Starting phenix.real_space_refine on Mon Dec 30 00:27:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8go9_34174/12_2024/8go9_34174.cif Found real_map, /net/cci-nas-00/data/ceres_data/8go9_34174/12_2024/8go9_34174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8go9_34174/12_2024/8go9_34174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8go9_34174/12_2024/8go9_34174.map" model { file = "/net/cci-nas-00/data/ceres_data/8go9_34174/12_2024/8go9_34174.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8go9_34174/12_2024/8go9_34174.cif" } resolution = 3.35 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= 0.000 sd= 0.039 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 P 12 5.49 5 S 26 5.16 5 C 7376 2.51 5 N 1988 2.21 5 O 2260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11662 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2888 Classifications: {'peptide': 363} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 24, 'TRANS': 335} Chain breaks: 1 Chain: "B" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1479 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1359 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1479 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1359 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "F" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2888 Classifications: {'peptide': 363} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 24, 'TRANS': 335} Chain breaks: 1 Chain: "G" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 7.54, per 1000 atoms: 0.65 Number of scatterers: 11662 At special positions: 0 Unit cell: (186.038, 87.6375, 121.463, 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) S 26 16.00 P 12 15.00 O 2260 8.00 N 1988 7.00 C 7376 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 206 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 206 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.6 seconds 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2868 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 30 sheets defined 7.0% alpha, 42.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.920A pdb=" N LEU A 49 " --> pdb=" O ASP A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 393 through 408 Processing helix chain 'B' and resid 90 through 94 removed outlier: 4.022A pdb=" N THR B 94 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 128 Processing helix chain 'C' and resid 184 through 190 removed outlier: 4.003A pdb=" N HIS C 190 " --> pdb=" O ASP C 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 removed outlier: 4.022A pdb=" N THR D 94 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 128 Processing helix chain 'E' and resid 184 through 190 removed outlier: 4.002A pdb=" N HIS E 190 " --> pdb=" O ASP E 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 50 removed outlier: 3.920A pdb=" N LEU F 49 " --> pdb=" O ASP F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 110 Processing helix chain 'F' and resid 393 through 408 Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 118 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.605A pdb=" N ILE A 169 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE A 145 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N LYS A 171 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 10.267A pdb=" N VAL A 143 " --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 63 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL A 54 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLN A 86 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL A 56 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASN A 84 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU A 58 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE A 82 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 60 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS A 78 " --> pdb=" O PHE A 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 128 through 130 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 189 removed outlier: 3.530A pdb=" N THR A 187 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 271 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 209 removed outlier: 3.845A pdb=" N VAL A 336 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR A 322 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU A 344 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 9.520A pdb=" N VAL A 320 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS A 231 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 232 " --> pdb=" O GLN A 259 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA A 255 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLN A 238 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ALA A 240 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LYS A 251 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ILE A 242 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLN A 249 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 6 through 10 removed outlier: 3.668A pdb=" N VAL B 8 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 24 " --> pdb=" O SER B 10 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 13 through 15 removed outlier: 3.729A pdb=" N ALA B 52 " --> pdb=" O TRP B 39 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG B 41 " --> pdb=" O TRP B 50 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N TRP B 50 " --> pdb=" O ARG B 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 13 through 15 Processing sheet with id=AA9, first strand: chain 'B' and resid 130 through 134 removed outlier: 3.735A pdb=" N GLY B 149 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR B 186 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 130 through 134 removed outlier: 3.735A pdb=" N GLY B 149 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR B 186 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 161 through 163 Processing sheet with id=AB3, first strand: chain 'C' and resid 5 through 8 Processing sheet with id=AB4, first strand: chain 'C' and resid 11 through 14 removed outlier: 3.581A pdb=" N GLU C 106 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.485A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR C 50 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 117 through 119 removed outlier: 6.331A pdb=" N TYR C 174 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 6 through 10 removed outlier: 3.668A pdb=" N VAL D 8 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER D 24 " --> pdb=" O SER D 10 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 13 through 15 removed outlier: 3.730A pdb=" N ALA D 52 " --> pdb=" O TRP D 39 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 13 through 15 Processing sheet with id=AC1, first strand: chain 'D' and resid 130 through 134 removed outlier: 3.735A pdb=" N GLY D 149 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR D 186 " --> pdb=" O ASP D 154 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 130 through 134 removed outlier: 3.735A pdb=" N GLY D 149 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TYR D 186 " --> pdb=" O ASP D 154 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 161 through 163 Processing sheet with id=AC4, first strand: chain 'E' and resid 5 through 8 Processing sheet with id=AC5, first strand: chain 'E' and resid 11 through 14 removed outlier: 3.581A pdb=" N GLU E 106 " --> pdb=" O LEU E 12 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 54 through 55 removed outlier: 6.484A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 117 through 119 removed outlier: 6.331A pdb=" N TYR E 174 " --> pdb=" O ASN E 139 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 113 through 118 Processing sheet with id=AC9, first strand: chain 'F' and resid 27 through 30 removed outlier: 3.605A pdb=" N ILE F 169 " --> pdb=" O PHE F 145 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE F 145 " --> pdb=" O ILE F 169 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N LYS F 171 " --> pdb=" O VAL F 143 " (cutoff:3.500A) removed outlier: 10.268A pdb=" N VAL F 143 " --> pdb=" O LYS F 171 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG F 63 " --> pdb=" O GLY F 142 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL F 54 " --> pdb=" O GLN F 86 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLN F 86 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL F 56 " --> pdb=" O ASN F 84 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASN F 84 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU F 58 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ILE F 82 " --> pdb=" O LEU F 58 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL F 60 " --> pdb=" O LEU F 80 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS F 78 " --> pdb=" O PHE F 62 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 128 through 130 Processing sheet with id=AD2, first strand: chain 'F' and resid 184 through 189 removed outlier: 3.529A pdb=" N THR F 187 " --> pdb=" O LEU F 200 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS F 271 " --> pdb=" O VAL F 219 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 208 through 209 removed outlier: 3.844A pdb=" N VAL F 336 " --> pdb=" O LEU F 328 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR F 322 " --> pdb=" O PHE F 342 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU F 344 " --> pdb=" O VAL F 320 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N VAL F 320 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS F 231 " --> pdb=" O VAL F 329 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE F 232 " --> pdb=" O GLN F 259 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA F 255 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLN F 238 " --> pdb=" O PRO F 253 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ALA F 240 " --> pdb=" O LYS F 251 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LYS F 251 " --> pdb=" O ALA F 240 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE F 242 " --> pdb=" O GLN F 249 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N GLN F 249 " --> pdb=" O ILE F 242 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1242 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: 4.08 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3752 1.34 - 1.46: 2723 1.46 - 1.58: 5375 1.58 - 1.69: 46 1.69 - 1.81: 34 Bond restraints: 11930 Sorted by residual: bond pdb=" OG1 TPO G 354 " pdb=" P TPO G 354 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" OG1 TPO H 354 " pdb=" P TPO H 354 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" O3P TPO G 354 " pdb=" P TPO G 354 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" O2P TPO G 354 " pdb=" P TPO G 354 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" O2P TPO H 354 " pdb=" P TPO H 354 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.66e+01 ... (remaining 11925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 16096 2.42 - 4.84: 134 4.84 - 7.25: 14 7.25 - 9.67: 4 9.67 - 12.09: 2 Bond angle restraints: 16250 Sorted by residual: angle pdb=" CB TPO H 354 " pdb=" OG1 TPO H 354 " pdb=" P TPO H 354 " ideal model delta sigma weight residual 119.31 107.22 12.09 3.00e+00 1.11e-01 1.62e+01 angle pdb=" CB TPO G 354 " pdb=" OG1 TPO G 354 " pdb=" P TPO G 354 " ideal model delta sigma weight residual 119.31 107.27 12.04 3.00e+00 1.11e-01 1.61e+01 angle pdb=" OG1 TPO G 354 " pdb=" P TPO G 354 " pdb=" O1P TPO G 354 " ideal model delta sigma weight residual 100.43 109.46 -9.03 3.00e+00 1.11e-01 9.06e+00 angle pdb=" OG1 TPO H 354 " pdb=" P TPO H 354 " pdb=" O1P TPO H 354 " ideal model delta sigma weight residual 100.43 109.43 -9.00 3.00e+00 1.11e-01 8.99e+00 angle pdb=" C LEU F 49 " pdb=" N LYS F 50 " pdb=" CA LYS F 50 " ideal model delta sigma weight residual 121.54 127.26 -5.72 1.91e+00 2.74e-01 8.97e+00 ... (remaining 16245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6599 17.99 - 35.99: 463 35.99 - 53.98: 86 53.98 - 71.97: 16 71.97 - 89.96: 8 Dihedral angle restraints: 7172 sinusoidal: 2730 harmonic: 4442 Sorted by residual: dihedral pdb=" CA ARG A 96 " pdb=" C ARG A 96 " pdb=" N PRO A 97 " pdb=" CA PRO A 97 " ideal model delta harmonic sigma weight residual 180.00 147.99 32.01 0 5.00e+00 4.00e-02 4.10e+01 dihedral pdb=" CA ARG F 96 " pdb=" C ARG F 96 " pdb=" N PRO F 97 " pdb=" CA PRO F 97 " ideal model delta harmonic sigma weight residual 180.00 148.06 31.94 0 5.00e+00 4.00e-02 4.08e+01 dihedral pdb=" CA PRO F 95 " pdb=" C PRO F 95 " pdb=" N ARG F 96 " pdb=" CA ARG F 96 " ideal model delta harmonic sigma weight residual 0.00 -30.10 30.10 0 5.00e+00 4.00e-02 3.62e+01 ... (remaining 7169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1290 0.035 - 0.071: 337 0.071 - 0.106: 157 0.106 - 0.141: 56 0.141 - 0.177: 4 Chirality restraints: 1844 Sorted by residual: chirality pdb=" CA LYS A 295 " pdb=" N LYS A 295 " pdb=" C LYS A 295 " pdb=" CB LYS A 295 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" CA LYS A 108 " pdb=" N LYS A 108 " pdb=" C LYS A 108 " pdb=" CB LYS A 108 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA LYS F 108 " pdb=" N LYS F 108 " pdb=" C LYS F 108 " pdb=" CB LYS F 108 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.95e-01 ... (remaining 1841 not shown) Planarity restraints: 2078 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 96 " 0.075 5.00e-02 4.00e+02 1.14e-01 2.10e+01 pdb=" N PRO A 97 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO A 97 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 97 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 96 " -0.075 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO F 97 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO F 97 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO F 97 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 91 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO A 92 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 92 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 92 " -0.027 5.00e-02 4.00e+02 ... (remaining 2075 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2837 2.80 - 3.33: 9646 3.33 - 3.85: 17971 3.85 - 4.38: 20008 4.38 - 4.90: 36855 Nonbonded interactions: 87317 Sorted by model distance: nonbonded pdb=" OE1 GLN C 7 " pdb=" OG1 THR C 103 " model vdw 2.277 3.040 nonbonded pdb=" OE1 GLN E 7 " pdb=" OG1 THR E 103 " model vdw 2.277 3.040 nonbonded pdb=" NZ LYS F 11 " pdb=" OE2 GLU H 349 " model vdw 2.279 3.120 nonbonded pdb=" O PHE E 140 " pdb=" OG1 THR E 173 " model vdw 2.282 3.040 nonbonded pdb=" O PHE C 140 " pdb=" OG1 THR C 173 " model vdw 2.282 3.040 ... (remaining 87312 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'G' 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=0.65 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 29.640 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 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 : 0.003 0.108 11930 Z= 0.188 Angle : 0.554 12.092 16250 Z= 0.275 Chirality : 0.042 0.177 1844 Planarity : 0.006 0.114 2078 Dihedral : 13.071 89.963 4286 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.32 % Allowed : 0.24 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.14 % Twisted Proline : 2.13 % Twisted General : 0.14 % 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: 0.51 (0.23), residues: 1472 helix: 2.08 (0.60), residues: 80 sheet: 1.27 (0.22), residues: 656 loop : -0.77 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 50 HIS 0.002 0.000 HIS F 346 PHE 0.008 0.001 PHE F 278 TYR 0.006 0.001 TYR A 250 ARG 0.007 0.000 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 124 time to evaluate : 1.280 Fit side-chains REVERT: A 108 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7923 (tttm) REVERT: B 77 THR cc_start: 0.8264 (p) cc_final: 0.8018 (p) REVERT: B 185 LEU cc_start: 0.7506 (mm) cc_final: 0.7219 (mm) REVERT: D 22 ARG cc_start: 0.7345 (ttt-90) cc_final: 0.7120 (tpt-90) REVERT: D 132 PHE cc_start: 0.6250 (m-10) cc_final: 0.5801 (m-80) REVERT: D 151 LEU cc_start: 0.7352 (tt) cc_final: 0.7145 (tt) REVERT: F 108 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7960 (ttpt) outliers start: 4 outliers final: 1 residues processed: 128 average time/residue: 0.2681 time to fit residues: 48.2245 Evaluate side-chains 107 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 295 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 0.0570 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 71 optimal weight: 0.1980 chunk 87 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN B 87 ASN C 7 GLN D 87 ASN E 7 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11930 Z= 0.187 Angle : 0.530 7.570 16250 Z= 0.271 Chirality : 0.044 0.146 1844 Planarity : 0.005 0.091 2078 Dihedral : 5.810 62.638 1688 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.20 % Allowed : 5.50 % Favored : 93.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.28 % 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: 0.49 (0.23), residues: 1472 helix: 2.05 (0.59), residues: 84 sheet: 1.06 (0.20), residues: 692 loop : -0.67 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 50 HIS 0.002 0.001 HIS F 114 PHE 0.022 0.001 PHE F 81 TYR 0.013 0.001 TYR C 92 ARG 0.006 0.000 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 1.291 Fit side-chains REVERT: D 185 LEU cc_start: 0.7534 (mm) cc_final: 0.6614 (mm) REVERT: F 153 LYS cc_start: 0.8684 (mtmm) cc_final: 0.8435 (mttp) REVERT: F 230 LYS cc_start: 0.7089 (mtmm) cc_final: 0.6515 (ttpp) REVERT: H 352 ILE cc_start: 0.7894 (mm) cc_final: 0.7670 (mt) outliers start: 15 outliers final: 14 residues processed: 122 average time/residue: 0.2974 time to fit residues: 49.9545 Evaluate side-chains 108 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 295 LYS Chi-restraints excluded: chain F residue 296 HIS Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain G residue 349 GLU Chi-restraints excluded: chain H residue 349 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 92 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 109 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN D 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11930 Z= 0.294 Angle : 0.570 7.118 16250 Z= 0.291 Chirality : 0.045 0.166 1844 Planarity : 0.005 0.064 2078 Dihedral : 5.935 65.014 1680 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.15 % Allowed : 7.97 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.27 (0.23), residues: 1472 helix: 2.15 (0.59), residues: 82 sheet: 0.90 (0.20), residues: 690 loop : -0.81 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 50 HIS 0.005 0.001 HIS F 346 PHE 0.021 0.002 PHE F 269 TYR 0.021 0.002 TYR E 92 ARG 0.003 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 1.281 Fit side-chains REVERT: A 230 LYS cc_start: 0.6743 (mtmm) cc_final: 0.6357 (mtpp) REVERT: C 106 GLU cc_start: 0.8040 (pm20) cc_final: 0.7788 (pm20) REVERT: E 119 PHE cc_start: 0.5207 (m-80) cc_final: 0.4826 (m-80) REVERT: F 153 LYS cc_start: 0.8706 (mtmm) cc_final: 0.8502 (mttp) REVERT: F 230 LYS cc_start: 0.7102 (mtmm) cc_final: 0.6696 (mtpp) outliers start: 27 outliers final: 19 residues processed: 126 average time/residue: 0.2935 time to fit residues: 51.0700 Evaluate side-chains 115 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain G residue 349 GLU Chi-restraints excluded: chain H residue 349 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 15 optimal weight: 0.0060 chunk 65 optimal weight: 0.1980 chunk 91 optimal weight: 8.9990 chunk 136 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 129 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS B 87 ASN D 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11930 Z= 0.175 Angle : 0.512 6.768 16250 Z= 0.258 Chirality : 0.043 0.145 1844 Planarity : 0.005 0.091 2078 Dihedral : 5.686 64.773 1676 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.83 % Allowed : 10.37 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.31 (0.23), residues: 1472 helix: 2.18 (0.59), residues: 84 sheet: 0.90 (0.20), residues: 690 loop : -0.77 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 50 HIS 0.002 0.000 HIS F 199 PHE 0.014 0.001 PHE F 81 TYR 0.013 0.001 TYR A 250 ARG 0.004 0.000 ARG C 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 1.363 Fit side-chains REVERT: C 119 PHE cc_start: 0.4903 (m-80) cc_final: 0.4679 (m-80) REVERT: D 185 LEU cc_start: 0.7338 (mm) cc_final: 0.6385 (mm) REVERT: E 119 PHE cc_start: 0.5087 (m-80) cc_final: 0.4872 (m-80) REVERT: F 230 LYS cc_start: 0.7082 (mtmm) cc_final: 0.6681 (mtpp) outliers start: 23 outliers final: 20 residues processed: 114 average time/residue: 0.3065 time to fit residues: 48.0762 Evaluate side-chains 112 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain G residue 349 GLU Chi-restraints excluded: chain H residue 349 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 3.9990 chunk 82 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN D 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 11930 Z= 0.408 Angle : 0.627 8.687 16250 Z= 0.321 Chirality : 0.047 0.180 1844 Planarity : 0.005 0.075 2078 Dihedral : 6.137 70.100 1676 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.15 % Allowed : 11.40 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.01 (0.23), residues: 1472 helix: 2.13 (0.60), residues: 84 sheet: 0.78 (0.20), residues: 676 loop : -1.04 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 50 HIS 0.007 0.001 HIS A 211 PHE 0.025 0.002 PHE A 269 TYR 0.026 0.002 TYR E 92 ARG 0.003 0.001 ARG F 406 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 1.472 Fit side-chains REVERT: A 230 LYS cc_start: 0.6759 (mtmm) cc_final: 0.6437 (mtpp) REVERT: B 68 LYS cc_start: 0.7867 (tptt) cc_final: 0.7637 (tptp) REVERT: C 119 PHE cc_start: 0.5028 (m-80) cc_final: 0.4710 (m-80) REVERT: D 68 LYS cc_start: 0.7865 (tptt) cc_final: 0.7642 (tptp) REVERT: F 230 LYS cc_start: 0.7076 (mtmm) cc_final: 0.6699 (mtpp) outliers start: 27 outliers final: 22 residues processed: 117 average time/residue: 0.3142 time to fit residues: 50.0763 Evaluate side-chains 111 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain G residue 349 GLU Chi-restraints excluded: chain H residue 349 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 145 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 139 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN D 87 ASN E 28 GLN F 190 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11930 Z= 0.205 Angle : 0.546 6.620 16250 Z= 0.276 Chirality : 0.044 0.143 1844 Planarity : 0.005 0.064 2078 Dihedral : 5.902 67.795 1676 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.23 % Allowed : 11.56 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.13 (0.23), residues: 1472 helix: 2.45 (0.61), residues: 82 sheet: 0.83 (0.20), residues: 676 loop : -0.96 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 50 HIS 0.002 0.001 HIS A 346 PHE 0.026 0.001 PHE A 269 TYR 0.014 0.001 TYR F 250 ARG 0.004 0.000 ARG D 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 1.315 Fit side-chains REVERT: A 230 LYS cc_start: 0.6807 (mtmm) cc_final: 0.6492 (mtpp) REVERT: B 68 LYS cc_start: 0.7804 (tptt) cc_final: 0.7570 (tptp) REVERT: D 68 LYS cc_start: 0.7818 (tptt) cc_final: 0.7588 (tptp) REVERT: E 106 GLU cc_start: 0.7952 (pm20) cc_final: 0.7723 (pm20) REVERT: F 230 LYS cc_start: 0.7080 (mtmm) cc_final: 0.6722 (mtpp) outliers start: 28 outliers final: 25 residues processed: 117 average time/residue: 0.3213 time to fit residues: 51.1147 Evaluate side-chains 115 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 28 GLN Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain G residue 349 GLU Chi-restraints excluded: chain H residue 349 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 0.6980 chunk 82 optimal weight: 0.0000 chunk 105 optimal weight: 0.6980 chunk 122 optimal weight: 6.9990 chunk 81 optimal weight: 0.4980 chunk 144 optimal weight: 2.9990 chunk 90 optimal weight: 0.0970 chunk 88 optimal weight: 0.0770 chunk 66 optimal weight: 2.9990 chunk 89 optimal weight: 0.0370 chunk 57 optimal weight: 0.9980 overall best weight: 0.1418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN D 87 ASN E 28 GLN F 190 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11930 Z= 0.131 Angle : 0.515 6.748 16250 Z= 0.258 Chirality : 0.043 0.140 1844 Planarity : 0.005 0.060 2078 Dihedral : 5.676 66.386 1676 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.20 % Allowed : 12.76 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.33 (0.23), residues: 1472 helix: 2.34 (0.60), residues: 84 sheet: 0.99 (0.20), residues: 676 loop : -0.82 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 36 HIS 0.002 0.000 HIS F 211 PHE 0.027 0.001 PHE A 269 TYR 0.014 0.001 TYR A 48 ARG 0.007 0.000 ARG C 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 1.196 Fit side-chains REVERT: A 200 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7760 (pt) REVERT: A 230 LYS cc_start: 0.6735 (mtmm) cc_final: 0.6428 (mtpp) REVERT: D 68 LYS cc_start: 0.7757 (tptt) cc_final: 0.7524 (tptp) REVERT: F 230 LYS cc_start: 0.7004 (mtmm) cc_final: 0.6379 (mtpp) outliers start: 15 outliers final: 11 residues processed: 108 average time/residue: 0.3163 time to fit residues: 45.9891 Evaluate side-chains 102 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain H residue 349 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 138 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN D 87 ASN D 174 HIS F 190 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 11930 Z= 0.425 Angle : 0.642 7.557 16250 Z= 0.329 Chirality : 0.047 0.178 1844 Planarity : 0.006 0.102 2078 Dihedral : 6.192 70.514 1676 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.47 % Allowed : 12.36 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.04 (0.23), residues: 1472 helix: 2.28 (0.60), residues: 84 sheet: 0.67 (0.20), residues: 692 loop : -0.92 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 50 HIS 0.009 0.001 HIS A 211 PHE 0.028 0.002 PHE A 269 TYR 0.025 0.002 TYR C 92 ARG 0.006 0.001 ARG C 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 1.431 Fit side-chains REVERT: A 230 LYS cc_start: 0.6835 (mtmm) cc_final: 0.6501 (mtpp) REVERT: B 68 LYS cc_start: 0.7806 (tptt) cc_final: 0.7591 (tptp) REVERT: D 68 LYS cc_start: 0.7879 (tptt) cc_final: 0.7670 (tptp) outliers start: 31 outliers final: 29 residues processed: 116 average time/residue: 0.2878 time to fit residues: 46.8357 Evaluate side-chains 115 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain H residue 349 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 81 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 121 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN D 87 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 11930 Z= 0.327 Angle : 0.598 8.851 16250 Z= 0.304 Chirality : 0.046 0.161 1844 Planarity : 0.006 0.100 2078 Dihedral : 6.146 70.310 1676 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.47 % Allowed : 12.28 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.03 (0.23), residues: 1472 helix: 2.21 (0.59), residues: 84 sheet: 0.75 (0.21), residues: 668 loop : -1.07 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 50 HIS 0.005 0.001 HIS F 211 PHE 0.032 0.002 PHE A 269 TYR 0.021 0.002 TYR C 92 ARG 0.005 0.000 ARG C 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 1.627 Fit side-chains REVERT: A 230 LYS cc_start: 0.6830 (mtmm) cc_final: 0.6484 (mtpp) REVERT: B 68 LYS cc_start: 0.7805 (tptt) cc_final: 0.7590 (tptp) REVERT: D 68 LYS cc_start: 0.7818 (tptt) cc_final: 0.7603 (tptp) REVERT: F 158 LYS cc_start: 0.6902 (pttp) cc_final: 0.6623 (pptt) outliers start: 31 outliers final: 27 residues processed: 112 average time/residue: 0.2909 time to fit residues: 46.0414 Evaluate side-chains 112 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 299 THR Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain G residue 349 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 chunk 137 optimal weight: 0.0570 chunk 118 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 72 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN C 28 GLN D 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11930 Z= 0.211 Angle : 0.556 8.451 16250 Z= 0.279 Chirality : 0.045 0.147 1844 Planarity : 0.005 0.095 2078 Dihedral : 5.994 69.326 1676 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.15 % Allowed : 12.60 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.03 (0.23), residues: 1472 helix: 2.34 (0.60), residues: 84 sheet: 0.67 (0.21), residues: 688 loop : -0.94 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 50 HIS 0.002 0.001 HIS A 346 PHE 0.031 0.002 PHE A 269 TYR 0.015 0.001 TYR A 48 ARG 0.004 0.000 ARG D 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2944 Ramachandran restraints generated. 1472 Oldfield, 0 Emsley, 1472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 1.395 Fit side-chains REVERT: A 230 LYS cc_start: 0.6767 (mtmm) cc_final: 0.6436 (mtpp) REVERT: B 68 LYS cc_start: 0.7795 (tptt) cc_final: 0.7573 (tptp) REVERT: D 68 LYS cc_start: 0.7798 (tptt) cc_final: 0.7585 (tptp) REVERT: F 158 LYS cc_start: 0.6849 (pttp) cc_final: 0.6591 (pptt) outliers start: 27 outliers final: 25 residues processed: 109 average time/residue: 0.2988 time to fit residues: 45.5990 Evaluate side-chains 113 residues out of total 1326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain C residue 28 GLN Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 5 MET Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 336 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 15 optimal weight: 0.0670 chunk 21 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN C 28 GLN D 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.178045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.142486 restraints weight = 13988.733| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.62 r_work: 0.3343 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11930 Z= 0.199 Angle : 0.550 8.396 16250 Z= 0.276 Chirality : 0.044 0.148 1844 Planarity : 0.005 0.095 2078 Dihedral : 5.948 69.186 1676 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.07 % Allowed : 12.76 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.10 (0.23), residues: 1472 helix: 2.33 (0.59), residues: 84 sheet: 0.73 (0.21), residues: 688 loop : -0.91 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 50 HIS 0.002 0.001 HIS A 199 PHE 0.029 0.001 PHE A 269 TYR 0.014 0.001 TYR A 48 ARG 0.004 0.000 ARG D 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2333.20 seconds wall clock time: 43 minutes 54.30 seconds (2634.30 seconds total)