop : 0.36 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 326 TYR 0.014 0.001 TYR G 365 PHE 0.016 0.001 PHE F 215 TRP 0.013 0.001 TRP B 106 HIS 0.005 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.20 (26104) covalent geometry : angle 0.59337 / 0.30 (35504) hydrogen bonds : bond 0.05665 / 3.75 ( 1504) hydrogen bonds : angle 4.45022 / 3.22 ( 4416) metal coordination : bond 0.00773 / 0.49 ( 32) metal coordination : angle 1.98563 / 1.10 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 291 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 PHE cc_start: 0.7193 (m-10) cc_final: 0.6992 (m-10) REVERT: B 199 PHE cc_start: 0.7292 (m-80) cc_final: 0.7012 (m-10) REVERT: E 315 PHE cc_start: 0.6760 (OUTLIER) cc_final: 0.6549 (t80) REVERT: E 449 LYS cc_start: 0.7362 (mmtt) cc_final: 0.6943 (ttpp) REVERT: G 315 PHE cc_start: 0.6863 (OUTLIER) cc_final: 0.6073 (t80) REVERT: F 53 ASP cc_start: 0.7622 (t0) cc_final: 0.7299 (t0) REVERT: F 315 PHE cc_start: 0.6863 (OUTLIER) cc_final: 0.6178 (t80) REVERT: F 321 ILE cc_start: 0.7697 (tp) cc_final: 0.7449 (tt) REVERT: F 331 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7950 (mm) REVERT: F 338 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7942 (mt) REVERT: F 445 LEU cc_start: 0.8270 (tp) cc_final: 0.8035 (tt) REVERT: H 331 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7984 (mm) REVERT: H 362 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7302 (mtp) REVERT: H 454 LYS cc_start: 0.6524 (mmtt) cc_final: 0.6298 (tppt) outliers start: 70 outliers final: 49 residues processed: 347 average time/residue: 0.1590 time to fit residues: 87.9583 Evaluate side-chains 321 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 265 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 252 CYS Chi-restraints excluded: chain E residue 315 PHE Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 252 CYS Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 441 MET Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 252 CYS Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 315 PHE Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 441 MET Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 252 CYS Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 362 MET Chi-restraints excluded: chain H residue 389 ILE Chi-restraints excluded: chain H residue 441 MET Chi-restraints excluded: chain H residue 460 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 123 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 250 optimal weight: 0.3980 chunk 31 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 HIS ** C 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN ** G 381 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 = 0.4545 r_free = 0.4545 target = 0.200682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.160594 restraints weight = 35812.507| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 1.69 r_work: 0.3595 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26136 Z= 0.137 Angle : 0.547 10.687 35528 Z= 0.271 Chirality : 0.041 0.354 3900 Planarity : 0.005 0.042 4432 Dihedral : 11.328 126.986 4068 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.53 % Allowed : 16.42 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.15), residues: 3076 helix: 1.50 (0.12), residues: 1944 sheet: -0.63 (0.53), residues: 96 loop : 0.38 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 326 TYR 0.014 0.001 TYR G 365 PHE 0.015 0.001 PHE H 215 TRP 0.014 0.001 TRP E 392 HIS 0.003 0.001 HIS F 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (26104) covalent geometry : angle 0.54517 / 0.27 (35504) hydrogen bonds : bond 0.04814 / 3.19 ( 1504) hydrogen bonds : angle 4.26996 / 3.10 ( 4416) metal coordination : bond 0.00464 / 0.30 ( 32) metal coordination : angle 1.61177 / 0.88 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 288 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 PHE cc_start: 0.7147 (m-10) cc_final: 0.6884 (m-10) REVERT: B 199 PHE cc_start: 0.7266 (m-80) cc_final: 0.6988 (m-10) REVERT: E 449 LYS cc_start: 0.7354 (mmtt) cc_final: 0.6878 (ttpp) REVERT: E 462 ARG cc_start: 0.6301 (ptt180) cc_final: 0.5964 (mtm180) REVERT: G 385 LYS cc_start: 0.6529 (mtmt) cc_final: 0.6286 (mmmt) REVERT: F 53 ASP cc_start: 0.7616 (t0) cc_final: 0.7299 (t0) REVERT: F 315 PHE cc_start: 0.6806 (OUTLIER) cc_final: 0.6143 (t80) REVERT: F 331 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7940 (mm) REVERT: F 338 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7791 (mt) REVERT: F 445 LEU cc_start: 0.8317 (tp) cc_final: 0.8049 (tt) REVERT: H 331 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7932 (mm) REVERT: H 362 MET cc_start: 0.7754 (tpt) cc_final: 0.7341 (mtp) REVERT: H 414 MET cc_start: 0.4724 (tpp) cc_final: 0.4354 (tpp) REVERT: H 445 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7536 (tt) outliers start: 64 outliers final: 45 residues processed: 339 average time/residue: 0.1605 time to fit residues: 86.5448 Evaluate side-chains 323 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 273 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 252 CYS Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 252 CYS Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 441 MET Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 252 CYS Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 315 PHE Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 441 MET Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 252 CYS Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 389 ILE Chi-restraints excluded: chain H residue 441 MET Chi-restraints excluded: chain H residue 445 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 249 optimal weight: 20.0000 chunk 258 optimal weight: 6.9990 chunk 302 optimal weight: 3.9990 chunk 276 optimal weight: 0.7980 chunk 226 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 280 optimal weight: 3.9990 chunk 262 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 HIS ** C 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 GLN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 GLN E 220 ASN G 220 ASN G 336 HIS G 381 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.198698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.160260 restraints weight = 35722.893| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 1.64 r_work: 0.3558 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 26136 Z= 0.191 Angle : 0.590 9.998 35528 Z= 0.293 Chirality : 0.043 0.316 3900 Planarity : 0.005 0.044 4432 Dihedral : 11.370 127.320 4068 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.25 % Allowed : 16.26 % Favored : 81.49 % 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: 1.39 (0.15), residues: 3076 helix: 1.40 (0.12), residues: 1944 sheet: -0.56 (0.43), residues: 136 loop : 0.40 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 326 TYR 0.014 0.001 TYR H 407 PHE 0.029 0.001 PHE E 315 TRP 0.010 0.001 TRP B 106 HIS 0.004 0.001 HIS F 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (26104) covalent geometry : angle 0.58807 / 0.29 (35504) hydrogen bonds : bond 0.05438 / 3.60 ( 1504) hydrogen bonds : angle 4.41176 / 3.20 ( 4416) metal coordination : bond 0.00744 / 0.47 ( 32) metal coordination : angle 1.82057 / 0.99 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 284 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 PHE cc_start: 0.7193 (m-10) cc_final: 0.6944 (m-10) REVERT: B 199 PHE cc_start: 0.7283 (m-80) cc_final: 0.6986 (m-10) REVERT: E 53 ASP cc_start: 0.7582 (t0) cc_final: 0.7219 (t0) REVERT: E 362 MET cc_start: 0.7576 (tpt) cc_final: 0.7294 (mtp) REVERT: E 449 LYS cc_start: 0.7290 (mmtt) cc_final: 0.6919 (ttpp) REVERT: E 462 ARG cc_start: 0.6340 (ptt180) cc_final: 0.5919 (mtm180) REVERT: G 315 PHE cc_start: 0.6798 (OUTLIER) cc_final: 0.5978 (t80) REVERT: G 385 LYS cc_start: 0.6558 (mtmt) cc_final: 0.6323 (mmmt) REVERT: F 53 ASP cc_start: 0.7690 (t0) cc_final: 0.7411 (t0) REVERT: F 315 PHE cc_start: 0.6841 (OUTLIER) cc_final: 0.6424 (t80) REVERT: F 321 ILE cc_start: 0.7664 (tp) cc_final: 0.7403 (tt) REVERT: F 323 LYS cc_start: 0.7493 (mmtm) cc_final: 0.6981 (mmtt) REVERT: F 338 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7838 (mt) REVERT: F 445 LEU cc_start: 0.8331 (tp) cc_final: 0.8057 (tt) REVERT: H 53 ASP cc_start: 0.7614 (t0) cc_final: 0.7258 (t0) REVERT: H 331 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7943 (mm) REVERT: H 362 MET cc_start: 0.7743 (tpt) cc_final: 0.7258 (mtp) REVERT: H 414 MET cc_start: 0.4787 (tpp) cc_final: 0.4411 (tpp) REVERT: H 445 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7533 (tt) REVERT: H 454 LYS cc_start: 0.6987 (tppt) cc_final: 0.6430 (mmtt) outliers start: 57 outliers final: 46 residues processed: 334 average time/residue: 0.1621 time to fit residues: 86.0048 Evaluate side-chains 322 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 271 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 252 CYS Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 252 CYS Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 441 MET Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 252 CYS Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 315 PHE Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 441 MET Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 252 CYS Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 389 ILE Chi-restraints excluded: chain H residue 441 MET Chi-restraints excluded: chain H residue 445 LEU Chi-restraints excluded: chain H residue 460 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 287 optimal weight: 8.9990 chunk 281 optimal weight: 0.7980 chunk 173 optimal weight: 7.9990 chunk 250 optimal weight: 9.9990 chunk 243 optimal weight: 0.8980 chunk 167 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 241 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 187 optimal weight: 0.9980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 HIS ** C 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 GLN E 220 ASN G 220 ASN H 336 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.197606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.158903 restraints weight = 35591.999| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 1.63 r_work: 0.3536 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 26136 Z= 0.224 Angle : 0.632 11.352 35528 Z= 0.316 Chirality : 0.044 0.292 3900 Planarity : 0.005 0.045 4432 Dihedral : 11.343 129.083 4068 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.18 % Allowed : 16.57 % Favored : 81.25 % 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: 1.10 (0.15), residues: 3076 helix: 1.17 (0.12), residues: 1960 sheet: -0.65 (0.43), residues: 136 loop : 0.25 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 326 TYR 0.014 0.001 TYR A 70 PHE 0.025 0.002 PHE E 315 TRP 0.024 0.001 TRP E 36 HIS 0.006 0.001 HIS G 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.22 (26104) covalent geometry : angle 0.62931 / 0.32 (35504) hydrogen bonds : bond 0.05857 / 3.88 ( 1504) hydrogen bonds : angle 4.55197 / 3.30 ( 4416) metal coordination : bond 0.00917 / 0.58 ( 32) metal coordination : angle 2.21950 / 1.20 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 284 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 PHE cc_start: 0.7286 (m-10) cc_final: 0.7032 (m-10) REVERT: C 41 ASP cc_start: 0.6151 (t0) cc_final: 0.5903 (p0) REVERT: B 199 PHE cc_start: 0.7396 (m-80) cc_final: 0.6624 (m-10) REVERT: D 41 ASP cc_start: 0.5802 (t0) cc_final: 0.5590 (p0) REVERT: E 53 ASP cc_start: 0.7692 (t0) cc_final: 0.7352 (t0) REVERT: E 398 MET cc_start: 0.7867 (tpt) cc_final: 0.7384 (tpp) REVERT: E 449 LYS cc_start: 0.7256 (mmtt) cc_final: 0.6926 (ttpp) REVERT: G 315 PHE cc_start: 0.6737 (OUTLIER) cc_final: 0.6243 (t80) REVERT: F 53 ASP cc_start: 0.7758 (t0) cc_final: 0.7511 (t0) REVERT: F 315 PHE cc_start: 0.6888 (OUTLIER) cc_final: 0.6164 (t80) REVERT: F 323 LYS cc_start: 0.7412 (mmtm) cc_final: 0.6933 (mmtt) REVERT: F 338 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7924 (mt) REVERT: F 445 LEU cc_start: 0.8337 (tp) cc_final: 0.8080 (tt) REVERT: H 53 ASP cc_start: 0.7729 (t0) cc_final: 0.7394 (t0) REVERT: H 331 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8021 (mm) REVERT: H 414 MET cc_start: 0.4801 (tpp) cc_final: 0.4555 (tpp) REVERT: H 445 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7573 (tt) REVERT: H 454 LYS cc_start: 0.7048 (tppt) cc_final: 0.6487 (mmtt) outliers start: 55 outliers final: 45 residues processed: 330 average time/residue: 0.1727 time to fit residues: 90.2473 Evaluate side-chains 319 residues out of total 2724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 269 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 252 CYS Chi-restraints excluded: chain E residue 365 TYR Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 252 CYS Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 441 MET Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 252 CYS Chi-restraints excluded: chain F residue 315 PHE Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 441 MET Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 252 CYS Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 338 LEU Chi-restraints excluded: chain H residue 389 ILE Chi-restraints excluded: chain H residue 441 MET Chi-restraints excluded: chain H residue 445 LEU Chi-restraints excluded: chain H residue 460 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 238 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 HIS ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN G 220 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.200659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.162756 restraints weight = 35602.431| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 1.64 r_work: 0.3590 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26136 Z= 0.133 Angle : 0.558 8.048 35528 Z= 0.276 Chirality : 0.041 0.262 3900 Planarity : 0.005 0.043 4432 Dihedral : 11.148 126.001 4068 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.94 % Allowed : 17.17 % Favored : 80.89 % 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: 1.41 (0.15), residues: 3076 helix: 1.39 (0.12), residues: 1956 sheet: -0.57 (0.53), residues: 96 loop : 0.40 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 332 TYR 0.014 0.001 TYR G 365 PHE 0.027 0.001 PHE E 315 TRP 0.028 0.001 TRP B 255 HIS 0.003 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (26104) covalent geometry : angle 0.55625 / 0.28 (35504) hydrogen bonds : bond 0.04761 / 3.15 ( 1504) hydrogen bonds : angle 4.28602 / 3.11 ( 4416) metal coordination : bond 0.00441 / 0.29 ( 32) metal coordination : angle 1.60984 / 0.89 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7262.99 seconds wall clock time: 124 minutes 34.43 seconds (7474.43 seconds total)