Starting phenix.real_space_refine on Fri Feb 16 10:24:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tci_25813/02_2024/7tci_25813_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tci_25813/02_2024/7tci_25813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tci_25813/02_2024/7tci_25813.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tci_25813/02_2024/7tci_25813.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tci_25813/02_2024/7tci_25813_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tci_25813/02_2024/7tci_25813_updated.pdb" } 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 Residue "A PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 8.15, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 6.51 Conformation dependent library (CDL) restraints added in 2.9 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... running ksdssp... Secondary structure from input PDB file: 96 helices and 4 sheets defined 74.3% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 110 through 134 Processing helix chain 'A' and resid 140 through 169 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) removed outlier: 4.340A pdb=" N GLY A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 187 through 205 Processing helix chain 'A' and resid 219 through 231 removed outlier: 4.419A pdb=" N GLN A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N HIS A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 238 through 247 Processing helix chain 'A' and resid 249 through 273 Processing helix chain 'A' and resid 289 through 301 Processing helix chain 'A' and resid 313 through 349 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 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 358 through 375 removed outlier: 3.882A pdb=" N GLU A 375 " --> pdb=" O CYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 522 Processing helix chain 'A' and resid 527 through 555 Processing helix chain 'B' and resid 11 through 21 Processing helix chain 'B' and resid 30 through 40 Processing helix chain 'B' and resid 46 through 56 Processing helix chain 'B' and resid 66 through 74 Processing helix chain 'B' and resid 80 through 93 Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'B' and resid 103 through 112 Processing helix chain 'B' and resid 119 through 129 Processing helix chain 'B' and resid 139 through 145 Processing helix chain 'E' and resid 96 through 105 Processing helix chain 'E' and resid 110 through 134 Processing helix chain 'E' and resid 140 through 169 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) removed outlier: 4.338A pdb=" N GLY E 169 " --> pdb=" O LEU E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 184 Processing helix chain 'E' and resid 187 through 205 Processing helix chain 'E' and resid 219 through 231 removed outlier: 4.369A pdb=" N GLN E 224 " --> pdb=" O ILE E 220 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU E 229 " --> pdb=" O ILE E 225 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N HIS E 230 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 235 No H-bonds generated for 'chain 'E' and resid 233 through 235' Processing helix chain 'E' and resid 238 through 247 Processing helix chain 'E' and resid 249 through 273 Processing helix chain 'E' and resid 289 through 301 Processing helix chain 'E' and resid 313 through 349 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 354 through 356 No H-bonds generated for 'chain 'E' and resid 354 through 356' Processing helix chain 'E' and resid 358 through 375 removed outlier: 3.884A pdb=" N GLU E 375 " --> pdb=" O CYS E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 522 Processing helix chain 'E' and resid 527 through 555 Processing helix chain 'F' and resid 11 through 21 Processing helix chain 'F' and resid 30 through 40 Processing helix chain 'F' and resid 46 through 56 Processing helix chain 'F' and resid 66 through 74 Processing helix chain 'F' and resid 80 through 93 Processing helix chain 'F' and resid 95 through 97 No H-bonds generated for 'chain 'F' and resid 95 through 97' Processing helix chain 'F' and resid 103 through 112 Processing helix chain 'F' and resid 119 through 129 Processing helix chain 'F' and resid 139 through 145 Processing helix chain 'C' and resid 96 through 105 Processing helix chain 'C' and resid 110 through 134 Processing helix chain 'C' and resid 140 through 169 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) removed outlier: 4.339A pdb=" N GLY C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 187 through 205 Processing helix chain 'C' and resid 219 through 231 removed outlier: 4.419A pdb=" N GLN C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU C 229 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N HIS C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL C 231 " --> pdb=" O ARG C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' Processing helix chain 'C' and resid 238 through 247 Processing helix chain 'C' and resid 249 through 273 Processing helix chain 'C' and resid 289 through 301 Processing helix chain 'C' and resid 313 through 349 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 354 through 356 No H-bonds generated for 'chain 'C' and resid 354 through 356' Processing helix chain 'C' and resid 358 through 375 removed outlier: 3.883A pdb=" N GLU C 375 " --> pdb=" O CYS C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 522 Processing helix chain 'C' and resid 527 through 555 Processing helix chain 'D' and resid 11 through 21 Processing helix chain 'D' and resid 30 through 40 Processing helix chain 'D' and resid 46 through 56 Processing helix chain 'D' and resid 66 through 74 Processing helix chain 'D' and resid 80 through 93 Processing helix chain 'D' and resid 95 through 97 No H-bonds generated for 'chain 'D' and resid 95 through 97' Processing helix chain 'D' and resid 103 through 112 Processing helix chain 'D' and resid 119 through 129 Processing helix chain 'D' and resid 139 through 145 Processing helix chain 'G' and resid 96 through 105 Processing helix chain 'G' and resid 110 through 134 Processing helix chain 'G' and resid 140 through 169 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) removed outlier: 4.340A pdb=" N GLY G 169 " --> pdb=" O LEU G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 184 Processing helix chain 'G' and resid 187 through 205 Processing helix chain 'G' and resid 219 through 231 removed outlier: 4.371A pdb=" N GLN G 224 " --> pdb=" O ILE G 220 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU G 229 " --> pdb=" O ILE G 225 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N HIS G 230 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL G 231 " --> pdb=" O ARG G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 235 No H-bonds generated for 'chain 'G' and resid 233 through 235' Processing helix chain 'G' and resid 238 through 247 Processing helix chain 'G' and resid 249 through 273 Processing helix chain 'G' and resid 289 through 301 Processing helix chain 'G' and resid 313 through 349 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 354 through 356 No H-bonds generated for 'chain 'G' and resid 354 through 356' Processing helix chain 'G' and resid 358 through 375 removed outlier: 3.878A pdb=" N GLU G 375 " --> pdb=" O CYS G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 522 Processing helix chain 'G' and resid 527 through 555 Processing helix chain 'H' and resid 11 through 21 Processing helix chain 'H' and resid 30 through 40 Processing helix chain 'H' and resid 46 through 56 Processing helix chain 'H' and resid 66 through 74 Processing helix chain 'H' and resid 80 through 93 Processing helix chain 'H' and resid 95 through 97 No H-bonds generated for 'chain 'H' and resid 95 through 97' Processing helix chain 'H' and resid 103 through 112 Processing helix chain 'H' and resid 119 through 129 Processing helix chain 'H' and resid 139 through 145 Processing sheet with id= A, 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= B, 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= C, 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= D, 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) 1004 hydrogen bonds defined for protein. 3012 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: 4.57 Time building geometry restraints manager: 6.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2380 1.31 - 1.44: 4408 1.44 - 1.56: 8488 1.56 - 1.69: 8 1.69 - 1.81: 124 Bond restraints: 15408 Sorted by residual: bond pdb=" CBE I0S G 701 " pdb=" SBF I0S G 701 " ideal model delta sigma weight residual 1.717 1.600 0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" CBE I0S E 701 " pdb=" SBF I0S E 701 " ideal model delta sigma weight residual 1.717 1.601 0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" CBE I0S A 701 " pdb=" SBF I0S A 701 " ideal model delta sigma weight residual 1.717 1.601 0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" CAT I0S C 701 " pdb=" SBF I0S C 701 " ideal model delta sigma weight residual 1.739 1.623 0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" CAT I0S A 701 " pdb=" SBF I0S A 701 " ideal model delta sigma weight residual 1.739 1.623 0.116 2.00e-02 2.50e+03 3.36e+01 ... (remaining 15403 not shown) Histogram of bond angle deviations from ideal: 98.97 - 105.97: 189 105.97 - 112.97: 8203 112.97 - 119.97: 5429 119.97 - 126.97: 6919 126.97 - 133.97: 152 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: 16411 3.33 - 3.85: 25698 3.85 - 4.38: 26459 4.38 - 4.90: 46375 Nonbonded interactions: 119035 Sorted by model distance: nonbonded pdb=" OE1 GLU A 150 " pdb=" NE2 GLN A 224 " model vdw 2.282 2.520 nonbonded pdb=" OE1 GLU C 150 " pdb=" NE2 GLN C 224 " model vdw 2.283 2.520 nonbonded pdb=" OE1 GLU E 150 " pdb=" NE2 GLN E 224 " model vdw 2.286 2.520 nonbonded pdb=" OE1 GLU G 150 " pdb=" NE2 GLN G 224 " model vdw 2.286 2.520 nonbonded pdb=" NH2 ARG E 522 " pdb=" OE1 GLU F 88 " model vdw 2.334 2.520 ... (remaining 119030 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.350 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: 0.050 Extract box with map and model: 10.950 Check model and map are aligned: 0.260 Set scattering table: 0.180 Process input model: 44.090 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.100 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.880 ------------------------------------------------------------------------------- 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= 0.361 Angle : 0.618 17.970 20892 Z= 0.275 Chirality : 0.036 0.238 2344 Planarity : 0.003 0.031 2628 Dihedral : 13.437 123.840 5436 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.95 % Allowed : 8.04 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.20), residues: 1884 helix: 2.67 (0.13), residues: 1476 sheet: None (None), residues: 0 loop : -0.79 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 295 HIS 0.001 0.000 HIS A 248 PHE 0.007 0.001 PHE C 322 TYR 0.012 0.001 TYR A 534 ARG 0.001 0.000 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 415 time to evaluate : 1.748 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: 0.2692 time to fit residues: 179.2680 Evaluate side-chains 376 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 351 time to evaluate : 1.732 ------------------------------------------------------------------------------- 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: 7.9990 chunk 142 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 147 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 chunk 170 optimal weight: 9.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS E 97 GLN ** E 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 HIS C 97 GLN ** C 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 HIS G 97 GLN ** G 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 15408 Z= 0.428 Angle : 0.659 9.327 20892 Z= 0.342 Chirality : 0.041 0.135 2344 Planarity : 0.004 0.035 2628 Dihedral : 11.656 123.299 2246 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 7.51 % Allowed : 17.49 % Favored : 75.00 % 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: 2.14 (0.20), residues: 1884 helix: 2.09 (0.14), residues: 1464 sheet: None (None), residues: 0 loop : -1.04 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 238 HIS 0.008 0.001 HIS B 108 PHE 0.023 0.002 PHE F 93 TYR 0.018 0.002 TYR E 534 ARG 0.003 0.000 ARG C 544 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 329 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 TYR cc_start: 0.6565 (m-80) cc_final: 0.6243 (m-10) REVERT: A 175 VAL cc_start: 0.8818 (m) cc_final: 0.8616 (p) REVERT: A 226 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8731 (tt) REVERT: A 322 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7527 (t80) REVERT: A 504 LYS cc_start: 0.8735 (pttm) cc_final: 0.8413 (ptpt) REVERT: E 138 TYR cc_start: 0.6616 (m-80) cc_final: 0.6222 (m-10) REVERT: E 175 VAL cc_start: 0.8814 (m) cc_final: 0.8610 (p) REVERT: E 226 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8739 (tt) REVERT: E 322 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7523 (t80) REVERT: E 504 LYS cc_start: 0.8745 (pttm) cc_final: 0.8407 (ptpt) REVERT: F 69 PHE cc_start: 0.8810 (t80) cc_final: 0.8541 (t80) REVERT: F 72 MET cc_start: 0.9027 (tmm) cc_final: 0.8632 (tmm) REVERT: F 73 MET cc_start: 0.7125 (mmm) cc_final: 0.6637 (mmm) REVERT: C 138 TYR cc_start: 0.6570 (m-80) cc_final: 0.6247 (m-10) REVERT: C 226 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8734 (tt) REVERT: C 322 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7530 (t80) REVERT: C 504 LYS cc_start: 0.8745 (pttm) cc_final: 0.8420 (ptpt) REVERT: C 523 LYS cc_start: 0.8028 (ttpp) cc_final: 0.7732 (mtpt) REVERT: C 534 TYR cc_start: 0.8628 (t80) cc_final: 0.8427 (t80) REVERT: G 138 TYR cc_start: 0.6579 (m-80) cc_final: 0.6199 (m-10) REVERT: G 175 VAL cc_start: 0.8816 (m) cc_final: 0.8616 (p) REVERT: G 226 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8739 (tt) REVERT: G 322 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7482 (t80) REVERT: G 329 PHE cc_start: 0.8126 (m-10) cc_final: 0.7700 (m-10) REVERT: G 504 LYS cc_start: 0.8741 (pttm) cc_final: 0.8416 (ptpt) REVERT: G 523 LYS cc_start: 0.8048 (ttpp) cc_final: 0.7747 (mtpt) REVERT: H 32 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7841 (tt0) outliers start: 112 outliers final: 81 residues processed: 407 average time/residue: 0.2751 time to fit residues: 163.1877 Evaluate side-chains 390 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 300 time to evaluate : 2.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 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 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 96 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 152 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 204 CYS Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain E residue 520 GLN Chi-restraints excluded: chain E residue 540 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 96 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 145 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 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 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 96 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 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 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 301 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 499 HIS Chi-restraints excluded: chain G residue 520 GLN Chi-restraints excluded: chain G residue 540 ASN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 108 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 184 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 169 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS E 97 GLN ** E 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 HIS C 97 GLN ** C 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 HIS G 97 GLN ** G 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.128 15408 Z= 0.510 Angle : 0.700 10.624 20892 Z= 0.364 Chirality : 0.042 0.142 2344 Planarity : 0.004 0.033 2628 Dihedral : 11.818 121.535 2246 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 8.24 % Allowed : 20.84 % 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: 1.63 (0.20), residues: 1884 helix: 1.73 (0.13), residues: 1448 sheet: None (None), residues: 0 loop : -1.12 (0.34), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 238 HIS 0.006 0.001 HIS D 108 PHE 0.030 0.003 PHE F 17 TYR 0.022 0.002 TYR A 534 ARG 0.005 0.001 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 315 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 TYR cc_start: 0.6623 (m-80) cc_final: 0.6261 (m-80) REVERT: A 226 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8755 (tt) REVERT: A 322 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7441 (t80) REVERT: A 504 LYS cc_start: 0.8711 (pttm) cc_final: 0.8312 (ptpt) REVERT: A 542 MET cc_start: 0.8691 (mmp) cc_final: 0.8491 (mmp) REVERT: B 50 GLN cc_start: 0.8739 (tp40) cc_final: 0.8059 (tp40) REVERT: E 138 TYR cc_start: 0.6618 (m-80) cc_final: 0.6296 (m-10) REVERT: E 226 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8758 (tt) REVERT: E 322 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7411 (t80) REVERT: E 504 LYS cc_start: 0.8708 (pttm) cc_final: 0.8341 (ptpt) REVERT: F 50 GLN cc_start: 0.8744 (tp40) cc_final: 0.8043 (tp40) REVERT: C 138 TYR cc_start: 0.6616 (m-80) cc_final: 0.6260 (m-80) REVERT: C 175 VAL cc_start: 0.8912 (OUTLIER) cc_final: 0.8690 (p) REVERT: C 226 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8755 (tt) REVERT: C 322 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7450 (t80) REVERT: C 504 LYS cc_start: 0.8715 (pttm) cc_final: 0.8320 (ptpt) REVERT: D 50 GLN cc_start: 0.8746 (tp40) cc_final: 0.8061 (tp40) REVERT: G 138 TYR cc_start: 0.6609 (m-80) cc_final: 0.6284 (m-10) REVERT: G 226 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8758 (tt) REVERT: G 322 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7409 (t80) REVERT: G 504 LYS cc_start: 0.8702 (pttm) cc_final: 0.8327 (ptpt) REVERT: H 32 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: H 50 GLN cc_start: 0.8741 (tp40) cc_final: 0.8055 (tp40) outliers start: 123 outliers final: 94 residues processed: 405 average time/residue: 0.2348 time to fit residues: 144.3432 Evaluate side-chains 405 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 301 time to evaluate : 1.794 ------------------------------------------------------------------------------- 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 132 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 204 CYS Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain E residue 520 GLN Chi-restraints excluded: chain E residue 540 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 108 HIS Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 204 CYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 98 ASN 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 132 LEU Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 204 CYS Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 230 HIS Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 299 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 499 HIS Chi-restraints excluded: chain G residue 520 GLN Chi-restraints excluded: chain G residue 540 ASN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 108 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 81 optimal weight: 6.9990 chunk 114 optimal weight: 0.6980 chunk 171 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 162 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS E 97 GLN ** E 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 HIS C 97 GLN ** C 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 HIS ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 HIS ** G 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 HIS ** H 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15408 Z= 0.179 Angle : 0.530 7.034 20892 Z= 0.269 Chirality : 0.037 0.189 2344 Planarity : 0.003 0.029 2628 Dihedral : 11.692 121.065 2238 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.56 % Allowed : 25.60 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.20), residues: 1884 helix: 2.05 (0.13), residues: 1456 sheet: None (None), residues: 0 loop : -1.18 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 295 HIS 0.003 0.001 HIS D 108 PHE 0.028 0.001 PHE F 17 TYR 0.012 0.001 TYR C 534 ARG 0.004 0.000 ARG A 544 *********************** 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 406 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 338 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 TYR cc_start: 0.6488 (m-80) cc_final: 0.6227 (m-80) REVERT: A 226 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8608 (tt) REVERT: A 322 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7468 (t80) REVERT: A 329 PHE cc_start: 0.8183 (m-10) cc_final: 0.7907 (m-10) REVERT: A 504 LYS cc_start: 0.8613 (pttm) cc_final: 0.8054 (ptpt) REVERT: A 534 TYR cc_start: 0.8519 (t80) cc_final: 0.8155 (t80) REVERT: E 138 TYR cc_start: 0.6505 (m-80) cc_final: 0.6238 (m-80) REVERT: E 226 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8635 (tt) REVERT: E 322 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.7448 (t80) REVERT: E 329 PHE cc_start: 0.7975 (m-10) cc_final: 0.7482 (m-10) REVERT: E 504 LYS cc_start: 0.8624 (pttm) cc_final: 0.8081 (ptpt) REVERT: F 73 MET cc_start: 0.7696 (mmm) cc_final: 0.7021 (mmt) REVERT: C 138 TYR cc_start: 0.6480 (m-80) cc_final: 0.6216 (m-80) REVERT: C 175 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8675 (p) REVERT: C 226 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8612 (tt) REVERT: C 322 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7479 (t80) REVERT: C 329 PHE cc_start: 0.8168 (m-10) cc_final: 0.7901 (m-10) REVERT: C 504 LYS cc_start: 0.8621 (pttm) cc_final: 0.8061 (ptpt) REVERT: C 534 TYR cc_start: 0.8592 (t80) cc_final: 0.8324 (t80) REVERT: G 138 TYR cc_start: 0.6500 (m-80) cc_final: 0.6228 (m-80) REVERT: G 226 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8638 (tt) REVERT: G 322 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7444 (t80) REVERT: G 329 PHE cc_start: 0.8002 (m-10) cc_final: 0.7483 (m-10) REVERT: G 504 LYS cc_start: 0.8607 (pttm) cc_final: 0.8068 (ptpt) outliers start: 68 outliers final: 46 residues processed: 381 average time/residue: 0.2410 time to fit residues: 138.9238 Evaluate side-chains 378 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 323 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU 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 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain E residue 124 LEU 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 301 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 353 HIS Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain E residue 520 GLN Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 108 HIS Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 353 HIS Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 230 HIS Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 353 HIS Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 499 HIS Chi-restraints excluded: chain G residue 520 GLN Chi-restraints excluded: chain G residue 540 ASN Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 108 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 135 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 155 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 163 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN B 108 HIS E 97 GLN ** E 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 347 GLN F 98 ASN F 108 HIS C 97 GLN ** C 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN ** C 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN D 108 HIS G 97 GLN ** G 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN H 108 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 15408 Z= 0.292 Angle : 0.576 7.298 20892 Z= 0.292 Chirality : 0.038 0.135 2344 Planarity : 0.003 0.030 2628 Dihedral : 11.429 120.646 2234 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 6.57 % Allowed : 24.33 % Favored : 69.10 % 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: 2.00 (0.20), residues: 1884 helix: 2.05 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : -1.21 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 238 HIS 0.004 0.001 HIS F 108 PHE 0.019 0.002 PHE D 17 TYR 0.013 0.001 TYR E 268 ARG 0.004 0.000 ARG A 544 *********************** 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 413 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 315 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 TYR cc_start: 0.6510 (m-80) cc_final: 0.6282 (m-80) REVERT: A 226 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8657 (tt) REVERT: A 322 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.7434 (t80) REVERT: A 329 PHE cc_start: 0.8210 (m-10) cc_final: 0.7993 (m-10) REVERT: A 504 LYS cc_start: 0.8649 (pttm) cc_final: 0.8058 (ptpt) REVERT: B 69 PHE cc_start: 0.8906 (t80) cc_final: 0.8678 (t80) REVERT: E 138 TYR cc_start: 0.6527 (m-80) cc_final: 0.6275 (m-80) REVERT: E 226 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8679 (tt) REVERT: E 322 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7436 (t80) REVERT: E 504 LYS cc_start: 0.8643 (pttm) cc_final: 0.8068 (ptpt) REVERT: F 73 MET cc_start: 0.7607 (mmm) cc_final: 0.6897 (mmt) REVERT: C 138 TYR cc_start: 0.6494 (m-80) cc_final: 0.6273 (m-80) REVERT: C 175 VAL cc_start: 0.8910 (OUTLIER) cc_final: 0.8692 (p) REVERT: C 226 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8658 (tt) REVERT: C 322 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7445 (t80) REVERT: C 329 PHE cc_start: 0.8197 (m-10) cc_final: 0.7983 (m-10) REVERT: C 504 LYS cc_start: 0.8642 (pttm) cc_final: 0.8057 (ptpt) REVERT: C 534 TYR cc_start: 0.8461 (t80) cc_final: 0.8247 (t80) REVERT: D 69 PHE cc_start: 0.8922 (t80) cc_final: 0.8685 (t80) REVERT: G 138 TYR cc_start: 0.6525 (m-80) cc_final: 0.6265 (m-80) REVERT: G 226 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8680 (tt) REVERT: G 322 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7431 (t80) REVERT: G 504 LYS cc_start: 0.8656 (pttm) cc_final: 0.8043 (ptpt) REVERT: H 69 PHE cc_start: 0.8904 (t80) cc_final: 0.8687 (t80) outliers start: 98 outliers final: 83 residues processed: 372 average time/residue: 0.2425 time to fit residues: 136.2202 Evaluate side-chains 401 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 309 time to evaluate : 1.695 ------------------------------------------------------------------------------- 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 132 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 226 LEU Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 353 HIS Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain E residue 520 GLN Chi-restraints excluded: chain E residue 540 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 108 HIS Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 132 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 226 LEU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 353 HIS Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 98 ASN 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 132 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 226 LEU Chi-restraints excluded: chain G residue 230 HIS Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 353 HIS Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 499 HIS Chi-restraints excluded: chain G residue 520 GLN Chi-restraints excluded: chain G residue 540 ASN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 96 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 61 optimal weight: 0.7980 chunk 163 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 106 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 15 optimal weight: 0.4980 chunk 60 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN A 347 GLN ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN B 108 HIS E 97 GLN ** E 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN F 98 ASN F 108 HIS C 97 GLN ** C 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 GLN ** C 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN D 108 HIS G 97 GLN ** G 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN G 347 GLN G 540 ASN H 98 ASN H 108 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15408 Z= 0.175 Angle : 0.540 7.675 20892 Z= 0.269 Chirality : 0.036 0.154 2344 Planarity : 0.003 0.030 2628 Dihedral : 11.085 120.099 2234 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 6.30 % Allowed : 25.80 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.20), residues: 1884 helix: 2.18 (0.13), residues: 1448 sheet: None (None), residues: 0 loop : -0.92 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 295 HIS 0.005 0.001 HIS F 108 PHE 0.015 0.001 PHE D 17 TYR 0.010 0.001 TYR G 271 ARG 0.003 0.000 ARG A 544 *********************** 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 413 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 319 time to evaluate : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 TYR cc_start: 0.6505 (m-80) cc_final: 0.6293 (m-80) REVERT: A 226 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8619 (tt) REVERT: A 322 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7692 (t80) REVERT: A 504 LYS cc_start: 0.8636 (pttm) cc_final: 0.8143 (ptpt) REVERT: E 138 TYR cc_start: 0.6476 (m-80) cc_final: 0.6268 (m-80) REVERT: E 226 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8600 (tt) REVERT: E 322 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7681 (t80) REVERT: E 504 LYS cc_start: 0.8617 (pttm) cc_final: 0.8227 (ptpt) REVERT: C 138 TYR cc_start: 0.6504 (m-80) cc_final: 0.6294 (m-80) REVERT: C 175 VAL cc_start: 0.8884 (OUTLIER) cc_final: 0.8664 (p) REVERT: C 226 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8619 (tt) REVERT: C 322 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7689 (t80) REVERT: C 504 LYS cc_start: 0.8638 (pttm) cc_final: 0.8152 (ptpt) REVERT: C 534 TYR cc_start: 0.8415 (t80) cc_final: 0.8088 (t80) REVERT: G 138 TYR cc_start: 0.6487 (m-80) cc_final: 0.6279 (m-80) REVERT: G 226 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8601 (tt) REVERT: G 322 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7636 (t80) REVERT: G 504 LYS cc_start: 0.8624 (pttm) cc_final: 0.8236 (ptpt) outliers start: 94 outliers final: 68 residues processed: 380 average time/residue: 0.2411 time to fit residues: 138.4130 Evaluate side-chains 385 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 308 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain E residue 132 LEU 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 301 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 353 HIS Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain E residue 520 GLN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 353 HIS Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 230 HIS Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 353 HIS Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 499 HIS Chi-restraints excluded: chain G residue 520 GLN 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 96 ASP Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 101 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 153 optimal weight: 0.7980 chunk 101 optimal weight: 0.2980 chunk 181 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN B 108 HIS E 97 GLN ** E 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 ASN C 97 GLN ** C 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN D 108 HIS G 97 GLN ** G 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 540 ASN H 98 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15408 Z= 0.174 Angle : 0.553 8.068 20892 Z= 0.269 Chirality : 0.036 0.171 2344 Planarity : 0.003 0.030 2628 Dihedral : 10.848 120.268 2228 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 6.17 % Allowed : 26.47 % Favored : 67.36 % 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: 2.34 (0.20), residues: 1884 helix: 2.24 (0.14), residues: 1448 sheet: None (None), residues: 0 loop : -0.87 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 295 HIS 0.006 0.001 HIS D 108 PHE 0.016 0.001 PHE E 246 TYR 0.014 0.001 TYR G 372 ARG 0.003 0.000 ARG A 544 *********************** 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 408 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 316 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 TYR cc_start: 0.6538 (m-80) cc_final: 0.6330 (m-80) REVERT: A 322 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7534 (t80) REVERT: B 69 PHE cc_start: 0.8934 (t80) cc_final: 0.8699 (t80) REVERT: E 138 TYR cc_start: 0.6522 (m-80) cc_final: 0.6318 (m-80) REVERT: E 322 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7540 (t80) REVERT: E 504 LYS cc_start: 0.8599 (pttm) cc_final: 0.8096 (ptpt) REVERT: C 138 TYR cc_start: 0.6514 (m-80) cc_final: 0.6311 (m-80) REVERT: C 175 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8661 (p) REVERT: C 322 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7539 (t80) REVERT: C 534 TYR cc_start: 0.8356 (t80) cc_final: 0.8086 (t80) REVERT: D 69 PHE cc_start: 0.8946 (t80) cc_final: 0.8707 (t80) REVERT: G 138 TYR cc_start: 0.6516 (m-80) cc_final: 0.6310 (m-80) REVERT: G 322 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7547 (t80) REVERT: G 504 LYS cc_start: 0.8602 (pttm) cc_final: 0.8091 (ptpt) REVERT: H 69 PHE cc_start: 0.8953 (t80) cc_final: 0.8720 (t80) outliers start: 92 outliers final: 74 residues processed: 375 average time/residue: 0.2417 time to fit residues: 136.5428 Evaluate side-chains 382 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 303 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 145 THR 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 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain E residue 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 226 LEU Chi-restraints excluded: chain E residue 230 HIS Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 353 HIS Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain E residue 520 GLN 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 102 SER Chi-restraints excluded: chain F residue 108 HIS 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 226 LEU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 353 HIS Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 226 LEU Chi-restraints excluded: chain G residue 230 HIS Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 353 HIS Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 499 HIS Chi-restraints excluded: chain G residue 520 GLN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 108 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 54 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 142 optimal weight: 8.9990 chunk 164 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN B 98 ASN E 97 GLN ** E 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 ASN C 97 GLN ** C 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN G 97 GLN ** G 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2729 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= 0.180 Angle : 0.562 7.942 20892 Z= 0.275 Chirality : 0.036 0.160 2344 Planarity : 0.003 0.031 2628 Dihedral : 10.686 120.124 2224 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 6.70 % Allowed : 25.20 % Favored : 68.10 % 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: 2.34 (0.20), residues: 1884 helix: 2.24 (0.13), residues: 1444 sheet: None (None), residues: 0 loop : -0.86 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 295 HIS 0.001 0.000 HIS B 108 PHE 0.014 0.001 PHE B 93 TYR 0.013 0.001 TYR G 372 ARG 0.003 0.000 ARG B 127 *********************** 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 402 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 302 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 TYR cc_start: 0.6553 (m-80) cc_final: 0.6351 (m-80) REVERT: A 178 TRP cc_start: 0.6768 (OUTLIER) cc_final: 0.6049 (m100) REVERT: A 322 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7606 (t80) REVERT: E 178 TRP cc_start: 0.6758 (OUTLIER) cc_final: 0.6055 (m100) REVERT: E 322 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7565 (t80) REVERT: F 69 PHE cc_start: 0.8911 (t80) cc_final: 0.8627 (t80) REVERT: C 175 VAL cc_start: 0.8917 (OUTLIER) cc_final: 0.8698 (p) REVERT: C 322 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.7599 (t80) REVERT: C 534 TYR cc_start: 0.8269 (t80) cc_final: 0.8010 (t80) REVERT: G 178 TRP cc_start: 0.6761 (OUTLIER) cc_final: 0.6052 (m100) REVERT: G 322 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7580 (t80) outliers start: 100 outliers final: 79 residues processed: 366 average time/residue: 0.2332 time to fit residues: 129.8060 Evaluate side-chains 376 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 289 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 TRP 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 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 96 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 132 LEU Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 178 TRP 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 301 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 367 THR Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain E residue 517 LYS Chi-restraints excluded: chain E residue 520 GLN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 108 HIS Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 353 HIS Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 178 TRP 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 301 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 367 THR Chi-restraints excluded: chain G residue 499 HIS Chi-restraints excluded: chain G residue 520 GLN 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 96 ASP Chi-restraints excluded: chain H residue 98 ASN 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 173 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 chunk 168 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 152 optimal weight: 0.0170 chunk 159 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 178 optimal weight: 8.9990 overall best weight: 1.9022 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN ** E 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 ASN C 97 GLN ** C 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN ** G 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 15408 Z= 0.292 Angle : 0.633 10.720 20892 Z= 0.309 Chirality : 0.038 0.156 2344 Planarity : 0.003 0.032 2628 Dihedral : 10.802 120.456 2224 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 7.04 % Allowed : 25.60 % Favored : 67.36 % 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: 2.18 (0.20), residues: 1884 helix: 2.10 (0.14), residues: 1452 sheet: None (None), residues: 0 loop : -0.86 (0.33), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 369 HIS 0.001 0.000 HIS A 248 PHE 0.021 0.002 PHE B 93 TYR 0.013 0.002 TYR C 268 ARG 0.003 0.000 ARG D 127 *********************** 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 400 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 295 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 TYR cc_start: 0.6609 (m-80) cc_final: 0.6396 (m-80) REVERT: A 178 TRP cc_start: 0.6812 (OUTLIER) cc_final: 0.6191 (m100) REVERT: A 226 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8646 (tt) REVERT: A 322 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.7729 (t80) REVERT: A 504 LYS cc_start: 0.8705 (pttm) cc_final: 0.8197 (ptpt) REVERT: E 178 TRP cc_start: 0.6814 (OUTLIER) cc_final: 0.6128 (m100) REVERT: E 226 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8656 (tt) REVERT: E 322 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.7686 (t80) REVERT: E 504 LYS cc_start: 0.8616 (pttm) cc_final: 0.7993 (ptpt) REVERT: F 69 PHE cc_start: 0.8956 (t80) cc_final: 0.8732 (t80) REVERT: C 175 VAL cc_start: 0.8920 (OUTLIER) cc_final: 0.8706 (p) REVERT: C 178 TRP cc_start: 0.6791 (OUTLIER) cc_final: 0.6099 (m100) REVERT: C 226 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8642 (tt) REVERT: C 322 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7704 (t80) REVERT: C 504 LYS cc_start: 0.8704 (pttm) cc_final: 0.8206 (ptpt) REVERT: C 534 TYR cc_start: 0.8372 (t80) cc_final: 0.8111 (t80) REVERT: D 13 PHE cc_start: 0.7668 (m-80) cc_final: 0.7335 (m-80) REVERT: G 178 TRP cc_start: 0.6807 (OUTLIER) cc_final: 0.6193 (m100) REVERT: G 226 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8662 (tt) REVERT: G 322 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.7692 (t80) REVERT: H 69 PHE cc_start: 0.8954 (t80) cc_final: 0.8746 (t80) outliers start: 105 outliers final: 85 residues processed: 365 average time/residue: 0.2502 time to fit residues: 136.5650 Evaluate side-chains 390 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 292 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 TRP 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 253 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 96 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 132 LEU Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 178 TRP 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 299 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 353 HIS Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain E residue 517 LYS Chi-restraints excluded: chain E residue 520 GLN Chi-restraints excluded: chain E residue 540 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 108 HIS Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 178 TRP 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 253 ILE Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 353 HIS Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 96 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 97 GLN Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 178 TRP 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 253 ILE Chi-restraints excluded: chain G residue 299 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 353 HIS Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 499 HIS Chi-restraints excluded: chain G residue 517 LYS Chi-restraints excluded: chain G residue 520 GLN 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 96 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 124 optimal weight: 0.3980 chunk 187 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 158 optimal weight: 0.0870 overall best weight: 0.8362 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN ** E 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 GLN ** C 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN ** G 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.147 15408 Z= 0.277 Angle : 1.015 59.198 20892 Z= 0.596 Chirality : 0.044 0.733 2344 Planarity : 0.004 0.076 2628 Dihedral : 10.823 120.617 2224 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 6.57 % Allowed : 25.60 % Favored : 67.83 % Cbeta Deviations : 0.17 % 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: 2.18 (0.20), residues: 1884 helix: 2.10 (0.14), residues: 1452 sheet: None (None), residues: 0 loop : -0.85 (0.33), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 369 HIS 0.001 0.000 HIS G 230 PHE 0.021 0.002 PHE B 93 TYR 0.013 0.001 TYR C 268 ARG 0.003 0.000 ARG E 544 ********************** 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 393 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 295 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8152 (tm-30) REVERT: A 138 TYR cc_start: 0.6604 (m-80) cc_final: 0.6393 (m-80) REVERT: A 178 TRP cc_start: 0.6804 (OUTLIER) cc_final: 0.6176 (m100) REVERT: A 226 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8641 (tt) REVERT: A 322 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7723 (t80) REVERT: A 504 LYS cc_start: 0.8699 (pttm) cc_final: 0.8195 (ptpt) REVERT: E 178 TRP cc_start: 0.6807 (OUTLIER) cc_final: 0.6119 (m100) REVERT: E 226 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8648 (tt) REVERT: E 322 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.7620 (t80) REVERT: F 69 PHE cc_start: 0.8970 (t80) cc_final: 0.8744 (t80) REVERT: C 175 VAL cc_start: 0.8917 (OUTLIER) cc_final: 0.8705 (p) REVERT: C 178 TRP cc_start: 0.6783 (OUTLIER) cc_final: 0.6093 (m100) REVERT: C 226 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8635 (tt) REVERT: C 322 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.7692 (t80) REVERT: C 504 LYS cc_start: 0.8700 (pttm) cc_final: 0.8204 (ptpt) REVERT: C 534 TYR cc_start: 0.8369 (t80) cc_final: 0.8106 (t80) REVERT: D 13 PHE cc_start: 0.7619 (m-80) cc_final: 0.7343 (m-80) REVERT: G 97 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8144 (tm-30) REVERT: G 178 TRP cc_start: 0.6799 (OUTLIER) cc_final: 0.6176 (m100) REVERT: G 226 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8662 (tt) REVERT: G 322 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.7630 (t80) REVERT: G 504 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8099 (ptpt) outliers start: 98 outliers final: 81 residues processed: 358 average time/residue: 0.2471 time to fit residues: 133.8656 Evaluate side-chains 390 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 293 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 178 TRP 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 253 ILE Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 322 PHE Chi-restraints excluded: chain A residue 353 HIS Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 517 LYS Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 96 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 132 LEU Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 178 TRP 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 253 ILE Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 322 PHE Chi-restraints excluded: chain E residue 353 HIS Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 499 HIS Chi-restraints excluded: chain E residue 517 LYS Chi-restraints excluded: chain E residue 520 GLN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 98 ASN Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 108 HIS Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 178 TRP 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 253 ILE Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 322 PHE Chi-restraints excluded: chain C residue 353 HIS Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 499 HIS Chi-restraints excluded: chain C residue 517 LYS Chi-restraints excluded: chain C residue 520 GLN Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 178 TRP 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 253 ILE Chi-restraints excluded: chain G residue 299 THR Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 322 PHE Chi-restraints excluded: chain G residue 353 HIS Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 499 HIS Chi-restraints excluded: chain G residue 504 LYS Chi-restraints excluded: chain G residue 520 GLN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 96 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 41 optimal weight: 0.0970 chunk 149 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 131 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN ** E 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 ASN ** C 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.188375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.159854 restraints weight = 24166.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.155895 restraints weight = 38855.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.155991 restraints weight = 38949.072| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15408 Z= 0.181 Angle : 0.591 9.677 20892 Z= 0.287 Chirality : 0.037 0.163 2344 Planarity : 0.003 0.031 2628 Dihedral : 10.708 120.367 2224 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 5.83 % Allowed : 26.68 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.20), residues: 1884 helix: 2.17 (0.14), residues: 1444 sheet: None (None), residues: 0 loop : -0.87 (0.32), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 369 HIS 0.001 0.000 HIS A 230 PHE 0.024 0.001 PHE B 93 TYR 0.012 0.001 TYR G 372 ARG 0.004 0.000 ARG C 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3333.18 seconds wall clock time: 61 minutes 2.98 seconds (3662.98 seconds total)