Starting phenix.real_space_refine on Tue Dec 31 06:55:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tci_25813/12_2024/7tci_25813.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tci_25813/12_2024/7tci_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tci_25813/12_2024/7tci_25813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tci_25813/12_2024/7tci_25813.map" model { file = "/net/cci-nas-00/data/ceres_data/7tci_25813/12_2024/7tci_25813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tci_25813/12_2024/7tci_25813.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 1} 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, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 1} 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, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 1} 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, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 4, 'ARG:plan': 1} 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: 9.72, per 1000 atoms: 0.64 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: 3.74 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.44 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: 4.17 Time building geometry restraints manager: 4.27 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' 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: 2.660 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: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 34.740 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.620 ------------------------------------------------------------------------------- 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= 0.332 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 : 6.98 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP A 295 HIS 0.001 0.000 HIS A 248 PHE 0.007 0.001 PHE C 322 TYR 0.012 0.001 TYR A 534 ARG 0.001 0.000 ARG C 171 *********************** 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 : 1.831 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: 0.6137 (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: 0.8113 (tp40) REVERT: B 98 ASN cc_start: 0.7169 (m-40) cc_final: 0.6898 (m110) REVERT: E 138 TYR cc_start: 0.6507 (m-80) cc_final: 0.6126 (m-10) REVERT: E 322 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.7406 (t80) REVERT: E 509 MET cc_start: 0.8766 (mtt) cc_final: 0.8050 (mtm) REVERT: F 69 PHE cc_start: 0.8674 (t80) cc_final: 0.8007 (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: 0.6125 (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: 0.2769 time to fit residues: 183.4693 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 : 1.876 ------------------------------------------------------------------------------- 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 158 optimal weight: 0.2980 chunk 142 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 147 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 170 optimal weight: 8.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 A 540 ASN B 108 HIS E 97 GLN E 224 GLN E 357 GLN F 108 HIS C 97 GLN C 224 GLN D 108 HIS G 97 GLN G 224 GLN G 357 GLN H 108 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1424 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= 0.209 Angle : 0.531 5.608 20892 Z= 0.277 Chirality : 0.037 0.120 2344 Planarity : 0.003 0.029 2628 Dihedral : 11.147 120.408 2246 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 5.97 % Allowed : 15.95 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.19), residues: 1884 helix: 2.48 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -0.96 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 369 HIS 0.008 0.001 HIS B 108 PHE 0.023 0.002 PHE H 17 TYR 0.018 0.001 TYR E 534 ARG 0.003 0.000 ARG C 544 *********************** 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 444 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 355 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 TYR cc_start: 0.6537 (m-80) cc_final: 0.6140 (m-10) REVERT: A 322 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7315 (t80) REVERT: A 329 PHE cc_start: 0.8000 (m-10) cc_final: 0.7632 (m-10) REVERT: A 504 LYS cc_start: 0.8683 (pttm) cc_final: 0.8352 (ptpt) REVERT: B 88 GLU cc_start: 0.7301 (tp30) cc_final: 0.6883 (mm-30) REVERT: E 138 TYR cc_start: 0.6543 (m-80) cc_final: 0.6154 (m-10) REVERT: E 322 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7366 (t80) REVERT: E 504 LYS cc_start: 0.8690 (pttm) cc_final: 0.8351 (ptpt) REVERT: F 69 PHE cc_start: 0.8716 (t80) cc_final: 0.8451 (t80) REVERT: F 72 MET cc_start: 0.8967 (tmm) cc_final: 0.8585 (tmm) REVERT: F 73 MET cc_start: 0.7142 (mmm) cc_final: 0.6697 (mmm) REVERT: F 88 GLU cc_start: 0.7323 (tp30) cc_final: 0.6884 (mm-30) REVERT: C 138 TYR cc_start: 0.6541 (m-80) cc_final: 0.6151 (m-10) REVERT: C 322 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7323 (t80) REVERT: C 329 PHE cc_start: 0.7980 (m-10) cc_final: 0.7629 (m-10) REVERT: C 504 LYS cc_start: 0.8690 (pttm) cc_final: 0.8360 (ptpt) REVERT: C 523 LYS cc_start: 0.7941 (ttpp) cc_final: 0.7602 (mtpt) REVERT: D 88 GLU cc_start: 0.7320 (tp30) cc_final: 0.6865 (mm-30) REVERT: G 138 TYR cc_start: 0.6522 (m-80) cc_final: 0.6132 (m-10) REVERT: G 322 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7363 (t80) REVERT: G 504 LYS cc_start: 0.8687 (pttm) cc_final: 0.8355 (ptpt) REVERT: G 523 LYS cc_start: 0.7948 (ttpp) cc_final: 0.7618 (mtpt) REVERT: H 88 GLU cc_start: 0.7308 (tp30) cc_final: 0.6829 (mm-30) outliers start: 89 outliers final: 52 residues processed: 414 average time/residue: 0.2802 time to fit residues: 168.0533 Evaluate side-chains 369 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 313 time to evaluate : 1.748 ------------------------------------------------------------------------------- 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 540 ASN 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 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 D residue 92 VAL 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 H residue 92 VAL 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 94 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 116 optimal weight: 0.4980 chunk 47 optimal weight: 5.9990 chunk 171 optimal weight: 4.9990 chunk 184 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 169 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- 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 A 540 ASN B 98 ASN B 108 HIS E 97 GLN E 357 GLN F 98 ASN F 108 HIS C 97 GLN D 98 ASN D 108 HIS G 97 GLN G 357 GLN H 98 ASN H 108 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.128 15408 Z= 0.495 Angle : 0.712 10.134 20892 Z= 0.371 Chirality : 0.043 0.147 2344 Planarity : 0.004 0.030 2628 Dihedral : 11.363 118.599 2244 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 7.17 % Allowed : 19.91 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.19), residues: 1884 helix: 1.96 (0.13), residues: 1460 sheet: None (None), residues: 0 loop : -1.02 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 238 HIS 0.008 0.001 HIS H 108 PHE 0.029 0.003 PHE F 17 TYR 0.016 0.002 TYR E 268 ARG 0.005 0.001 ARG B 38 *********************** 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 417 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 310 time to evaluate : 1.736 Fit side-chains REVERT: A 138 TYR cc_start: 0.6638 (m-80) cc_final: 0.6235 (m-10) REVERT: A 322 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7497 (t80) REVERT: A 367 THR cc_start: 0.8213 (p) cc_final: 0.7807 (p) REVERT: A 504 LYS cc_start: 0.8688 (pttm) cc_final: 0.8282 (ptpt) REVERT: A 542 MET cc_start: 0.8751 (mmp) cc_final: 0.8410 (mmp) REVERT: B 50 GLN cc_start: 0.8739 (tp40) cc_final: 0.8040 (tp40) REVERT: B 83 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7761 (mp0) REVERT: E 138 TYR cc_start: 0.6604 (m-80) cc_final: 0.6226 (m-10) REVERT: E 226 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8713 (tt) REVERT: E 322 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7476 (t80) REVERT: E 329 PHE cc_start: 0.8181 (m-10) cc_final: 0.7820 (m-10) REVERT: E 367 THR cc_start: 0.8188 (p) cc_final: 0.7792 (p) REVERT: E 504 LYS cc_start: 0.8682 (pttm) cc_final: 0.8309 (ptpt) REVERT: E 542 MET cc_start: 0.8806 (mmp) cc_final: 0.8528 (mmp) REVERT: F 83 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: C 138 TYR cc_start: 0.6640 (m-80) cc_final: 0.6237 (m-10) REVERT: C 322 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7511 (t80) REVERT: C 367 THR cc_start: 0.8202 (p) cc_final: 0.7798 (p) REVERT: C 504 LYS cc_start: 0.8690 (pttm) cc_final: 0.8286 (ptpt) REVERT: C 542 MET cc_start: 0.8733 (mmp) cc_final: 0.8503 (mmp) REVERT: D 50 GLN cc_start: 0.8744 (tp40) cc_final: 0.8041 (tp40) REVERT: D 83 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: G 138 TYR cc_start: 0.6587 (m-80) cc_final: 0.6212 (m-10) REVERT: G 322 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7471 (t80) REVERT: G 329 PHE cc_start: 0.8199 (m-10) cc_final: 0.7812 (m-10) REVERT: G 367 THR cc_start: 0.8213 (p) cc_final: 0.7810 (p) REVERT: G 504 LYS cc_start: 0.8681 (pttm) cc_final: 0.8295 (ptpt) REVERT: G 542 MET cc_start: 0.8820 (mmp) cc_final: 0.8482 (mmp) REVERT: H 83 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7755 (mp0) outliers start: 107 outliers final: 70 residues processed: 389 average time/residue: 0.2823 time to fit residues: 166.3532 Evaluate side-chains 381 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 302 time to evaluate : 1.788 ------------------------------------------------------------------------------- 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 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 252 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 92 VAL 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 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 226 LEU Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain E residue 530 VAL 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 92 VAL 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 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 297 VAL Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 92 VAL 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 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 252 LEU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 499 HIS Chi-restraints excluded: chain G residue 530 VAL 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 92 VAL 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 168 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 81 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 162 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 B 108 HIS E 97 GLN E 346 GLN E 347 GLN F 108 HIS C 346 GLN C 347 GLN D 108 HIS G 346 GLN G 347 GLN H 108 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15408 Z= 0.201 Angle : 0.539 7.051 20892 Z= 0.278 Chirality : 0.037 0.122 2344 Planarity : 0.003 0.031 2628 Dihedral : 11.234 121.137 2240 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.70 % Allowed : 21.05 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.19), residues: 1884 helix: 2.21 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -1.12 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 295 HIS 0.006 0.001 HIS B 108 PHE 0.027 0.001 PHE F 17 TYR 0.010 0.001 TYR A 271 ARG 0.005 0.000 ARG F 38 *********************** 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 409 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 324 time to evaluate : 1.879 Fit side-chains REVERT: A 126 CYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7622 (t) REVERT: A 138 TYR cc_start: 0.6551 (m-80) cc_final: 0.6180 (m-10) REVERT: A 322 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7486 (t80) REVERT: A 329 PHE cc_start: 0.8123 (m-10) cc_final: 0.7812 (m-10) REVERT: A 504 LYS cc_start: 0.8606 (pttm) cc_final: 0.8063 (ptpt) REVERT: B 50 GLN cc_start: 0.8654 (tp40) cc_final: 0.7940 (tp40) REVERT: B 88 GLU cc_start: 0.7509 (tp30) cc_final: 0.6812 (mm-30) REVERT: E 126 CYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7648 (t) REVERT: E 138 TYR cc_start: 0.6538 (m-80) cc_final: 0.6169 (m-10) REVERT: E 226 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8642 (tt) REVERT: E 322 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7544 (t80) REVERT: E 504 LYS cc_start: 0.8626 (pttm) cc_final: 0.8084 (ptpt) REVERT: F 69 PHE cc_start: 0.8955 (t80) cc_final: 0.8680 (t80) REVERT: F 73 MET cc_start: 0.7748 (mmm) cc_final: 0.7310 (mmm) REVERT: F 88 GLU cc_start: 0.7529 (tp30) cc_final: 0.6865 (mm-30) REVERT: C 126 CYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7628 (t) REVERT: C 138 TYR cc_start: 0.6554 (m-80) cc_final: 0.6189 (m-10) REVERT: C 322 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7527 (t80) REVERT: C 329 PHE cc_start: 0.8110 (m-10) cc_final: 0.7809 (m-10) REVERT: C 504 LYS cc_start: 0.8608 (pttm) cc_final: 0.8067 (ptpt) REVERT: D 13 PHE cc_start: 0.7845 (m-80) cc_final: 0.7640 (m-80) REVERT: D 50 GLN cc_start: 0.8669 (tp40) cc_final: 0.7955 (tp40) REVERT: D 88 GLU cc_start: 0.7526 (tp30) cc_final: 0.6865 (mm-30) REVERT: G 126 CYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7623 (t) REVERT: G 138 TYR cc_start: 0.6518 (m-80) cc_final: 0.6151 (m-10) REVERT: G 322 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7505 (t80) REVERT: G 504 LYS cc_start: 0.8601 (pttm) cc_final: 0.8052 (ptpt) REVERT: H 69 PHE cc_start: 0.8918 (t80) cc_final: 0.8715 (t80) REVERT: H 88 GLU cc_start: 0.7490 (tp30) cc_final: 0.6821 (mm-30) outliers start: 85 outliers final: 52 residues processed: 383 average time/residue: 0.2480 time to fit residues: 143.4479 Evaluate side-chains 369 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 308 time to evaluate : 1.623 ------------------------------------------------------------------------------- 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 155 VAL Chi-restraints excluded: chain A residue 190 VAL 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 363 SER Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 94 ASP 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 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 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 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 124 LEU Chi-restraints excluded: chain C residue 126 CYS 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 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 523 LYS Chi-restraints excluded: chain D residue 53 ILE 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 155 VAL Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 190 VAL 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 363 SER Chi-restraints excluded: chain G residue 499 HIS Chi-restraints excluded: chain G residue 540 ASN Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 108 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 163 optimal weight: 0.5980 chunk 45 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN B 108 HIS F 108 HIS C 97 GLN D 108 HIS G 97 GLN H 108 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15408 Z= 0.245 Angle : 0.572 7.589 20892 Z= 0.293 Chirality : 0.038 0.141 2344 Planarity : 0.003 0.029 2628 Dihedral : 10.923 120.161 2236 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 8.11 % Allowed : 20.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.19), residues: 1884 helix: 2.16 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -1.14 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 295 HIS 0.005 0.001 HIS B 108 PHE 0.022 0.002 PHE B 93 TYR 0.011 0.001 TYR E 268 ARG 0.003 0.000 ARG F 38 *********************** 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 439 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 318 time to evaluate : 1.704 Fit side-chains REVERT: A 126 CYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7649 (t) REVERT: A 138 TYR cc_start: 0.6589 (m-80) cc_final: 0.6220 (m-10) REVERT: A 322 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7558 (t80) REVERT: A 329 PHE cc_start: 0.8148 (m-10) cc_final: 0.7883 (m-10) REVERT: A 504 LYS cc_start: 0.8617 (pttm) cc_final: 0.8268 (ptpt) REVERT: A 542 MET cc_start: 0.8755 (mmp) cc_final: 0.8527 (mmp) REVERT: B 50 GLN cc_start: 0.8632 (tp40) cc_final: 0.7821 (tp40) REVERT: B 53 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8650 (tp) REVERT: B 88 GLU cc_start: 0.7562 (tp30) cc_final: 0.6819 (mm-30) REVERT: E 126 CYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7680 (t) REVERT: E 138 TYR cc_start: 0.6579 (m-80) cc_final: 0.6212 (m-10) REVERT: E 226 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8652 (tt) REVERT: E 322 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7547 (t80) REVERT: E 504 LYS cc_start: 0.8597 (pttm) cc_final: 0.8270 (ptpt) REVERT: E 542 MET cc_start: 0.8768 (mmp) cc_final: 0.8514 (mmp) REVERT: F 69 PHE cc_start: 0.8982 (t80) cc_final: 0.8762 (t80) REVERT: F 73 MET cc_start: 0.7789 (mmm) cc_final: 0.7354 (mmm) REVERT: F 88 GLU cc_start: 0.7575 (tp30) cc_final: 0.6850 (mm-30) REVERT: C 126 CYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7660 (t) REVERT: C 138 TYR cc_start: 0.6578 (m-80) cc_final: 0.6216 (m-10) REVERT: C 322 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7534 (t80) REVERT: C 329 PHE cc_start: 0.8135 (m-10) cc_final: 0.7888 (m-10) REVERT: C 504 LYS cc_start: 0.8620 (pttm) cc_final: 0.8274 (ptpt) REVERT: C 542 MET cc_start: 0.8832 (mmp) cc_final: 0.8590 (mmp) REVERT: D 50 GLN cc_start: 0.8647 (tp40) cc_final: 0.7944 (tp40) REVERT: D 88 GLU cc_start: 0.7575 (tp30) cc_final: 0.6845 (mm-30) REVERT: G 126 CYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7657 (t) REVERT: G 138 TYR cc_start: 0.6560 (m-80) cc_final: 0.6190 (m-10) REVERT: G 322 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7571 (t80) REVERT: G 504 LYS cc_start: 0.8609 (pttm) cc_final: 0.8285 (ptpt) REVERT: G 542 MET cc_start: 0.8779 (mmp) cc_final: 0.8530 (mmp) REVERT: H 88 GLU cc_start: 0.7572 (tp30) cc_final: 0.6844 (mm-30) outliers start: 121 outliers final: 80 residues processed: 399 average time/residue: 0.2433 time to fit residues: 147.3450 Evaluate side-chains 399 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 309 time to evaluate : 1.806 ------------------------------------------------------------------------------- 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 253 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 297 VAL 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 B residue 30 THR Chi-restraints excluded: chain B residue 53 ILE 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 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 226 LEU Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 297 VAL 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 92 VAL 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 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 253 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 297 VAL 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 540 ASN Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 53 ILE 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 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 253 ILE 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 84 optimal weight: 0.0570 chunk 15 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- 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 E 355 ASN C 97 GLN C 540 ASN G 97 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15408 Z= 0.174 Angle : 0.561 9.097 20892 Z= 0.280 Chirality : 0.037 0.154 2344 Planarity : 0.003 0.029 2628 Dihedral : 10.548 119.448 2236 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 5.90 % Allowed : 23.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.19), residues: 1884 helix: 2.21 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -1.09 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 295 HIS 0.001 0.000 HIS E 499 PHE 0.016 0.001 PHE A 246 TYR 0.009 0.001 TYR C 271 ARG 0.003 0.000 ARG F 38 *********************** 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 410 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 322 time to evaluate : 1.580 Fit side-chains REVERT: A 126 CYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7624 (t) REVERT: A 138 TYR cc_start: 0.6524 (m-80) cc_final: 0.6221 (m-10) REVERT: A 322 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7473 (t80) REVERT: A 504 LYS cc_start: 0.8622 (pttm) cc_final: 0.8134 (ptpt) REVERT: B 38 ARG cc_start: 0.8377 (mtm-85) cc_final: 0.8169 (ptp-110) REVERT: B 88 GLU cc_start: 0.7487 (tp30) cc_final: 0.6775 (mm-30) REVERT: B 117 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7700 (mt) REVERT: E 126 CYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7646 (t) REVERT: E 138 TYR cc_start: 0.6518 (m-80) cc_final: 0.6225 (m-10) REVERT: E 226 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8636 (tt) REVERT: E 322 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7465 (t80) REVERT: E 504 LYS cc_start: 0.8598 (pttm) cc_final: 0.8235 (ptpt) REVERT: F 73 MET cc_start: 0.7792 (mmm) cc_final: 0.7337 (mmm) REVERT: F 88 GLU cc_start: 0.7503 (tp30) cc_final: 0.6782 (mm-30) REVERT: C 126 CYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7631 (t) REVERT: C 138 TYR cc_start: 0.6527 (m-80) cc_final: 0.6230 (m-10) REVERT: C 322 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7455 (t80) REVERT: C 504 LYS cc_start: 0.8624 (pttm) cc_final: 0.8130 (ptpt) REVERT: D 88 GLU cc_start: 0.7504 (tp30) cc_final: 0.6781 (mm-30) REVERT: G 126 CYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7622 (t) REVERT: G 138 TYR cc_start: 0.6501 (m-80) cc_final: 0.6204 (m-10) REVERT: G 322 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7500 (t80) REVERT: G 504 LYS cc_start: 0.8620 (pttm) cc_final: 0.8238 (ptpt) REVERT: H 88 GLU cc_start: 0.7494 (tp30) cc_final: 0.6781 (mm-30) outliers start: 88 outliers final: 62 residues processed: 382 average time/residue: 0.2593 time to fit residues: 148.3290 Evaluate side-chains 373 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 301 time to evaluate : 1.949 ------------------------------------------------------------------------------- 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 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 92 VAL 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 B residue 117 LEU 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 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 92 VAL 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 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 C residue 540 ASN 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 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 499 HIS Chi-restraints excluded: chain G residue 540 ASN 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 175 optimal weight: 20.0000 chunk 20 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 153 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 110 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN C 97 GLN C 540 ASN G 97 GLN G 540 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15408 Z= 0.186 Angle : 0.576 8.415 20892 Z= 0.286 Chirality : 0.038 0.169 2344 Planarity : 0.003 0.029 2628 Dihedral : 10.342 119.871 2234 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 5.97 % Allowed : 23.79 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.19), residues: 1884 helix: 2.19 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -1.11 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 295 HIS 0.001 0.000 HIS B 108 PHE 0.025 0.001 PHE F 93 TYR 0.016 0.001 TYR C 372 ARG 0.007 0.000 ARG H 38 *********************** 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 400 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 311 time to evaluate : 1.870 Fit side-chains revert: symmetry clash REVERT: A 126 CYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7645 (t) REVERT: A 138 TYR cc_start: 0.6517 (m-80) cc_final: 0.6205 (m-10) REVERT: A 175 VAL cc_start: 0.8815 (OUTLIER) cc_final: 0.8577 (p) REVERT: A 322 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7468 (t80) REVERT: A 542 MET cc_start: 0.8855 (mmp) cc_final: 0.8530 (mmp) REVERT: B 88 GLU cc_start: 0.7460 (tp30) cc_final: 0.6672 (mm-30) REVERT: B 117 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7701 (mt) REVERT: E 126 CYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7672 (t) REVERT: E 138 TYR cc_start: 0.6496 (m-80) cc_final: 0.6179 (m-10) REVERT: E 175 VAL cc_start: 0.8809 (OUTLIER) cc_final: 0.8573 (p) REVERT: E 226 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8619 (tt) REVERT: E 322 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7483 (t80) REVERT: F 73 MET cc_start: 0.7799 (mmm) cc_final: 0.7423 (mmm) REVERT: F 88 GLU cc_start: 0.7502 (tp30) cc_final: 0.6729 (mm-30) REVERT: C 126 CYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7653 (t) REVERT: C 138 TYR cc_start: 0.6507 (m-80) cc_final: 0.6183 (m-10) REVERT: C 322 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7486 (t80) REVERT: C 504 LYS cc_start: 0.8624 (pttm) cc_final: 0.7987 (ptpt) REVERT: D 88 GLU cc_start: 0.7507 (tp30) cc_final: 0.6720 (mm-30) REVERT: G 126 CYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7648 (t) REVERT: G 138 TYR cc_start: 0.6479 (m-80) cc_final: 0.6158 (m-10) REVERT: G 175 VAL cc_start: 0.8808 (OUTLIER) cc_final: 0.8570 (p) REVERT: G 322 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7472 (t80) REVERT: G 504 LYS cc_start: 0.8618 (pttm) cc_final: 0.8000 (ptpt) REVERT: H 69 PHE cc_start: 0.8950 (t80) cc_final: 0.8697 (t80) REVERT: H 88 GLU cc_start: 0.7497 (tp30) cc_final: 0.6723 (mm-30) outliers start: 89 outliers final: 59 residues processed: 372 average time/residue: 0.2452 time to fit residues: 140.2216 Evaluate side-chains 361 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 289 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN 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 363 SER Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 523 LYS Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 117 LEU 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 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 F residue 98 ASN Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 108 HIS Chi-restraints excluded: chain C residue 97 GLN 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 C residue 540 ASN Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain G residue 97 GLN 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 499 HIS Chi-restraints excluded: chain G residue 540 ASN Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 102 SER 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 112 optimal weight: 1.9990 chunk 72 optimal weight: 0.0470 chunk 108 optimal weight: 5.9990 chunk 54 optimal weight: 0.0070 chunk 35 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 142 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 overall best weight: 0.4296 ------------------------------------------------------------------------------- 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 E 97 GLN E 355 ASN C 97 GLN C 355 ASN C 540 ASN G 97 GLN G 355 ASN G 540 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15408 Z= 0.169 Angle : 0.592 10.941 20892 Z= 0.291 Chirality : 0.037 0.163 2344 Planarity : 0.003 0.029 2628 Dihedral : 10.135 119.624 2234 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 5.23 % Allowed : 25.47 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.19), residues: 1884 helix: 2.20 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -1.10 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 238 HIS 0.002 0.000 HIS C 538 PHE 0.019 0.001 PHE D 93 TYR 0.016 0.001 TYR E 372 ARG 0.005 0.000 ARG H 38 *********************** 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 378 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 300 time to evaluate : 2.400 Fit side-chains revert: symmetry clash REVERT: A 126 CYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7692 (t) REVERT: A 138 TYR cc_start: 0.6503 (m-80) cc_final: 0.6156 (m-10) REVERT: A 175 VAL cc_start: 0.8869 (OUTLIER) cc_final: 0.8606 (p) REVERT: A 322 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7531 (t80) REVERT: B 48 GLU cc_start: 0.8825 (tp30) cc_final: 0.8616 (tp30) REVERT: B 69 PHE cc_start: 0.8640 (t80) cc_final: 0.8439 (t80) REVERT: B 88 GLU cc_start: 0.7457 (tp30) cc_final: 0.6649 (mm-30) REVERT: B 117 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7641 (mt) REVERT: E 126 CYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7721 (t) REVERT: E 138 TYR cc_start: 0.6496 (m-80) cc_final: 0.6154 (m-10) REVERT: E 175 VAL cc_start: 0.8868 (OUTLIER) cc_final: 0.8596 (p) REVERT: E 226 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8603 (tt) REVERT: E 322 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7593 (t80) REVERT: F 73 MET cc_start: 0.7724 (mmm) cc_final: 0.7368 (mmm) REVERT: F 88 GLU cc_start: 0.7503 (tp30) cc_final: 0.6700 (mm-30) REVERT: C 126 CYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7700 (t) REVERT: C 138 TYR cc_start: 0.6505 (m-80) cc_final: 0.6165 (m-10) REVERT: C 175 VAL cc_start: 0.8859 (OUTLIER) cc_final: 0.8618 (p) REVERT: C 322 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7517 (t80) REVERT: D 88 GLU cc_start: 0.7487 (tp30) cc_final: 0.6691 (mm-30) REVERT: G 126 CYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7703 (t) REVERT: G 138 TYR cc_start: 0.6480 (m-80) cc_final: 0.6142 (m-10) REVERT: G 175 VAL cc_start: 0.8865 (OUTLIER) cc_final: 0.8600 (p) REVERT: G 322 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7505 (t80) REVERT: H 88 GLU cc_start: 0.7489 (tp30) cc_final: 0.6693 (mm-30) outliers start: 78 outliers final: 51 residues processed: 357 average time/residue: 0.2671 time to fit residues: 145.7462 Evaluate side-chains 346 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 281 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 230 HIS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 330 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 B residue 94 ASP Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 97 GLN 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 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 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 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 230 HIS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 330 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 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 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 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 499 HIS Chi-restraints excluded: chain G residue 517 LYS Chi-restraints excluded: chain G residue 540 ASN Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 98 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 4.9990 chunk 158 optimal weight: 0.0060 chunk 168 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 178 optimal weight: 8.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN E 97 GLN C 97 GLN C 540 ASN G 97 GLN G 540 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 15408 Z= 0.408 Angle : 0.710 11.028 20892 Z= 0.357 Chirality : 0.042 0.218 2344 Planarity : 0.003 0.031 2628 Dihedral : 10.482 120.112 2228 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 6.64 % Allowed : 24.73 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.19), residues: 1884 helix: 1.97 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -1.34 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 238 HIS 0.002 0.000 HIS H 108 PHE 0.028 0.002 PHE B 93 TYR 0.017 0.002 TYR E 268 ARG 0.005 0.001 ARG H 38 *********************** 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 386 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 287 time to evaluate : 1.943 Fit side-chains revert: symmetry clash REVERT: A 126 CYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7689 (t) REVERT: A 138 TYR cc_start: 0.6579 (m-80) cc_final: 0.6208 (m-10) REVERT: A 175 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8628 (p) REVERT: A 322 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7534 (t80) REVERT: A 504 LYS cc_start: 0.8727 (pttm) cc_final: 0.8014 (ptpt) REVERT: B 117 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7770 (mt) REVERT: E 126 CYS cc_start: 0.8429 (OUTLIER) cc_final: 0.7719 (t) REVERT: E 138 TYR cc_start: 0.6573 (m-80) cc_final: 0.6213 (m-10) REVERT: E 175 VAL cc_start: 0.8839 (OUTLIER) cc_final: 0.8625 (p) REVERT: E 322 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7608 (t80) REVERT: E 504 LYS cc_start: 0.8642 (pttm) cc_final: 0.8032 (ptpt) REVERT: C 126 CYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7699 (t) REVERT: C 138 TYR cc_start: 0.6560 (m-80) cc_final: 0.6212 (m-10) REVERT: C 175 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8636 (p) REVERT: C 322 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7534 (t80) REVERT: C 504 LYS cc_start: 0.8725 (pttm) cc_final: 0.8006 (ptpt) REVERT: D 13 PHE cc_start: 0.7660 (m-80) cc_final: 0.7322 (m-80) REVERT: G 126 CYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7699 (t) REVERT: G 138 TYR cc_start: 0.6552 (m-80) cc_final: 0.6197 (m-10) REVERT: G 175 VAL cc_start: 0.8830 (OUTLIER) cc_final: 0.8622 (p) REVERT: G 322 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7514 (t80) REVERT: H 73 MET cc_start: 0.7878 (tpp) cc_final: 0.7642 (tpp) outliers start: 99 outliers final: 72 residues processed: 357 average time/residue: 0.2551 time to fit residues: 137.9890 Evaluate side-chains 370 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 285 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 132 LEU 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 253 ILE 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 363 SER Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 523 LYS 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 102 SER Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 132 LEU 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 253 ILE 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 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 102 SER Chi-restraints excluded: chain F residue 108 HIS Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 132 LEU 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 253 ILE 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 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 108 HIS Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 132 LEU 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 253 ILE 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 G residue 540 ASN 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 102 SER 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 108 optimal weight: 4.9990 chunk 84 optimal weight: 30.0000 chunk 124 optimal weight: 0.9990 chunk 187 optimal weight: 8.9990 chunk 172 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 158 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 E 97 GLN E 355 ASN C 97 GLN C 355 ASN G 97 GLN G 355 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 15408 Z= 0.214 Angle : 0.641 10.930 20892 Z= 0.317 Chirality : 0.039 0.194 2344 Planarity : 0.003 0.031 2628 Dihedral : 10.433 120.598 2228 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.89 % Allowed : 26.47 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.19), residues: 1884 helix: 2.07 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -1.25 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 369 HIS 0.001 0.000 HIS G 499 PHE 0.023 0.002 PHE F 142 TYR 0.015 0.001 TYR E 372 ARG 0.004 0.000 ARG H 38 ********************** 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 369 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 296 time to evaluate : 2.296 Fit side-chains REVERT: A 126 CYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7612 (t) REVERT: A 138 TYR cc_start: 0.6491 (m-80) cc_final: 0.6168 (m-10) REVERT: A 175 VAL cc_start: 0.8818 (OUTLIER) cc_final: 0.8590 (p) REVERT: A 322 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7536 (t80) REVERT: A 504 LYS cc_start: 0.8687 (pttm) cc_final: 0.8169 (ptpt) REVERT: B 88 GLU cc_start: 0.7642 (tp30) cc_final: 0.6923 (mm-30) REVERT: E 126 CYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7615 (t) REVERT: E 138 TYR cc_start: 0.6494 (m-80) cc_final: 0.6164 (m-10) REVERT: E 175 VAL cc_start: 0.8813 (OUTLIER) cc_final: 0.8589 (p) REVERT: E 322 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7520 (t80) REVERT: F 13 PHE cc_start: 0.7520 (m-80) cc_final: 0.7239 (m-80) REVERT: C 126 CYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7615 (t) REVERT: C 138 TYR cc_start: 0.6478 (m-80) cc_final: 0.6152 (m-10) REVERT: C 175 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8640 (p) REVERT: C 322 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7399 (t80) REVERT: C 504 LYS cc_start: 0.8670 (pttm) cc_final: 0.8163 (ptpt) REVERT: C 517 LYS cc_start: 0.9240 (mmtm) cc_final: 0.8965 (mmtp) REVERT: D 13 PHE cc_start: 0.7527 (m-80) cc_final: 0.7295 (m-80) REVERT: D 50 GLN cc_start: 0.8847 (tp40) cc_final: 0.8110 (tp40) REVERT: G 126 CYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7620 (t) REVERT: G 138 TYR cc_start: 0.6480 (m-80) cc_final: 0.6140 (m-10) REVERT: G 175 VAL cc_start: 0.8813 (OUTLIER) cc_final: 0.8585 (p) REVERT: G 322 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7553 (t80) REVERT: G 504 LYS cc_start: 0.8680 (pttm) cc_final: 0.7945 (ptpt) REVERT: H 73 MET cc_start: 0.7845 (tpp) cc_final: 0.7596 (tpp) outliers start: 73 outliers final: 50 residues processed: 355 average time/residue: 0.2788 time to fit residues: 154.8893 Evaluate side-chains 347 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 285 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 230 HIS Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 254 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 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 102 SER Chi-restraints excluded: chain E residue 97 GLN 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 330 PHE Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 102 SER 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 230 HIS Chi-restraints excluded: chain C residue 254 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 540 ASN Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 98 ASN 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 230 HIS Chi-restraints excluded: chain G residue 253 ILE 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 363 SER Chi-restraints excluded: chain G residue 499 HIS Chi-restraints excluded: chain G residue 517 LYS 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 102 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 0.0470 chunk 137 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN E 97 GLN E 234 GLN C 97 GLN G 97 GLN G 234 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.188006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.158835 restraints weight = 24742.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.157545 restraints weight = 35127.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.156106 restraints weight = 28967.831| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 15408 Z= 0.202 Angle : 0.630 11.972 20892 Z= 0.311 Chirality : 0.038 0.191 2344 Planarity : 0.003 0.030 2628 Dihedral : 10.203 119.987 2228 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.69 % Allowed : 26.41 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.19), residues: 1884 helix: 2.14 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -1.19 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP G 369 HIS 0.001 0.000 HIS C 538 PHE 0.024 0.001 PHE D 142 TYR 0.014 0.001 TYR E 372 ARG 0.004 0.000 ARG D 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3377.19 seconds wall clock time: 62 minutes 9.18 seconds (3729.18 seconds total)