Starting phenix.real_space_refine on Fri Jun 13 13:41:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tci_25813/06_2025/7tci_25813.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tci_25813/06_2025/7tci_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_25813/06_2025/7tci_25813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tci_25813/06_2025/7tci_25813.map" model { file = "/net/cci-nas-00/data/ceres_data/7tci_25813/06_2025/7tci_25813.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tci_25813/06_2025/7tci_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 10.17, per 1000 atoms: 0.67 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: 4.23 Conformation dependent library (CDL) restraints added in 1.9 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: 4.58 Time building geometry restraints manager: 4.93 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: 0.11 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.240 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: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 36.900 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 15408 Z= 0.277 Angle : 0.618 17.970 20892 Z= 0.275 Chirality : 0.036 0.238 2344 Planarity : 0.003 0.031 2628 Dihedral : 13.437 123.840 5436 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 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 Details of bonding type rmsd hydrogen bonds : bond 0.07677 ( 1145) hydrogen bonds : angle 3.92992 ( 3411) covalent geometry : bond 0.00558 (15408) covalent geometry : angle 0.61838 (20892) *********************** 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 : 1.547 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: 0.2565 time to fit residues: 170.0254 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 : 1.537 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.182451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.153535 restraints weight = 24560.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.150085 restraints weight = 36698.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.149772 restraints weight = 36433.995| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1423 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= 0.142 Angle : 0.531 5.607 20892 Z= 0.277 Chirality : 0.037 0.120 2344 Planarity : 0.003 0.029 2628 Dihedral : 11.144 120.324 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 : 15.88 % Favored : 78.15 % 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 0.009 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 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 1145) hydrogen bonds : angle 3.97881 ( 3411) covalent geometry : bond 0.00327 (15408) covalent geometry : angle 0.53106 (20892) *********************** 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 : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 TYR cc_start: 0.6389 (m-80) cc_final: 0.6145 (m-10) REVERT: A 322 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.7302 (t80) REVERT: A 329 PHE cc_start: 0.7874 (m-10) cc_final: 0.7467 (m-10) REVERT: A 504 LYS cc_start: 0.8028 (pttm) cc_final: 0.7808 (ptpt) REVERT: A 541 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8868 (tt) REVERT: E 138 TYR cc_start: 0.6403 (m-80) cc_final: 0.6157 (m-10) REVERT: E 322 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7386 (t80) REVERT: E 504 LYS cc_start: 0.8056 (pttm) cc_final: 0.7775 (ptpt) REVERT: E 541 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8878 (tt) REVERT: C 138 TYR cc_start: 0.6408 (m-80) cc_final: 0.6156 (m-10) REVERT: C 322 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.7322 (t80) REVERT: C 329 PHE cc_start: 0.7895 (m-10) cc_final: 0.7522 (m-10) REVERT: C 504 LYS cc_start: 0.8066 (pttm) cc_final: 0.7835 (ptpt) REVERT: C 523 LYS cc_start: 0.8204 (ttpp) cc_final: 0.7815 (mtpt) REVERT: C 541 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8875 (tt) REVERT: G 138 TYR cc_start: 0.6371 (m-80) cc_final: 0.6126 (m-10) REVERT: G 322 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7382 (t80) REVERT: G 504 LYS cc_start: 0.8074 (pttm) cc_final: 0.7834 (ptpt) REVERT: G 523 LYS cc_start: 0.8207 (ttpp) cc_final: 0.7828 (mtpt) REVERT: G 541 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8866 (tt) outliers start: 89 outliers final: 52 residues processed: 414 average time/residue: 0.2725 time to fit residues: 163.6077 Evaluate side-chains 373 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 313 time to evaluate : 1.649 ------------------------------------------------------------------------------- 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 A residue 541 LEU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 204 CYS Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain E residue 541 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 108 HIS Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 541 LEU 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 G residue 541 LEU 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 168 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 108 HIS E 97 GLN E 357 GLN F 108 HIS C 97 GLN D 108 HIS G 97 GLN G 357 GLN H 108 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.186817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.157485 restraints weight = 24067.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.155269 restraints weight = 34619.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.154213 restraints weight = 30434.554| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15408 Z= 0.176 Angle : 0.565 6.408 20892 Z= 0.292 Chirality : 0.038 0.120 2344 Planarity : 0.003 0.029 2628 Dihedral : 10.954 118.876 2244 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 6.30 % Allowed : 19.64 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.42 (0.19), residues: 1884 helix: 2.26 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -0.90 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 295 HIS 0.006 0.001 HIS D 108 PHE 0.029 0.002 PHE F 17 TYR 0.016 0.001 TYR G 534 ARG 0.004 0.000 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 1145) hydrogen bonds : angle 4.14354 ( 3411) covalent geometry : bond 0.00420 (15408) covalent geometry : angle 0.56475 (20892) *********************** 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 406 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 312 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8705 (tt) REVERT: A 322 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7669 (t80) REVERT: A 504 LYS cc_start: 0.8041 (pttm) cc_final: 0.7716 (ptpt) REVERT: A 542 MET cc_start: 0.8203 (mmp) cc_final: 0.7963 (mmp) REVERT: E 226 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8672 (tt) REVERT: E 322 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7600 (t80) REVERT: E 504 LYS cc_start: 0.8045 (pttm) cc_final: 0.7760 (ptpt) REVERT: E 542 MET cc_start: 0.8214 (mmp) cc_final: 0.7939 (mmp) REVERT: C 226 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8707 (tt) REVERT: C 322 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7565 (t80) REVERT: C 504 LYS cc_start: 0.8047 (pttm) cc_final: 0.7720 (ptpt) REVERT: C 523 LYS cc_start: 0.8060 (ttpp) cc_final: 0.7797 (mtpt) REVERT: C 542 MET cc_start: 0.8176 (mmp) cc_final: 0.7904 (mmp) REVERT: G 226 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8688 (tt) REVERT: G 322 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7340 (t80) REVERT: G 504 LYS cc_start: 0.8019 (pttm) cc_final: 0.7700 (ptpt) REVERT: G 542 MET cc_start: 0.8291 (mmp) cc_final: 0.8013 (mmp) outliers start: 94 outliers final: 61 residues processed: 382 average time/residue: 0.2450 time to fit residues: 140.9216 Evaluate side-chains 369 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 300 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 204 CYS Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain E residue 540 ASN Chi-restraints excluded: chain F residue 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 F residue 117 LEU 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 155 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 297 VAL 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 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 145 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 230 HIS Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 499 HIS Chi-restraints excluded: chain G residue 540 ASN Chi-restraints excluded: chain 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 96 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 169 optimal weight: 9.9990 chunk 162 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 HIS E 97 GLN E 347 GLN F 108 HIS C 346 GLN D 108 HIS H 108 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.186968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.158677 restraints weight = 24166.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.156086 restraints weight = 35152.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.155710 restraints weight = 33807.249| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15408 Z= 0.150 Angle : 0.546 6.893 20892 Z= 0.282 Chirality : 0.037 0.120 2344 Planarity : 0.003 0.030 2628 Dihedral : 10.834 119.734 2244 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 6.50 % Allowed : 19.64 % Favored : 73.86 % 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: 2.35 (0.19), residues: 1884 helix: 2.27 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -1.08 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 295 HIS 0.010 0.001 HIS D 108 PHE 0.026 0.002 PHE F 17 TYR 0.011 0.001 TYR A 268 ARG 0.004 0.000 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 1145) hydrogen bonds : angle 4.11424 ( 3411) covalent geometry : bond 0.00351 (15408) covalent geometry : angle 0.54560 (20892) *********************** 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 416 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 319 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 CYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7622 (t) REVERT: A 226 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8678 (tt) REVERT: A 322 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7600 (t80) REVERT: A 329 PHE cc_start: 0.7999 (m-10) cc_final: 0.7627 (m-10) REVERT: A 504 LYS cc_start: 0.7940 (pttm) cc_final: 0.7685 (ptpt) REVERT: B 13 PHE cc_start: 0.6186 (m-80) cc_final: 0.5909 (m-80) REVERT: E 126 CYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7632 (t) REVERT: E 226 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8693 (tt) REVERT: E 322 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7581 (t80) REVERT: E 504 LYS cc_start: 0.8004 (pttm) cc_final: 0.7721 (ptpt) REVERT: C 126 CYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7627 (t) REVERT: C 226 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8674 (tt) REVERT: C 322 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7571 (t80) REVERT: C 329 PHE cc_start: 0.7992 (m-10) cc_final: 0.7647 (m-10) REVERT: C 504 LYS cc_start: 0.7924 (pttm) cc_final: 0.7687 (ptpt) REVERT: C 523 LYS cc_start: 0.8063 (ttpp) cc_final: 0.7822 (mtpt) REVERT: D 13 PHE cc_start: 0.6229 (m-80) cc_final: 0.5968 (m-80) REVERT: G 126 CYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7627 (t) REVERT: G 226 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8693 (tt) REVERT: G 322 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7593 (t80) REVERT: G 504 LYS cc_start: 0.7933 (pttm) cc_final: 0.7690 (ptpt) REVERT: H 13 PHE cc_start: 0.6431 (m-80) cc_final: 0.6139 (m-80) outliers start: 97 outliers final: 66 residues processed: 385 average time/residue: 0.2387 time to fit residues: 138.7020 Evaluate side-chains 383 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 305 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 523 LYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 204 CYS Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 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 101 ILE Chi-restraints excluded: chain F residue 108 HIS Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 353 HIS Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 230 HIS Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 297 VAL 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 101 ILE 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 152 optimal weight: 0.3980 chunk 126 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 181 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 F 108 HIS C 347 GLN D 108 HIS G 346 GLN G 347 GLN G 540 ASN H 108 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.188424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.161288 restraints weight = 24635.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.159223 restraints weight = 38155.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.159674 restraints weight = 33369.921| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15408 Z= 0.128 Angle : 0.542 7.546 20892 Z= 0.275 Chirality : 0.037 0.115 2344 Planarity : 0.003 0.030 2628 Dihedral : 10.578 119.621 2244 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 6.84 % Allowed : 19.91 % 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: 2.42 (0.19), residues: 1884 helix: 2.31 (0.13), residues: 1464 sheet: None (None), residues: 0 loop : -1.03 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 295 HIS 0.008 0.001 HIS H 108 PHE 0.019 0.001 PHE H 17 TYR 0.009 0.001 TYR A 268 ARG 0.003 0.000 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.03691 ( 1145) hydrogen bonds : angle 4.03627 ( 3411) covalent geometry : bond 0.00290 (15408) covalent geometry : angle 0.54151 (20892) *********************** 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 431 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 329 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 CYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7593 (t) REVERT: A 226 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8658 (tt) REVERT: A 322 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7582 (t80) REVERT: A 329 PHE cc_start: 0.7979 (m-10) cc_final: 0.7596 (m-10) REVERT: A 504 LYS cc_start: 0.7840 (pttm) cc_final: 0.7620 (ptpt) REVERT: E 126 CYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7598 (t) REVERT: E 226 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8645 (tt) REVERT: E 322 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7429 (t80) REVERT: E 504 LYS cc_start: 0.7859 (pttm) cc_final: 0.7631 (ptpt) REVERT: E 542 MET cc_start: 0.8002 (mmp) cc_final: 0.7765 (mmp) REVERT: C 126 CYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7601 (t) REVERT: C 226 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8633 (tt) REVERT: C 322 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7358 (t80) REVERT: C 329 PHE cc_start: 0.7959 (m-10) cc_final: 0.7581 (m-10) REVERT: C 504 LYS cc_start: 0.7825 (pttm) cc_final: 0.7611 (ptpt) REVERT: C 523 LYS cc_start: 0.8068 (ttpp) cc_final: 0.7807 (mtpt) REVERT: C 542 MET cc_start: 0.7943 (mmp) cc_final: 0.7711 (mmp) REVERT: G 126 CYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7585 (t) REVERT: G 226 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8654 (tt) REVERT: G 322 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7663 (t80) outliers start: 102 outliers final: 56 residues processed: 396 average time/residue: 0.2423 time to fit residues: 144.4736 Evaluate side-chains 360 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 292 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 499 HIS 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 E residue 118 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 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 108 HIS Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 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 92 VAL Chi-restraints excluded: chain D residue 94 ASP 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 190 VAL Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 230 HIS Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 330 PHE Chi-restraints excluded: chain G residue 353 HIS Chi-restraints excluded: chain G residue 363 SER Chi-restraints excluded: chain G residue 499 HIS Chi-restraints excluded: chain G residue 540 ASN Chi-restraints excluded: chain H residue 92 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 96 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 160 optimal weight: 0.3980 chunk 163 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 142 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 E 97 GLN F 108 HIS C 97 GLN D 108 HIS G 97 GLN G 540 ASN H 108 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.189649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.162614 restraints weight = 24552.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.160730 restraints weight = 39685.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.161482 restraints weight = 35951.138| |-----------------------------------------------------------------------------| r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 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 0.031 15408 Z= 0.125 Angle : 0.553 8.914 20892 Z= 0.282 Chirality : 0.037 0.203 2344 Planarity : 0.003 0.030 2628 Dihedral : 10.163 118.278 2236 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 6.10 % Allowed : 21.65 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.35 (0.19), residues: 1884 helix: 2.25 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -1.05 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 295 HIS 0.003 0.001 HIS B 108 PHE 0.020 0.001 PHE F 93 TYR 0.009 0.001 TYR C 268 ARG 0.007 0.000 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.03632 ( 1145) hydrogen bonds : angle 4.01571 ( 3411) covalent geometry : bond 0.00275 (15408) covalent geometry : angle 0.55278 (20892) *********************** 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 405 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 314 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 CYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7563 (t) REVERT: A 226 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8619 (tt) REVERT: A 322 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7295 (t80) REVERT: A 329 PHE cc_start: 0.7907 (m-10) cc_final: 0.7519 (m-10) REVERT: A 504 LYS cc_start: 0.7912 (pttm) cc_final: 0.7636 (ptpt) REVERT: B 125 MET cc_start: 0.8799 (mmm) cc_final: 0.8422 (mmm) REVERT: E 126 CYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7570 (t) REVERT: E 226 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8613 (tt) REVERT: E 322 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7300 (t80) REVERT: C 126 CYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7580 (t) REVERT: C 226 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8627 (tt) REVERT: C 322 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7243 (t80) REVERT: C 329 PHE cc_start: 0.7882 (m-10) cc_final: 0.7529 (m-10) REVERT: C 504 LYS cc_start: 0.7898 (pttm) cc_final: 0.7643 (ptpt) REVERT: C 523 LYS cc_start: 0.8004 (ttpp) cc_final: 0.7766 (mtpt) REVERT: G 126 CYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7557 (t) REVERT: G 226 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8636 (tt) REVERT: G 322 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7351 (t80) REVERT: H 125 MET cc_start: 0.8798 (mmm) cc_final: 0.8398 (mmm) outliers start: 91 outliers final: 62 residues processed: 376 average time/residue: 0.2468 time to fit residues: 140.8482 Evaluate side-chains 358 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 284 time to evaluate : 1.776 ------------------------------------------------------------------------------- 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 226 LEU Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 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 A residue 540 ASN Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain E residue 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 363 SER 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 108 HIS Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 330 PHE Chi-restraints excluded: chain C residue 353 HIS Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 230 HIS Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 330 PHE Chi-restraints excluded: chain G residue 353 HIS Chi-restraints excluded: chain G residue 363 SER Chi-restraints excluded: chain G residue 499 HIS Chi-restraints excluded: chain G residue 540 ASN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 101 ILE 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 82 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 60 optimal weight: 0.0570 overall best weight: 1.5904 ------------------------------------------------------------------------------- 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 E 97 GLN F 108 HIS C 97 GLN D 108 HIS G 97 GLN H 108 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.187251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.155963 restraints weight = 24481.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.153970 restraints weight = 36057.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.152467 restraints weight = 27938.543| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2518 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= 0.165 Angle : 0.594 10.605 20892 Z= 0.300 Chirality : 0.039 0.249 2344 Planarity : 0.003 0.030 2628 Dihedral : 10.155 118.151 2236 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 6.43 % Allowed : 21.72 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.24 (0.19), residues: 1884 helix: 2.18 (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 0.010 0.001 TRP E 369 HIS 0.007 0.001 HIS H 108 PHE 0.024 0.002 PHE F 93 TYR 0.017 0.001 TYR G 372 ARG 0.004 0.000 ARG B 38 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 1145) hydrogen bonds : angle 4.15916 ( 3411) covalent geometry : bond 0.00394 (15408) covalent geometry : angle 0.59410 (20892) *********************** 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 390 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 294 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 CYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7630 (t) REVERT: A 322 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7575 (t80) REVERT: A 504 LYS cc_start: 0.8254 (pttm) cc_final: 0.7847 (ptpt) REVERT: E 126 CYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7624 (t) REVERT: E 322 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7568 (t80) REVERT: E 504 LYS cc_start: 0.8241 (pttm) cc_final: 0.7846 (ptpt) REVERT: C 126 CYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7657 (t) REVERT: C 226 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8747 (tt) REVERT: C 322 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7577 (t80) REVERT: C 504 LYS cc_start: 0.8244 (pttm) cc_final: 0.7842 (ptpt) REVERT: C 523 LYS cc_start: 0.7946 (ttpp) cc_final: 0.7724 (mtpt) REVERT: C 542 MET cc_start: 0.8450 (mmp) cc_final: 0.8093 (mmp) REVERT: D 125 MET cc_start: 0.8646 (mmm) cc_final: 0.8394 (mmm) REVERT: G 126 CYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7634 (t) REVERT: G 322 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.7568 (t80) outliers start: 96 outliers final: 73 residues processed: 358 average time/residue: 0.2493 time to fit residues: 134.0779 Evaluate side-chains 369 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 287 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 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 94 ASP Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 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 363 SER Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain E residue 540 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 353 HIS Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 230 HIS Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 330 PHE Chi-restraints excluded: chain G residue 353 HIS Chi-restraints excluded: chain G residue 363 SER Chi-restraints excluded: chain G residue 499 HIS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 53 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.196883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.157609 restraints weight = 24640.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.157309 restraints weight = 27561.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.159050 restraints weight = 21576.528| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15408 Z= 0.126 Angle : 0.584 11.196 20892 Z= 0.290 Chirality : 0.037 0.220 2344 Planarity : 0.003 0.030 2628 Dihedral : 9.972 118.663 2236 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 5.97 % Allowed : 21.85 % Favored : 72.18 % 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: 2.22 (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 0.013 0.001 TRP A 369 HIS 0.001 0.000 HIS A 499 PHE 0.020 0.001 PHE H 93 TYR 0.016 0.001 TYR G 372 ARG 0.004 0.000 ARG G 544 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 1145) hydrogen bonds : angle 4.08018 ( 3411) covalent geometry : bond 0.00285 (15408) covalent geometry : angle 0.58435 (20892) *********************** 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 379 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 290 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 CYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7616 (t) REVERT: A 322 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7596 (t80) REVERT: B 125 MET cc_start: 0.8451 (mmm) cc_final: 0.7950 (tpp) REVERT: E 126 CYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7601 (t) REVERT: E 322 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7518 (t80) REVERT: E 504 LYS cc_start: 0.8367 (pttm) cc_final: 0.7862 (ptpt) REVERT: F 125 MET cc_start: 0.8579 (mmm) cc_final: 0.8342 (mmm) REVERT: C 126 CYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7659 (t) REVERT: C 226 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8652 (tt) REVERT: C 322 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7610 (t80) REVERT: G 126 CYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7614 (t) REVERT: G 175 VAL cc_start: 0.8798 (OUTLIER) cc_final: 0.8543 (p) REVERT: G 322 PHE cc_start: 0.8148 (OUTLIER) cc_final: 0.7573 (t80) REVERT: H 125 MET cc_start: 0.8430 (mmm) cc_final: 0.7968 (tpp) outliers start: 89 outliers final: 68 residues processed: 353 average time/residue: 0.2498 time to fit residues: 132.4573 Evaluate side-chains 366 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 288 time to evaluate : 1.818 ------------------------------------------------------------------------------- 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 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 30 THR Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 204 CYS Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 330 PHE Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain E residue 517 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 108 HIS Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 330 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 D residue 101 ILE Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 230 HIS Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 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 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 101 ILE Chi-restraints excluded: chain H residue 108 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 102 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 22 optimal weight: 0.0570 chunk 182 optimal weight: 0.6980 overall best weight: 2.1504 ------------------------------------------------------------------------------- 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 G 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.183908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.150278 restraints weight = 24538.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.149520 restraints weight = 32342.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.146752 restraints weight = 22204.286| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 15408 Z= 0.200 Angle : 0.647 10.519 20892 Z= 0.323 Chirality : 0.039 0.167 2344 Planarity : 0.003 0.031 2628 Dihedral : 10.235 118.886 2236 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 6.10 % Allowed : 22.32 % 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: 2.06 (0.19), residues: 1884 helix: 2.07 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -1.23 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 369 HIS 0.002 0.000 HIS C 499 PHE 0.024 0.002 PHE H 93 TYR 0.015 0.002 TYR E 372 ARG 0.004 0.000 ARG E 544 Details of bonding type rmsd hydrogen bonds : bond 0.04017 ( 1145) hydrogen bonds : angle 4.28204 ( 3411) covalent geometry : bond 0.00487 (15408) covalent geometry : angle 0.64720 (20892) *********************** 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 378 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 287 time to evaluate : 1.749 Fit side-chains revert: symmetry clash REVERT: A 126 CYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7629 (t) REVERT: A 175 VAL cc_start: 0.8783 (OUTLIER) cc_final: 0.8551 (p) REVERT: A 322 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7705 (t80) REVERT: A 504 LYS cc_start: 0.8408 (pttm) cc_final: 0.7983 (ptpt) REVERT: E 126 CYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7654 (t) REVERT: E 175 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8552 (p) REVERT: E 322 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7680 (t80) REVERT: E 504 LYS cc_start: 0.8405 (pttm) cc_final: 0.7982 (pttm) REVERT: C 126 CYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7668 (t) REVERT: C 322 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7686 (t80) REVERT: C 504 LYS cc_start: 0.8427 (pttm) cc_final: 0.7994 (ptpt) REVERT: G 126 CYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7637 (t) REVERT: G 175 VAL cc_start: 0.8788 (OUTLIER) cc_final: 0.8556 (p) REVERT: G 322 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7372 (t80) REVERT: G 353 HIS cc_start: 0.7463 (OUTLIER) cc_final: 0.7051 (m-70) outliers start: 91 outliers final: 62 residues processed: 348 average time/residue: 0.2600 time to fit residues: 135.8535 Evaluate side-chains 358 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 284 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 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 30 THR Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 204 CYS Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain E residue 517 LYS 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 108 HIS Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 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 D residue 101 ILE Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 230 HIS Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 353 HIS 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 108 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 13 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 184 optimal weight: 0.8980 chunk 177 optimal weight: 3.9990 chunk 24 optimal weight: 0.0000 chunk 11 optimal weight: 10.0000 chunk 181 optimal weight: 0.0980 chunk 119 optimal weight: 0.0030 overall best weight: 0.3394 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.187796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.161597 restraints weight = 24704.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.160407 restraints weight = 41938.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.161480 restraints weight = 33537.487| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2709 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= 0.123 Angle : 0.604 10.218 20892 Z= 0.298 Chirality : 0.037 0.202 2344 Planarity : 0.003 0.031 2628 Dihedral : 9.938 118.960 2236 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.89 % Allowed : 24.20 % Favored : 70.91 % 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: 2.22 (0.19), residues: 1884 helix: 2.18 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -1.16 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 295 HIS 0.002 0.000 HIS F 108 PHE 0.015 0.001 PHE F 93 TYR 0.016 0.001 TYR E 372 ARG 0.006 0.000 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 1145) hydrogen bonds : angle 4.08660 ( 3411) covalent geometry : bond 0.00266 (15408) covalent geometry : angle 0.60401 (20892) ********************** 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 368 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 295 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 CYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7524 (t) REVERT: A 175 VAL cc_start: 0.8754 (OUTLIER) cc_final: 0.8396 (p) REVERT: A 322 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7523 (t80) REVERT: A 504 LYS cc_start: 0.8011 (pttm) cc_final: 0.7647 (ptpt) REVERT: B 13 PHE cc_start: 0.6051 (m-80) cc_final: 0.5846 (m-80) REVERT: E 126 CYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7527 (t) REVERT: E 175 VAL cc_start: 0.8751 (OUTLIER) cc_final: 0.8410 (p) REVERT: E 322 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7485 (t80) REVERT: C 126 CYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7567 (t) REVERT: C 322 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7576 (t80) REVERT: C 504 LYS cc_start: 0.8035 (pttm) cc_final: 0.7658 (ptpt) REVERT: G 126 CYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7519 (t) REVERT: G 175 VAL cc_start: 0.8754 (OUTLIER) cc_final: 0.8403 (p) REVERT: G 322 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7452 (t80) REVERT: G 353 HIS cc_start: 0.7177 (OUTLIER) cc_final: 0.6782 (m-70) outliers start: 73 outliers final: 49 residues processed: 353 average time/residue: 0.2252 time to fit residues: 122.5804 Evaluate side-chains 341 residues out of total 1640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 280 time to evaluate : 1.710 ------------------------------------------------------------------------------- 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 363 SER Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 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 E residue 517 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 108 HIS Chi-restraints excluded: chain F residue 117 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 330 PHE Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 499 HIS 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 353 HIS Chi-restraints excluded: chain G residue 363 SER Chi-restraints excluded: chain G residue 499 HIS Chi-restraints excluded: chain G residue 517 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 94 ASP 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 41 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4276 r_free = 0.4276 target = 0.187034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.158200 restraints weight = 24475.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.157146 restraints weight = 33118.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.157352 restraints weight = 29046.548| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15408 Z= 0.135 Angle : 0.637 10.280 20892 Z= 0.313 Chirality : 0.038 0.193 2344 Planarity : 0.003 0.033 2628 Dihedral : 9.716 118.460 2228 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.96 % Allowed : 24.46 % Favored : 70.58 % 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: 2.23 (0.19), residues: 1884 helix: 2.21 (0.13), residues: 1460 sheet: None (None), residues: 0 loop : -1.21 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 369 HIS 0.002 0.000 HIS B 108 PHE 0.024 0.001 PHE F 142 TYR 0.015 0.001 TYR G 372 ARG 0.008 0.000 ARG A 528 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 1145) hydrogen bonds : angle 4.08213 ( 3411) covalent geometry : bond 0.00314 (15408) covalent geometry : angle 0.63686 (20892) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4794.83 seconds wall clock time: 83 minutes 34.19 seconds (5014.19 seconds total)