Starting phenix.real_space_refine on Wed Mar 4 17:05:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tci_25813/03_2026/7tci_25813.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tci_25813/03_2026/7tci_25813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tci_25813/03_2026/7tci_25813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tci_25813/03_2026/7tci_25813.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tci_25813/03_2026/7tci_25813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tci_25813/03_2026/7tci_25813.map" } resolution = 3.9 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= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 12 9.91 5 S 76 5.16 5 C 9780 2.51 5 N 2572 2.21 5 O 2644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15084 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2703 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 7, 'TRANS': 334} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 4, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1033 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 134} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 2703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2703 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 7, 'TRANS': 334} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 4, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "F" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1033 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 134} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 2703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2703 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 7, 'TRANS': 334} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 4, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1033 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 134} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 31 Chain: "G" Number of atoms: 2703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2703 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 7, 'TRANS': 334} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 4, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 43 Chain: "H" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1033 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 134} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Classifications: {'peptide': 1} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Classifications: {'peptide': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Classifications: {'peptide': 1} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.42, per 1000 atoms: 0.23 Number of scatterers: 15084 At special positions: 0 Unit cell: (104.375, 104.375, 121.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 12 19.99 S 76 16.00 O 2644 8.00 N 2572 7.00 C 9780 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: 1.41 Conformation dependent library (CDL) restraints added in 532.6 milliseconds 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB I0S A 701 " pdb=" CB I0S E 701 " pdb=" CB I0S C 701 " pdb=" CB I0S G 701 " Number of C-beta restraints generated: 3560 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 4 sheets defined 82.1% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 109 through 135 Processing helix chain 'A' and resid 139 through 168 removed outlier: 4.811A pdb=" N GLU A 144 " --> pdb=" O ASN A 140 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N THR A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 186 through 206 Processing helix chain 'A' and resid 218 through 228 removed outlier: 4.419A pdb=" N GLN A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 removed outlier: 4.141A pdb=" N ARG A 233 " --> pdb=" O HIS A 230 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLN A 234 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 235 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY A 236 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 248 Processing helix chain 'A' and resid 248 through 274 Processing helix chain 'A' and resid 288 through 301 Processing helix chain 'A' and resid 312 through 350 removed outlier: 4.923A pdb=" N SER A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N PHE A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 353 through 356 Processing helix chain 'A' and resid 357 through 376 removed outlier: 3.882A pdb=" N GLU A 375 " --> pdb=" O CYS A 371 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN A 376 " --> pdb=" O TYR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 523 Processing helix chain 'A' and resid 526 through 556 Processing helix chain 'B' and resid 11 through 22 Processing helix chain 'B' and resid 29 through 41 Processing helix chain 'B' and resid 45 through 57 Processing helix chain 'B' and resid 65 through 75 Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 95 through 98 removed outlier: 3.669A pdb=" N ASN B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 95 through 98' Processing helix chain 'B' and resid 103 through 113 Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 139 through 146 Processing helix chain 'E' and resid 96 through 106 Processing helix chain 'E' and resid 109 through 135 Processing helix chain 'E' and resid 139 through 168 removed outlier: 4.807A pdb=" N GLU E 144 " --> pdb=" O ASN E 140 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N THR E 145 " --> pdb=" O LEU E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 185 Processing helix chain 'E' and resid 186 through 206 Processing helix chain 'E' and resid 218 through 228 removed outlier: 4.369A pdb=" N GLN E 224 " --> pdb=" O ILE E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 236 removed outlier: 4.150A pdb=" N ARG E 233 " --> pdb=" O HIS E 230 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLN E 234 " --> pdb=" O VAL E 231 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY E 235 " --> pdb=" O ASP E 232 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY E 236 " --> pdb=" O ARG E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 248 Processing helix chain 'E' and resid 248 through 274 Processing helix chain 'E' and resid 288 through 301 Processing helix chain 'E' and resid 312 through 350 removed outlier: 4.923A pdb=" N SER E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N PHE E 329 " --> pdb=" O PHE E 325 " (cutoff:3.500A) Proline residue: E 333 - end of helix Processing helix chain 'E' and resid 353 through 356 Processing helix chain 'E' and resid 357 through 376 removed outlier: 3.884A pdb=" N GLU E 375 " --> pdb=" O CYS E 371 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASN E 376 " --> pdb=" O TYR E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 523 Processing helix chain 'E' and resid 526 through 556 Processing helix chain 'F' and resid 11 through 22 Processing helix chain 'F' and resid 29 through 41 Processing helix chain 'F' and resid 45 through 57 Processing helix chain 'F' and resid 65 through 75 Processing helix chain 'F' and resid 79 through 94 Processing helix chain 'F' and resid 95 through 98 removed outlier: 3.670A pdb=" N ASN F 98 " --> pdb=" O LYS F 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 95 through 98' Processing helix chain 'F' and resid 103 through 113 Processing helix chain 'F' and resid 118 through 130 Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'C' and resid 96 through 106 Processing helix chain 'C' and resid 109 through 135 Processing helix chain 'C' and resid 139 through 168 removed outlier: 4.812A pdb=" N GLU C 144 " --> pdb=" O ASN C 140 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N THR C 145 " --> pdb=" O LEU C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 186 through 206 Processing helix chain 'C' and resid 218 through 228 removed outlier: 4.419A pdb=" N GLN C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 236 removed outlier: 4.139A pdb=" N ARG C 233 " --> pdb=" O HIS C 230 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLN C 234 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C 235 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY C 236 " --> pdb=" O ARG C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 248 Processing helix chain 'C' and resid 248 through 274 Processing helix chain 'C' and resid 288 through 301 Processing helix chain 'C' and resid 312 through 350 removed outlier: 4.922A pdb=" N SER C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N PHE C 329 " --> pdb=" O PHE C 325 " (cutoff:3.500A) Proline residue: C 333 - end of helix Processing helix chain 'C' and resid 353 through 356 Processing helix chain 'C' and resid 357 through 376 removed outlier: 3.883A pdb=" N GLU C 375 " --> pdb=" O CYS C 371 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN C 376 " --> pdb=" O TYR C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 523 Processing helix chain 'C' and resid 526 through 556 Processing helix chain 'D' and resid 11 through 22 Processing helix chain 'D' and resid 29 through 41 Processing helix chain 'D' and resid 45 through 57 Processing helix chain 'D' and resid 65 through 75 Processing helix chain 'D' and resid 79 through 94 Processing helix chain 'D' and resid 95 through 98 removed outlier: 3.670A pdb=" N ASN D 98 " --> pdb=" O LYS D 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 95 through 98' Processing helix chain 'D' and resid 103 through 113 Processing helix chain 'D' and resid 118 through 130 Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'G' and resid 96 through 106 Processing helix chain 'G' and resid 109 through 135 Processing helix chain 'G' and resid 139 through 168 removed outlier: 4.805A pdb=" N GLU G 144 " --> pdb=" O ASN G 140 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N THR G 145 " --> pdb=" O LEU G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 185 Processing helix chain 'G' and resid 186 through 206 Processing helix chain 'G' and resid 218 through 228 removed outlier: 4.371A pdb=" N GLN G 224 " --> pdb=" O ILE G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 236 removed outlier: 4.149A pdb=" N ARG G 233 " --> pdb=" O HIS G 230 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLN G 234 " --> pdb=" O VAL G 231 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY G 235 " --> pdb=" O ASP G 232 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY G 236 " --> pdb=" O ARG G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 248 Processing helix chain 'G' and resid 248 through 274 Processing helix chain 'G' and resid 288 through 301 Processing helix chain 'G' and resid 312 through 350 removed outlier: 4.921A pdb=" N SER G 328 " --> pdb=" O VAL G 324 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N PHE G 329 " --> pdb=" O PHE G 325 " (cutoff:3.500A) Proline residue: G 333 - end of helix Processing helix chain 'G' and resid 353 through 356 Processing helix chain 'G' and resid 357 through 376 removed outlier: 3.878A pdb=" N GLU G 375 " --> pdb=" O CYS G 371 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASN G 376 " --> pdb=" O TYR G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 523 Processing helix chain 'G' and resid 526 through 556 Processing helix chain 'H' and resid 11 through 22 Processing helix chain 'H' and resid 29 through 41 Processing helix chain 'H' and resid 45 through 57 Processing helix chain 'H' and resid 65 through 75 Processing helix chain 'H' and resid 79 through 94 Processing helix chain 'H' and resid 95 through 98 removed outlier: 3.670A pdb=" N ASN H 98 " --> pdb=" O LYS H 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 95 through 98' Processing helix chain 'H' and resid 103 through 113 Processing helix chain 'H' and resid 118 through 130 Processing helix chain 'H' and resid 139 through 146 Processing sheet with id=AA1, first strand: chain 'B' and resid 100 through 102 removed outlier: 3.747A pdb=" N ILE B 101 " --> pdb=" O VAL B 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 100 through 102 removed outlier: 3.748A pdb=" N ILE F 101 " --> pdb=" O VAL F 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 100 through 102 removed outlier: 3.748A pdb=" N ILE D 101 " --> pdb=" O VAL D 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 100 through 102 removed outlier: 3.747A pdb=" N ILE H 101 " --> pdb=" O VAL H 137 " (cutoff:3.500A) 1145 hydrogen bonds defined for protein. 3411 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: 2.43 Time building geometry restraints manager: 1.81 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: 2380 1.31 - 1.44: 4408 1.44 - 1.56: 8488 1.56 - 1.69: 8 1.69 - 1.81: 124 Bond restraints: 15408 Sorted by residual: bond pdb=" CBE I0S G 701 " pdb=" SBF I0S G 701 " ideal model delta sigma weight residual 1.717 1.600 0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" CBE I0S E 701 " pdb=" SBF I0S E 701 " ideal model delta sigma weight residual 1.717 1.601 0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" CBE I0S A 701 " pdb=" SBF I0S A 701 " ideal model delta sigma weight residual 1.717 1.601 0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" CAT I0S C 701 " pdb=" SBF I0S C 701 " ideal model delta sigma weight residual 1.739 1.623 0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" CAT I0S A 701 " pdb=" SBF I0S A 701 " ideal model delta sigma weight residual 1.739 1.623 0.116 2.00e-02 2.50e+03 3.36e+01 ... (remaining 15403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.59: 20786 3.59 - 7.19: 88 7.19 - 10.78: 10 10.78 - 14.38: 4 14.38 - 17.97: 4 Bond angle restraints: 20892 Sorted by residual: angle pdb=" OAQ I0S A 701 " pdb=" SAI I0S A 701 " pdb=" OAR I0S A 701 " ideal model delta sigma weight residual 119.45 101.48 17.97 3.00e+00 1.11e-01 3.59e+01 angle pdb=" OAQ I0S C 701 " pdb=" SAI I0S C 701 " pdb=" OAR I0S C 701 " ideal model delta sigma weight residual 119.45 101.48 17.97 3.00e+00 1.11e-01 3.59e+01 angle pdb=" OAQ I0S E 701 " pdb=" SAI I0S E 701 " pdb=" OAR I0S E 701 " ideal model delta sigma weight residual 119.45 101.50 17.95 3.00e+00 1.11e-01 3.58e+01 angle pdb=" OAQ I0S G 701 " pdb=" SAI I0S G 701 " pdb=" OAR I0S G 701 " ideal model delta sigma weight residual 119.45 101.51 17.94 3.00e+00 1.11e-01 3.58e+01 angle pdb=" CA I0S G 701 " pdb=" N I0S G 701 " pdb=" CAG I0S G 701 " ideal model delta sigma weight residual 121.42 109.40 12.02 3.00e+00 1.11e-01 1.60e+01 ... (remaining 20887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.77: 8608 24.77 - 49.54: 329 49.54 - 74.30: 39 74.30 - 99.07: 12 99.07 - 123.84: 8 Dihedral angle restraints: 8996 sinusoidal: 3468 harmonic: 5528 Sorted by residual: dihedral pdb=" CB I0S A 701 " pdb=" CAE I0S A 701 " pdb=" CAF I0S A 701 " pdb=" CAG I0S A 701 " ideal model delta sinusoidal sigma weight residual 68.95 -54.89 123.84 1 3.00e+01 1.11e-03 1.66e+01 dihedral pdb=" CB I0S G 701 " pdb=" CAE I0S G 701 " pdb=" CAF I0S G 701 " pdb=" CAG I0S G 701 " ideal model delta sinusoidal sigma weight residual 68.95 -54.89 123.84 1 3.00e+01 1.11e-03 1.66e+01 dihedral pdb=" CB I0S E 701 " pdb=" CAE I0S E 701 " pdb=" CAF I0S E 701 " pdb=" CAG I0S E 701 " ideal model delta sinusoidal sigma weight residual 68.95 -54.82 123.77 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 8993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1915 0.048 - 0.095: 377 0.095 - 0.143: 48 0.143 - 0.191: 0 0.191 - 0.238: 4 Chirality restraints: 2344 Sorted by residual: chirality pdb=" CA I0S E 701 " pdb=" N I0S E 701 " pdb=" C I0S E 701 " pdb=" CB I0S E 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA I0S C 701 " pdb=" N I0S C 701 " pdb=" C I0S C 701 " pdb=" CB I0S C 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA I0S G 701 " pdb=" N I0S G 701 " pdb=" C I0S G 701 " pdb=" CB I0S G 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 2341 not shown) Planarity restraints: 2628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 523 " -0.021 5.00e-02 4.00e+02 3.11e-02 1.54e+00 pdb=" N PRO E 524 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO E 524 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 524 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 523 " 0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO A 524 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 524 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 524 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 523 " -0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO C 524 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO C 524 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 524 " -0.017 5.00e-02 4.00e+02 ... (remaining 2625 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 4092 2.81 - 3.33: 16274 3.33 - 3.85: 25496 3.85 - 4.38: 26242 4.38 - 4.90: 46367 Nonbonded interactions: 118471 Sorted by model distance: nonbonded pdb=" OE1 GLU A 150 " pdb=" NE2 GLN A 224 " model vdw 2.282 3.120 nonbonded pdb=" OE1 GLU C 150 " pdb=" NE2 GLN C 224 " model vdw 2.283 3.120 nonbonded pdb=" OE1 GLU E 150 " pdb=" NE2 GLN E 224 " model vdw 2.286 3.120 nonbonded pdb=" OE1 GLU G 150 " pdb=" NE2 GLN G 224 " model vdw 2.286 3.120 nonbonded pdb=" NH2 ARG E 522 " pdb=" OE1 GLU F 88 " model vdw 2.334 3.120 ... (remaining 118466 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.620 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.380 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 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 : 0.006 0.117 15408 Z= 0.277 Angle : 0.618 17.970 20892 Z= 0.275 Chirality : 0.036 0.238 2344 Planarity : 0.003 0.031 2628 Dihedral : 13.437 123.840 5436 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.95 % Allowed : 8.04 % Favored : 89.01 % 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: 2.98 (0.20), residues: 1884 helix: 2.67 (0.13), residues: 1476 sheet: None (None), residues: 0 loop : -0.79 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 171 TYR 0.012 0.001 TYR A 534 PHE 0.007 0.001 PHE C 322 TRP 0.006 0.001 TRP A 295 HIS 0.001 0.000 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00558 (15408) covalent geometry : angle 0.61838 (20892) hydrogen bonds : bond 0.07677 ( 1145) hydrogen bonds : angle 3.92992 ( 3411) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 415 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 TYR cc_start: 0.6517 (m-80) cc_final: 0.6136 (m-10) REVERT: A 322 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7412 (t80) REVERT: A 329 PHE cc_start: 0.7951 (m-10) cc_final: 0.7749 (m-10) REVERT: A 509 MET cc_start: 0.8764 (mtt) cc_final: 0.8073 (mtm) REVERT: B 50 GLN cc_start: 0.8826 (tp40) cc_final: 0.8114 (tp40) REVERT: B 98 ASN cc_start: 0.7170 (m-40) cc_final: 0.6898 (m110) REVERT: E 138 TYR cc_start: 0.6506 (m-80) cc_final: 0.6125 (m-10) REVERT: E 322 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.7406 (t80) REVERT: E 509 MET cc_start: 0.8765 (mtt) cc_final: 0.8050 (mtm) REVERT: F 69 PHE cc_start: 0.8674 (t80) cc_final: 0.8010 (t80) REVERT: F 98 ASN cc_start: 0.7174 (m-40) cc_final: 0.6895 (m110) REVERT: C 138 TYR cc_start: 0.6517 (m-80) cc_final: 0.6137 (m-10) REVERT: C 322 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7408 (t80) REVERT: C 329 PHE cc_start: 0.7943 (m-10) cc_final: 0.7743 (m-10) REVERT: C 509 MET cc_start: 0.8779 (mtt) cc_final: 0.8099 (mtm) REVERT: D 98 ASN cc_start: 0.7171 (m-40) cc_final: 0.6903 (m110) REVERT: G 138 TYR cc_start: 0.6496 (m-80) cc_final: 0.6126 (m-10) REVERT: G 322 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7382 (t80) REVERT: G 509 MET cc_start: 0.8766 (mtt) cc_final: 0.8059 (mtm) REVERT: H 98 ASN cc_start: 0.7177 (m-40) cc_final: 0.6894 (m110) outliers start: 44 outliers final: 21 residues processed: 451 average time/residue: 0.1191 time to fit residues: 79.9973 Evaluate side-chains 376 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 351 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 230 HIS Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 499 HIS Chi-restraints excluded: chain H residue 101 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 224 GLN A 357 GLN B 108 HIS E 97 GLN E 224 GLN E 357 GLN F 108 HIS C 97 GLN C 224 GLN C 540 ASN D 108 HIS G 97 GLN G 224 GLN G 357 GLN G 540 ASN H 108 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.190496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 122)---------------| | r_work = 0.3973 r_free = 0.3973 target = 0.156132 restraints weight = 24124.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.155048 restraints weight = 30619.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.156270 restraints weight = 20044.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.156230 restraints weight = 15795.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.156203 restraints weight = 14202.459| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15408 Z= 0.131 Angle : 0.517 5.563 20892 Z= 0.270 Chirality : 0.036 0.118 2344 Planarity : 0.003 0.029 2628 Dihedral : 11.062 119.204 2246 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 5.83 % Allowed : 15.82 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.19), residues: 1884 helix: 2.53 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -0.95 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 544 TYR 0.018 0.001 TYR E 534 PHE 0.022 0.002 PHE H 17 TRP 0.008 0.001 TRP E 369 HIS 0.009 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00288 (15408) covalent geometry : angle 0.51715 (20892) hydrogen bonds : bond 0.03570 ( 1145) hydrogen bonds : angle 3.92696 ( 3411) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 355 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 TYR cc_start: 0.6430 (m-80) cc_final: 0.6152 (m-10) REVERT: A 322 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.7345 (t80) REVERT: A 329 PHE cc_start: 0.7896 (m-10) cc_final: 0.7561 (m-10) REVERT: A 504 LYS cc_start: 0.8341 (pttm) cc_final: 0.8060 (ptpt) REVERT: A 541 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8876 (tt) REVERT: E 138 TYR cc_start: 0.6419 (m-80) cc_final: 0.6144 (m-10) REVERT: E 322 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7396 (t80) REVERT: E 504 LYS cc_start: 0.8344 (pttm) cc_final: 0.8010 (ptpt) REVERT: E 541 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8849 (tt) REVERT: F 69 PHE cc_start: 0.8301 (t80) cc_final: 0.7958 (t80) REVERT: F 72 MET cc_start: 0.8609 (tmm) cc_final: 0.8321 (tmm) REVERT: F 73 MET cc_start: 0.6914 (mmm) cc_final: 0.6690 (mmm) REVERT: F 88 GLU cc_start: 0.7101 (tp30) cc_final: 0.6884 (mm-30) REVERT: C 138 TYR cc_start: 0.6447 (m-80) cc_final: 0.6166 (m-10) REVERT: C 322 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7350 (t80) REVERT: C 329 PHE cc_start: 0.7867 (m-10) cc_final: 0.7558 (m-10) REVERT: C 504 LYS cc_start: 0.8347 (pttm) cc_final: 0.8060 (ptpt) REVERT: C 523 LYS cc_start: 0.8109 (ttpp) cc_final: 0.7739 (mtpt) REVERT: C 541 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8879 (tt) REVERT: D 88 GLU cc_start: 0.7075 (tp30) cc_final: 0.6858 (mm-30) REVERT: G 138 TYR cc_start: 0.6413 (m-80) cc_final: 0.6075 (m-10) REVERT: G 322 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7386 (t80) REVERT: G 504 LYS cc_start: 0.8344 (pttm) cc_final: 0.8056 (ptpt) REVERT: G 523 LYS cc_start: 0.8124 (ttpp) cc_final: 0.7753 (mtpt) REVERT: G 541 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8861 (tt) REVERT: H 88 GLU cc_start: 0.7080 (tp30) cc_final: 0.6854 (mm-30) outliers start: 87 outliers final: 51 residues processed: 411 average time/residue: 0.1264 time to fit residues: 76.3104 Evaluate side-chains 376 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 317 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 204 CYS Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 108 HIS Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 230 HIS Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 499 HIS Chi-restraints excluded: chain G residue 540 ASN Chi-restraints excluded: chain G residue 541 LEU Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 108 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 145 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 31 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 357 GLN B 98 ASN B 108 HIS E 97 GLN E 357 GLN F 108 HIS C 97 GLN C 540 ASN D 98 ASN D 108 HIS G 97 GLN G 357 GLN G 540 ASN H 98 ASN H 108 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.187880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.159440 restraints weight = 24276.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.158069 restraints weight = 36086.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.158301 restraints weight = 31252.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.157591 restraints weight = 27336.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.157939 restraints weight = 22792.482| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15408 Z= 0.164 Angle : 0.553 6.392 20892 Z= 0.288 Chirality : 0.037 0.118 2344 Planarity : 0.003 0.028 2628 Dihedral : 10.860 118.682 2244 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 5.97 % Allowed : 19.97 % Favored : 74.06 % 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: 2.38 (0.19), residues: 1884 helix: 2.26 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -0.98 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 171 TYR 0.017 0.001 TYR G 534 PHE 0.029 0.002 PHE F 17 TRP 0.006 0.001 TRP E 295 HIS 0.005 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00384 (15408) covalent geometry : angle 0.55285 (20892) hydrogen bonds : bond 0.03777 ( 1145) hydrogen bonds : angle 4.11363 ( 3411) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 322 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 TYR cc_start: 0.6346 (m-80) cc_final: 0.6113 (m-10) REVERT: A 226 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8658 (tt) REVERT: A 322 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7409 (t80) REVERT: A 504 LYS cc_start: 0.7994 (pttm) cc_final: 0.7694 (ptpt) REVERT: A 542 MET cc_start: 0.8176 (mmp) cc_final: 0.7912 (mmp) REVERT: E 226 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8678 (tt) REVERT: E 322 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7323 (t80) REVERT: E 504 LYS cc_start: 0.7987 (pttm) cc_final: 0.7744 (ptpt) REVERT: E 542 MET cc_start: 0.8209 (mmp) cc_final: 0.7942 (mmp) REVERT: F 88 GLU cc_start: 0.7178 (tp30) cc_final: 0.6865 (mm-30) REVERT: C 138 TYR cc_start: 0.6337 (m-80) cc_final: 0.6108 (m-10) REVERT: C 226 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8660 (tt) REVERT: C 322 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7605 (t80) REVERT: C 504 LYS cc_start: 0.7999 (pttm) cc_final: 0.7700 (ptpt) REVERT: C 542 MET cc_start: 0.8137 (mmp) cc_final: 0.7854 (mmp) REVERT: D 88 GLU cc_start: 0.7161 (tp30) cc_final: 0.6859 (mm-30) REVERT: G 138 TYR cc_start: 0.6345 (m-80) cc_final: 0.6140 (m-10) REVERT: G 226 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8666 (tt) REVERT: G 322 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7450 (t80) REVERT: G 504 LYS cc_start: 0.7980 (pttm) cc_final: 0.7683 (ptpt) REVERT: G 542 MET cc_start: 0.8164 (mmp) cc_final: 0.7877 (mmp) REVERT: H 88 GLU cc_start: 0.7156 (tp30) cc_final: 0.6857 (mm-30) outliers start: 89 outliers final: 58 residues processed: 385 average time/residue: 0.1162 time to fit residues: 67.6057 Evaluate side-chains 375 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 309 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 204 CYS Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 108 HIS Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 230 HIS Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 499 HIS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 108 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 51 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 179 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN B 108 HIS E 540 ASN F 108 HIS D 108 HIS H 108 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.187940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.159006 restraints weight = 24520.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.156366 restraints weight = 34687.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.154813 restraints weight = 30292.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.154595 restraints weight = 29658.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.155060 restraints weight = 22623.454| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15408 Z= 0.140 Angle : 0.545 7.190 20892 Z= 0.277 Chirality : 0.037 0.122 2344 Planarity : 0.003 0.027 2628 Dihedral : 10.672 118.689 2244 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 5.36 % Allowed : 20.24 % Favored : 74.40 % 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: 2.39 (0.19), residues: 1884 helix: 2.22 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -0.81 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 38 TYR 0.010 0.001 TYR C 268 PHE 0.026 0.001 PHE F 17 TRP 0.008 0.001 TRP G 295 HIS 0.008 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00324 (15408) covalent geometry : angle 0.54514 (20892) hydrogen bonds : bond 0.03689 ( 1145) hydrogen bonds : angle 4.03835 ( 3411) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 330 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 CYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7587 (t) REVERT: A 226 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8641 (tt) REVERT: A 322 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7313 (t80) REVERT: A 329 PHE cc_start: 0.7996 (m-10) cc_final: 0.7642 (m-10) REVERT: A 504 LYS cc_start: 0.8102 (pttm) cc_final: 0.7751 (ptpt) REVERT: B 13 PHE cc_start: 0.6578 (m-80) cc_final: 0.6338 (m-80) REVERT: B 145 MET cc_start: 0.7519 (ppp) cc_final: 0.7227 (ppp) REVERT: E 126 CYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7623 (t) REVERT: E 226 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8645 (tt) REVERT: E 322 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7341 (t80) REVERT: E 504 LYS cc_start: 0.8158 (pttm) cc_final: 0.7786 (ptpt) REVERT: F 88 GLU cc_start: 0.7175 (tp30) cc_final: 0.6835 (mm-30) REVERT: F 145 MET cc_start: 0.7523 (ppp) cc_final: 0.7215 (ppp) REVERT: C 126 CYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7600 (t) REVERT: C 226 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8642 (tt) REVERT: C 322 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7261 (t80) REVERT: C 329 PHE cc_start: 0.7974 (m-10) cc_final: 0.7605 (m-10) REVERT: C 504 LYS cc_start: 0.8112 (pttm) cc_final: 0.7761 (ptpt) REVERT: D 13 PHE cc_start: 0.6572 (m-80) cc_final: 0.6300 (m-80) REVERT: D 88 GLU cc_start: 0.7160 (tp30) cc_final: 0.6776 (mm-30) REVERT: D 145 MET cc_start: 0.7533 (ppp) cc_final: 0.7231 (ppp) REVERT: G 126 CYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7591 (t) REVERT: G 138 TYR cc_start: 0.6376 (m-80) cc_final: 0.6153 (m-10) REVERT: G 226 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8667 (tt) REVERT: G 322 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7382 (t80) REVERT: G 504 LYS cc_start: 0.8110 (pttm) cc_final: 0.7768 (ptpt) REVERT: H 13 PHE cc_start: 0.6703 (m-80) cc_final: 0.6424 (m-80) REVERT: H 88 GLU cc_start: 0.7152 (tp30) cc_final: 0.6837 (mm-30) REVERT: H 145 MET cc_start: 0.7534 (ppp) cc_final: 0.7222 (ppp) outliers start: 80 outliers final: 50 residues processed: 386 average time/residue: 0.1154 time to fit residues: 67.2780 Evaluate side-chains 373 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 311 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 523 LYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain E residue 540 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 230 HIS Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 499 HIS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 101 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 166 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 159 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 112 optimal weight: 0.0980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN E 97 GLN E 346 GLN E 347 GLN E 540 ASN C 97 GLN C 346 GLN G 97 GLN G 347 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.186940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.158077 restraints weight = 24497.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.154735 restraints weight = 35640.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.153794 restraints weight = 30665.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.153626 restraints weight = 28576.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.153938 restraints weight = 22582.564| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15408 Z= 0.149 Angle : 0.546 7.429 20892 Z= 0.278 Chirality : 0.037 0.119 2344 Planarity : 0.003 0.027 2628 Dihedral : 10.493 118.770 2244 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 6.90 % Allowed : 19.97 % Favored : 73.12 % 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: 2.33 (0.19), residues: 1884 helix: 2.20 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -0.91 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 38 TYR 0.011 0.001 TYR A 268 PHE 0.022 0.001 PHE F 17 TRP 0.007 0.001 TRP C 295 HIS 0.002 0.000 HIS C 538 Details of bonding type rmsd covalent geometry : bond 0.00350 (15408) covalent geometry : angle 0.54610 (20892) hydrogen bonds : bond 0.03741 ( 1145) hydrogen bonds : angle 4.06066 ( 3411) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 311 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 CYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7614 (t) REVERT: A 226 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8679 (tt) REVERT: A 322 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7585 (t80) REVERT: A 504 LYS cc_start: 0.8078 (pttm) cc_final: 0.7804 (ptpt) REVERT: E 126 CYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7633 (t) REVERT: E 226 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8677 (tt) REVERT: E 322 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7553 (t80) REVERT: E 504 LYS cc_start: 0.8141 (pttm) cc_final: 0.7877 (ptpt) REVERT: F 88 GLU cc_start: 0.7271 (tp30) cc_final: 0.6774 (mm-30) REVERT: C 126 CYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7637 (t) REVERT: C 226 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8675 (tt) REVERT: C 322 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7563 (t80) REVERT: C 504 LYS cc_start: 0.8081 (pttm) cc_final: 0.7813 (ptpt) REVERT: C 542 MET cc_start: 0.8208 (mmp) cc_final: 0.7967 (mmp) REVERT: D 88 GLU cc_start: 0.7283 (tp30) cc_final: 0.6782 (mm-30) REVERT: G 126 CYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7596 (t) REVERT: G 226 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8688 (tt) REVERT: G 322 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7530 (t80) REVERT: G 504 LYS cc_start: 0.8087 (pttm) cc_final: 0.7834 (ptpt) REVERT: G 542 MET cc_start: 0.8224 (mmp) cc_final: 0.7973 (mmp) REVERT: H 88 GLU cc_start: 0.7254 (tp30) cc_final: 0.6779 (mm-30) outliers start: 103 outliers final: 69 residues processed: 377 average time/residue: 0.1172 time to fit residues: 66.6410 Evaluate side-chains 378 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 297 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 523 LYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 204 CYS Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 353 HIS Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain E residue 540 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 108 HIS Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 353 HIS Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 230 HIS Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 353 HIS Chi-restraints excluded: chain G residue 499 HIS Chi-restraints excluded: chain G residue 540 ASN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 108 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 46 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 346 GLN A 347 GLN A 540 ASN E 97 GLN E 540 ASN C 97 GLN C 347 GLN G 97 GLN G 346 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.184685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.152412 restraints weight = 24517.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.147949 restraints weight = 32464.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.145757 restraints weight = 23472.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.146129 restraints weight = 21678.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.146171 restraints weight = 19102.436| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 15408 Z= 0.206 Angle : 0.618 7.949 20892 Z= 0.315 Chirality : 0.039 0.124 2344 Planarity : 0.003 0.028 2628 Dihedral : 10.552 119.441 2242 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 7.24 % Allowed : 21.05 % Favored : 71.72 % 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: 2.07 (0.19), residues: 1884 helix: 2.06 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -1.16 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 38 TYR 0.014 0.001 TYR A 268 PHE 0.032 0.002 PHE B 93 TRP 0.007 0.001 TRP A 238 HIS 0.002 0.000 HIS H 108 Details of bonding type rmsd covalent geometry : bond 0.00494 (15408) covalent geometry : angle 0.61845 (20892) hydrogen bonds : bond 0.04003 ( 1145) hydrogen bonds : angle 4.26249 ( 3411) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 308 time to evaluate : 0.554 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 126 CYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7694 (t) REVERT: A 322 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7561 (t80) REVERT: A 329 PHE cc_start: 0.8128 (m-10) cc_final: 0.7843 (m-10) REVERT: A 504 LYS cc_start: 0.8486 (pttm) cc_final: 0.7987 (ptpt) REVERT: B 145 MET cc_start: 0.7788 (ppp) cc_final: 0.7555 (ppp) REVERT: E 126 CYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7687 (t) REVERT: E 226 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8783 (tt) REVERT: E 322 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7624 (t80) REVERT: E 504 LYS cc_start: 0.8510 (pttm) cc_final: 0.8186 (ptpt) REVERT: F 73 MET cc_start: 0.7320 (mmm) cc_final: 0.7012 (mmt) REVERT: F 88 GLU cc_start: 0.7517 (tp30) cc_final: 0.6827 (mm-30) REVERT: F 145 MET cc_start: 0.7765 (ppp) cc_final: 0.7479 (ppp) REVERT: C 126 CYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7705 (t) REVERT: C 322 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7559 (t80) REVERT: C 329 PHE cc_start: 0.8083 (m-10) cc_final: 0.7784 (m-10) REVERT: C 504 LYS cc_start: 0.8505 (pttm) cc_final: 0.8013 (ptpt) REVERT: C 542 MET cc_start: 0.8632 (mmp) cc_final: 0.8400 (mmp) REVERT: D 145 MET cc_start: 0.7759 (ppp) cc_final: 0.7479 (ppp) REVERT: G 126 CYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7687 (t) REVERT: G 322 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7554 (t80) REVERT: G 504 LYS cc_start: 0.8506 (pttm) cc_final: 0.8157 (ptpt) REVERT: H 88 GLU cc_start: 0.7475 (tp30) cc_final: 0.6810 (mm-30) REVERT: H 145 MET cc_start: 0.7774 (ppp) cc_final: 0.7487 (ppp) outliers start: 108 outliers final: 77 residues processed: 376 average time/residue: 0.1068 time to fit residues: 60.7547 Evaluate side-chains 384 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 298 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 523 LYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 204 CYS Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 353 HIS Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain E residue 540 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 108 HIS Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 353 HIS Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 230 HIS Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 299 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 353 HIS Chi-restraints excluded: chain G residue 363 SER Chi-restraints excluded: chain G residue 499 HIS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 108 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 184 optimal weight: 8.9990 chunk 96 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 540 ASN E 97 GLN E 355 ASN E 540 ASN C 97 GLN D 98 ASN G 97 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.188234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.157287 restraints weight = 24254.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.156518 restraints weight = 31163.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.156402 restraints weight = 27298.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.155408 restraints weight = 25718.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.155971 restraints weight = 20885.337| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15408 Z= 0.131 Angle : 0.568 9.953 20892 Z= 0.285 Chirality : 0.037 0.121 2344 Planarity : 0.003 0.029 2628 Dihedral : 10.283 119.475 2236 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 5.90 % Allowed : 21.65 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.19), residues: 1884 helix: 2.15 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -1.09 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 38 TYR 0.010 0.001 TYR G 534 PHE 0.023 0.001 PHE D 93 TRP 0.010 0.001 TRP A 295 HIS 0.001 0.000 HIS G 499 Details of bonding type rmsd covalent geometry : bond 0.00296 (15408) covalent geometry : angle 0.56813 (20892) hydrogen bonds : bond 0.03755 ( 1145) hydrogen bonds : angle 4.12039 ( 3411) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 303 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 CYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7575 (t) REVERT: A 322 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.7592 (t80) REVERT: A 504 LYS cc_start: 0.8105 (pttm) cc_final: 0.7752 (ptpt) REVERT: B 94 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7737 (t0) REVERT: E 126 CYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7598 (t) REVERT: E 226 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8698 (tt) REVERT: E 322 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7554 (t80) REVERT: E 504 LYS cc_start: 0.8125 (pttm) cc_final: 0.7778 (ptpt) REVERT: F 88 GLU cc_start: 0.7237 (tp30) cc_final: 0.6667 (mm-30) REVERT: C 126 CYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7595 (t) REVERT: C 322 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7549 (t80) REVERT: C 329 PHE cc_start: 0.8008 (m-10) cc_final: 0.7644 (m-10) REVERT: C 504 LYS cc_start: 0.8122 (pttm) cc_final: 0.7771 (ptpt) REVERT: D 88 GLU cc_start: 0.7303 (tp30) cc_final: 0.7001 (mm-30) REVERT: G 126 CYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7575 (t) REVERT: G 322 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7570 (t80) REVERT: G 504 LYS cc_start: 0.8125 (pttm) cc_final: 0.7753 (ptpt) REVERT: H 88 GLU cc_start: 0.7203 (tp30) cc_final: 0.6658 (mm-30) outliers start: 88 outliers final: 64 residues processed: 363 average time/residue: 0.1159 time to fit residues: 63.2169 Evaluate side-chains 366 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 292 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 523 LYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 204 CYS Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 330 PHE Chi-restraints excluded: chain E residue 353 HIS Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain E residue 540 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 108 HIS Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 353 HIS Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 230 HIS Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 330 PHE Chi-restraints excluded: chain G residue 353 HIS Chi-restraints excluded: chain G residue 363 SER Chi-restraints excluded: chain G residue 499 HIS Chi-restraints excluded: chain G residue 540 ASN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 83 GLU Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 108 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 169 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 175 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 540 ASN E 97 GLN E 540 ASN C 97 GLN C 355 ASN G 97 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.186703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.159012 restraints weight = 24586.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.155825 restraints weight = 36885.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.153731 restraints weight = 33021.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.153631 restraints weight = 29030.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.153948 restraints weight = 25808.715| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 15408 Z= 0.203 Angle : 0.654 9.410 20892 Z= 0.327 Chirality : 0.039 0.158 2344 Planarity : 0.003 0.042 2628 Dihedral : 10.320 119.060 2236 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 6.37 % Allowed : 21.78 % Favored : 71.85 % 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: 2.06 (0.19), residues: 1884 helix: 2.10 (0.13), residues: 1460 sheet: None (None), residues: 0 loop : -1.31 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 544 TYR 0.014 0.001 TYR C 268 PHE 0.028 0.002 PHE H 93 TRP 0.009 0.001 TRP A 369 HIS 0.002 0.000 HIS A 538 Details of bonding type rmsd covalent geometry : bond 0.00491 (15408) covalent geometry : angle 0.65356 (20892) hydrogen bonds : bond 0.04048 ( 1145) hydrogen bonds : angle 4.27303 ( 3411) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 293 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 CYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7587 (t) REVERT: A 175 VAL cc_start: 0.8800 (OUTLIER) cc_final: 0.8513 (p) REVERT: A 322 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7632 (t80) REVERT: A 329 PHE cc_start: 0.8108 (m-10) cc_final: 0.7779 (m-10) REVERT: A 504 LYS cc_start: 0.8258 (pttm) cc_final: 0.7842 (pttm) REVERT: E 126 CYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7652 (t) REVERT: E 175 VAL cc_start: 0.8824 (OUTLIER) cc_final: 0.8535 (p) REVERT: E 322 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7697 (t80) REVERT: E 504 LYS cc_start: 0.8286 (pttm) cc_final: 0.7901 (ptpt) REVERT: F 125 MET cc_start: 0.8612 (mmm) cc_final: 0.8333 (mmm) REVERT: C 126 CYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7601 (t) REVERT: C 322 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7615 (t80) REVERT: C 329 PHE cc_start: 0.8091 (m-10) cc_final: 0.7768 (m-10) REVERT: C 504 LYS cc_start: 0.8313 (pttm) cc_final: 0.7899 (pttm) REVERT: D 88 GLU cc_start: 0.7474 (tp30) cc_final: 0.7052 (mm-30) REVERT: D 125 MET cc_start: 0.8618 (mmm) cc_final: 0.8282 (mmm) REVERT: G 126 CYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7584 (t) REVERT: G 175 VAL cc_start: 0.8796 (OUTLIER) cc_final: 0.8517 (p) REVERT: G 322 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7691 (t80) REVERT: G 504 LYS cc_start: 0.8292 (pttm) cc_final: 0.7872 (ptpt) REVERT: H 125 MET cc_start: 0.8598 (mmm) cc_final: 0.8277 (mmm) outliers start: 95 outliers final: 69 residues processed: 360 average time/residue: 0.1163 time to fit residues: 63.2533 Evaluate side-chains 364 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 284 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 523 LYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 204 CYS Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 353 HIS Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain E residue 540 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 108 HIS Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 353 HIS Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 230 HIS Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 299 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 363 SER Chi-restraints excluded: chain G residue 499 HIS Chi-restraints excluded: chain G residue 517 LYS Chi-restraints excluded: chain G residue 540 ASN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 108 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 131 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 173 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 355 ASN A 540 ASN E 97 GLN E 355 ASN E 540 ASN C 97 GLN G 97 GLN G 355 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.185337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.156399 restraints weight = 24477.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.154571 restraints weight = 35241.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.153790 restraints weight = 31981.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.153275 restraints weight = 29596.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.153864 restraints weight = 22984.914| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15408 Z= 0.158 Angle : 0.639 10.682 20892 Z= 0.315 Chirality : 0.038 0.171 2344 Planarity : 0.003 0.029 2628 Dihedral : 10.167 118.941 2236 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 6.64 % Allowed : 21.78 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.19), residues: 1884 helix: 2.14 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -1.24 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 38 TYR 0.011 0.001 TYR A 268 PHE 0.024 0.002 PHE H 93 TRP 0.012 0.001 TRP C 369 HIS 0.002 0.000 HIS A 538 Details of bonding type rmsd covalent geometry : bond 0.00373 (15408) covalent geometry : angle 0.63897 (20892) hydrogen bonds : bond 0.03906 ( 1145) hydrogen bonds : angle 4.20024 ( 3411) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 292 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 CYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7559 (t) REVERT: A 175 VAL cc_start: 0.8731 (OUTLIER) cc_final: 0.8430 (p) REVERT: A 322 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7696 (t80) REVERT: A 504 LYS cc_start: 0.8111 (pttm) cc_final: 0.7716 (pttm) REVERT: E 126 CYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7563 (t) REVERT: E 175 VAL cc_start: 0.8746 (OUTLIER) cc_final: 0.8452 (p) REVERT: E 322 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7641 (t80) REVERT: C 126 CYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7564 (t) REVERT: C 175 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8441 (p) REVERT: C 322 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7616 (t80) REVERT: C 329 PHE cc_start: 0.8050 (m-10) cc_final: 0.7701 (m-10) REVERT: C 504 LYS cc_start: 0.8131 (pttm) cc_final: 0.7735 (pttm) REVERT: D 88 GLU cc_start: 0.7407 (tp30) cc_final: 0.7042 (mm-30) REVERT: D 125 MET cc_start: 0.8404 (mmm) cc_final: 0.8194 (mmm) REVERT: G 126 CYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7560 (t) REVERT: G 175 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8462 (p) REVERT: G 322 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7598 (t80) REVERT: H 125 MET cc_start: 0.8421 (mmm) cc_final: 0.8201 (mmm) outliers start: 99 outliers final: 70 residues processed: 362 average time/residue: 0.1073 time to fit residues: 59.3288 Evaluate side-chains 372 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 290 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 523 LYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 204 CYS Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 330 PHE Chi-restraints excluded: chain E residue 353 HIS Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain E residue 517 LYS Chi-restraints excluded: chain E residue 540 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 108 HIS Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 230 HIS Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 363 SER Chi-restraints excluded: chain G residue 499 HIS Chi-restraints excluded: chain G residue 517 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 108 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 0.0570 chunk 175 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 167 optimal weight: 4.9990 chunk 128 optimal weight: 9.9990 overall best weight: 2.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 540 ASN E 97 GLN E 540 ASN C 97 GLN C 355 ASN G 97 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.181694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.152697 restraints weight = 24765.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.151082 restraints weight = 40828.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.151500 restraints weight = 36468.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.151028 restraints weight = 29840.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.151113 restraints weight = 26899.067| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 15408 Z= 0.224 Angle : 0.713 10.875 20892 Z= 0.354 Chirality : 0.041 0.210 2344 Planarity : 0.003 0.029 2628 Dihedral : 10.303 118.759 2236 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 6.57 % Allowed : 22.59 % Favored : 70.84 % 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: 1.92 (0.19), residues: 1884 helix: 2.01 (0.13), residues: 1460 sheet: None (None), residues: 0 loop : -1.41 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 38 TYR 0.014 0.001 TYR G 268 PHE 0.028 0.002 PHE H 93 TRP 0.028 0.001 TRP A 369 HIS 0.002 0.000 HIS A 538 Details of bonding type rmsd covalent geometry : bond 0.00544 (15408) covalent geometry : angle 0.71333 (20892) hydrogen bonds : bond 0.04172 ( 1145) hydrogen bonds : angle 4.37228 ( 3411) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 287 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 CYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7567 (t) REVERT: A 175 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8425 (p) REVERT: A 322 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7671 (t80) REVERT: A 353 HIS cc_start: 0.7143 (OUTLIER) cc_final: 0.6766 (m-70) REVERT: A 504 LYS cc_start: 0.8093 (pttm) cc_final: 0.7698 (pttm) REVERT: B 125 MET cc_start: 0.8577 (tpp) cc_final: 0.8136 (mmm) REVERT: E 126 CYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7554 (t) REVERT: E 175 VAL cc_start: 0.8739 (OUTLIER) cc_final: 0.8442 (p) REVERT: E 322 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7688 (t80) REVERT: E 504 LYS cc_start: 0.8091 (pttm) cc_final: 0.7656 (ptpt) REVERT: C 126 CYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7617 (t) REVERT: C 175 VAL cc_start: 0.8746 (OUTLIER) cc_final: 0.8437 (p) REVERT: C 322 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7628 (t80) REVERT: C 329 PHE cc_start: 0.8106 (m-10) cc_final: 0.7873 (m-10) REVERT: C 353 HIS cc_start: 0.7234 (OUTLIER) cc_final: 0.6849 (m-70) REVERT: C 504 LYS cc_start: 0.8066 (pttm) cc_final: 0.7662 (pttm) REVERT: D 88 GLU cc_start: 0.7419 (tp30) cc_final: 0.7041 (mm-30) REVERT: D 125 MET cc_start: 0.8418 (mmm) cc_final: 0.8128 (mmm) REVERT: G 126 CYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7604 (t) REVERT: G 175 VAL cc_start: 0.8749 (OUTLIER) cc_final: 0.8461 (p) REVERT: G 322 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7655 (t80) REVERT: G 504 LYS cc_start: 0.8068 (pttm) cc_final: 0.7624 (ptpt) REVERT: H 125 MET cc_start: 0.8407 (mmm) cc_final: 0.8107 (mmm) outliers start: 98 outliers final: 70 residues processed: 357 average time/residue: 0.1128 time to fit residues: 61.2539 Evaluate side-chains 365 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 281 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 523 LYS Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 204 CYS Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain E residue 517 LYS Chi-restraints excluded: chain E residue 540 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 108 HIS Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 353 HIS Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 230 HIS Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 299 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 363 SER Chi-restraints excluded: chain G residue 499 HIS Chi-restraints excluded: chain G residue 517 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 108 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 10.0000 chunk 36 optimal weight: 0.0970 chunk 39 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 116 optimal weight: 0.5980 chunk 166 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN A 540 ASN E 97 GLN E 540 ASN C 97 GLN G 97 GLN G 355 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.184992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.150951 restraints weight = 24428.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.150019 restraints weight = 34160.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.151326 restraints weight = 26768.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.150941 restraints weight = 19733.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.151102 restraints weight = 17843.002| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15408 Z= 0.135 Angle : 0.666 11.636 20892 Z= 0.325 Chirality : 0.038 0.202 2344 Planarity : 0.003 0.029 2628 Dihedral : 10.112 119.003 2236 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 5.43 % Allowed : 23.86 % Favored : 70.71 % 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: 2.11 (0.19), residues: 1884 helix: 2.14 (0.13), residues: 1460 sheet: None (None), residues: 0 loop : -1.33 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 38 TYR 0.011 0.001 TYR G 534 PHE 0.021 0.001 PHE D 93 TRP 0.026 0.001 TRP A 369 HIS 0.001 0.000 HIS F 108 Details of bonding type rmsd covalent geometry : bond 0.00303 (15408) covalent geometry : angle 0.66593 (20892) hydrogen bonds : bond 0.03920 ( 1145) hydrogen bonds : angle 4.17659 ( 3411) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2481.21 seconds wall clock time: 43 minutes 38.54 seconds (2618.54 seconds total)