Starting phenix.real_space_refine on Mon May 12 16:38:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i0n_35104/05_2025/8i0n_35104.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i0n_35104/05_2025/8i0n_35104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i0n_35104/05_2025/8i0n_35104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i0n_35104/05_2025/8i0n_35104.map" model { file = "/net/cci-nas-00/data/ceres_data/8i0n_35104/05_2025/8i0n_35104.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i0n_35104/05_2025/8i0n_35104.cif" } resolution = 3.26 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= 0.040 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 10 5.49 5 S 32 5.16 5 C 5798 2.51 5 N 1546 2.21 5 O 1755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9141 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2775 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 28, 'TRANS': 333} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 6, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2767 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 28, 'TRANS': 333} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "H" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113} Chain: "I" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113} Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 799 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "U" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 90 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'TPO:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "V" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 90 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'TPO:plan-1': 3} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 5.49, per 1000 atoms: 0.60 Number of scatterers: 9141 At special positions: 0 Unit cell: (113.436, 168.104, 84.7354, 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 32 16.00 P 10 15.00 O 1755 8.00 N 1546 7.00 C 5798 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS I 25 " - pdb=" SG CYS I 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 24 " - pdb=" SG CYS M 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: 2.06 Conformation dependent library (CDL) restraints added in 1.0 seconds 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 22 sheets defined 5.6% alpha, 47.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.686A pdb=" N ARG A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 278 through 282 removed outlier: 4.114A pdb=" N ARG A 282 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.912A pdb=" N LYS B 94 " --> pdb=" O PRO B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 removed outlier: 3.700A pdb=" N ARG B 103 " --> pdb=" O ARG B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 278 through 282 removed outlier: 4.108A pdb=" N ARG B 282 " --> pdb=" O ALA B 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 94 removed outlier: 4.176A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 68 removed outlier: 3.640A pdb=" N LYS I 68 " --> pdb=" O ASP I 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 65 through 68' Processing helix chain 'I' and resid 77 through 79 No H-bonds generated for 'chain 'I' and resid 77 through 79' Processing helix chain 'I' and resid 90 through 94 removed outlier: 4.142A pdb=" N THR I 94 " --> pdb=" O ALA I 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 84 removed outlier: 4.260A pdb=" N PHE M 84 " --> pdb=" O PRO M 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 117 Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.742A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 10.117A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 55 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASN A 83 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU A 57 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL A 81 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N CYS A 59 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.742A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 10.117A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N CYS A 140 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 189 Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 208 removed outlier: 4.215A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LEU A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N VAL A 319 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE A 231 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N GLU A 257 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE A 233 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N MET A 255 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL A 235 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A 249 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 112 through 117 Processing sheet with id=AA7, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.750A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LYS B 170 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 10.142A pdb=" N VAL B 142 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL B 55 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASN B 83 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B 57 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL B 81 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N CYS B 59 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.750A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LYS B 170 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 10.142A pdb=" N VAL B 142 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N CYS B 140 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 183 through 189 Processing sheet with id=AB1, first strand: chain 'B' and resid 207 through 208 removed outlier: 3.518A pdb=" N PHE B 349 " --> pdb=" O TYR B 321 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU B 351 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N VAL B 319 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE B 231 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU B 257 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE B 233 " --> pdb=" O MET B 255 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N MET B 255 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL B 235 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR B 249 " --> pdb=" O ALA B 239 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AB3, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.892A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.892A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 6 through 10 Processing sheet with id=AB6, first strand: chain 'I' and resid 60 through 63 removed outlier: 6.885A pdb=" N TRP I 39 " --> pdb=" O VAL I 51 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N SER I 53 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE I 37 " --> pdb=" O SER I 53 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N SER I 55 " --> pdb=" O SER I 35 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N SER I 35 " --> pdb=" O SER I 55 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR I 112 " --> pdb=" O ARG I 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 60 through 63 removed outlier: 6.885A pdb=" N TRP I 39 " --> pdb=" O VAL I 51 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N SER I 53 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE I 37 " --> pdb=" O SER I 53 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N SER I 55 " --> pdb=" O SER I 35 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N SER I 35 " --> pdb=" O SER I 55 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AB9, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.505A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.874A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 5 through 8 Processing sheet with id=AC3, first strand: chain 'M' and resid 11 through 13 removed outlier: 6.484A pdb=" N VAL M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TYR M 50 " --> pdb=" O VAL M 34 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 11 through 13 removed outlier: 3.838A pdb=" N THR M 98 " --> pdb=" O GLN M 91 " (cutoff:3.500A) 397 hydrogen bonds defined for protein. 1035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.79 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1767 1.33 - 1.45: 2226 1.45 - 1.57: 5284 1.57 - 1.69: 28 1.69 - 1.81: 42 Bond restraints: 9347 Sorted by residual: bond pdb=" OG1 TPO V 339 " pdb=" P TPO V 339 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" OG1 TPO U 339 " pdb=" P TPO U 339 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" OG1 TPO V 336 " pdb=" P TPO V 336 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" OG1 TPO U 336 " pdb=" P TPO U 336 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" OG1 TPO V 342 " pdb=" P TPO V 342 " ideal model delta sigma weight residual 1.717 1.616 0.101 2.00e-02 2.50e+03 2.56e+01 ... (remaining 9342 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 12561 2.52 - 5.04: 138 5.04 - 7.55: 20 7.55 - 10.07: 8 10.07 - 12.59: 6 Bond angle restraints: 12733 Sorted by residual: angle pdb=" N PRO B 360 " pdb=" CA PRO B 360 " pdb=" C PRO B 360 " ideal model delta sigma weight residual 110.70 103.37 7.33 1.22e+00 6.72e-01 3.61e+01 angle pdb=" CB TPO V 339 " pdb=" OG1 TPO V 339 " pdb=" P TPO V 339 " ideal model delta sigma weight residual 119.31 106.72 12.59 3.00e+00 1.11e-01 1.76e+01 angle pdb=" CB TPO U 339 " pdb=" OG1 TPO U 339 " pdb=" P TPO U 339 " ideal model delta sigma weight residual 119.31 107.13 12.18 3.00e+00 1.11e-01 1.65e+01 angle pdb=" CB TPO V 336 " pdb=" OG1 TPO V 336 " pdb=" P TPO V 336 " ideal model delta sigma weight residual 119.31 107.38 11.93 3.00e+00 1.11e-01 1.58e+01 angle pdb=" OG1 TPO U 342 " pdb=" P TPO U 342 " pdb=" O1P TPO U 342 " ideal model delta sigma weight residual 100.43 112.33 -11.90 3.00e+00 1.11e-01 1.57e+01 ... (remaining 12728 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5117 17.97 - 35.94: 389 35.94 - 53.90: 77 53.90 - 71.87: 20 71.87 - 89.84: 16 Dihedral angle restraints: 5619 sinusoidal: 2151 harmonic: 3468 Sorted by residual: dihedral pdb=" CA GLU A 364 " pdb=" C GLU A 364 " pdb=" N VAL A 365 " pdb=" CA VAL A 365 " ideal model delta harmonic sigma weight residual 180.00 -163.83 -16.17 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CB GLU B 206 " pdb=" CG GLU B 206 " pdb=" CD GLU B 206 " pdb=" OE1 GLU B 206 " ideal model delta sinusoidal sigma weight residual 0.00 87.52 -87.52 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CA GLU B 364 " pdb=" C GLU B 364 " pdb=" N VAL B 365 " pdb=" CA VAL B 365 " ideal model delta harmonic sigma weight residual -180.00 -164.07 -15.93 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 5616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1040 0.040 - 0.080: 260 0.080 - 0.121: 131 0.121 - 0.161: 18 0.161 - 0.201: 1 Chirality restraints: 1450 Sorted by residual: chirality pdb=" CA PRO B 360 " pdb=" N PRO B 360 " pdb=" C PRO B 360 " pdb=" CB PRO B 360 " both_signs ideal model delta sigma weight residual False 2.72 2.92 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA VAL A 84 " pdb=" N VAL A 84 " pdb=" C VAL A 84 " pdb=" CB VAL A 84 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA ILE A 318 " pdb=" N ILE A 318 " pdb=" C ILE A 318 " pdb=" CB ILE A 318 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 1447 not shown) Planarity restraints: 1622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 359 " 0.015 2.00e-02 2.50e+03 3.00e-02 8.99e+00 pdb=" C GLU A 359 " -0.052 2.00e-02 2.50e+03 pdb=" O GLU A 359 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO A 360 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 337 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.74e+00 pdb=" C ASP A 337 " 0.045 2.00e-02 2.50e+03 pdb=" O ASP A 337 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU A 338 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 359 " 0.009 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C GLU B 359 " -0.029 2.00e-02 2.50e+03 pdb=" O GLU B 359 " 0.011 2.00e-02 2.50e+03 pdb=" N PRO B 360 " 0.010 2.00e-02 2.50e+03 ... (remaining 1619 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2245 2.80 - 3.32: 7626 3.32 - 3.85: 14136 3.85 - 4.37: 15956 4.37 - 4.90: 30113 Nonbonded interactions: 70076 Sorted by model distance: nonbonded pdb=" NH1 ARG B 76 " pdb=" OD1 ASP B 78 " model vdw 2.273 3.120 nonbonded pdb=" N GLU L 82 " pdb=" OE1 GLU L 82 " model vdw 2.284 3.120 nonbonded pdb=" O ALA A 301 " pdb=" OH TYR A 321 " model vdw 2.317 3.040 nonbonded pdb=" O ALA B 301 " pdb=" OH TYR B 321 " model vdw 2.325 3.040 nonbonded pdb=" NZ LYS A 292 " pdb=" OG1 THR A 298 " model vdw 2.347 3.120 ... (remaining 70071 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' and (resid 7 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 68 or (resid 69 and (name N or name \ CA or name C or name O or name CB )) or resid 70 through 133 or (resid 134 and \ (name N or name CA or name C or name O or name CB )) or resid 135 through 175 or \ (resid 176 through 177 and (name N or name CA or name C or name O or name CB )) \ or resid 178 through 368)) selection = (chain 'B' and (resid 7 through 203 or (resid 204 and (name N or name CA or name \ C or name O or name CB )) or resid 205 through 214 or (resid 215 and (name N or \ name CA or name C or name O or name CB )) or resid 216 through 336 or (resid 33 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 338 through \ 368)) } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = (chain 'L' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 50 or (resid 51 through 52 and (name N \ or name CA or name C or name O or name CB )) or resid 53 through 107)) selection = chain 'M' } ncs_group { reference = chain 'U' selection = chain 'V' } 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 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: 1.510 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.480 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 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 0.110 9351 Z= 0.289 Angle : 0.714 12.591 12741 Z= 0.331 Chirality : 0.044 0.201 1450 Planarity : 0.004 0.040 1622 Dihedral : 14.608 89.840 3379 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.62 % Allowed : 12.13 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.18 % 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: 0.08 (0.25), residues: 1160 helix: 0.07 (1.25), residues: 20 sheet: 0.53 (0.23), residues: 534 loop : -0.33 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 39 HIS 0.005 0.001 HIS A 353 PHE 0.013 0.002 PHE A 349 TYR 0.012 0.001 TYR M 92 ARG 0.008 0.001 ARG A 363 Details of bonding type rmsd hydrogen bonds : bond 0.22026 ( 345) hydrogen bonds : angle 8.89481 ( 1035) SS BOND : bond 0.00210 ( 4) SS BOND : angle 0.36433 ( 8) covalent geometry : bond 0.00595 ( 9347) covalent geometry : angle 0.71421 (12733) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 1.052 Fit side-chains REVERT: B 204 ASP cc_start: 0.7870 (m-30) cc_final: 0.7634 (m-30) REVERT: L 43 LYS cc_start: 0.8519 (mmmm) cc_final: 0.8207 (mmtp) REVERT: M 43 LYS cc_start: 0.8434 (mmmm) cc_final: 0.8151 (mmtp) outliers start: 6 outliers final: 4 residues processed: 97 average time/residue: 0.2841 time to fit residues: 37.8032 Evaluate side-chains 87 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain I residue 21 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 89 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 0.1980 chunk 66 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.144232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.115057 restraints weight = 12830.255| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.57 r_work: 0.3199 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9351 Z= 0.115 Angle : 0.546 4.867 12741 Z= 0.287 Chirality : 0.044 0.144 1450 Planarity : 0.004 0.030 1622 Dihedral : 5.876 66.853 1320 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.26 % Allowed : 10.79 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.18 % 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: 0.36 (0.25), residues: 1160 helix: -0.01 (1.15), residues: 20 sheet: 0.74 (0.23), residues: 534 loop : -0.14 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 50 HIS 0.004 0.001 HIS A 353 PHE 0.012 0.002 PHE M 84 TYR 0.014 0.001 TYR A 21 ARG 0.004 0.000 ARG M 25 Details of bonding type rmsd hydrogen bonds : bond 0.03851 ( 345) hydrogen bonds : angle 5.41889 ( 1035) SS BOND : bond 0.00347 ( 4) SS BOND : angle 0.25720 ( 8) covalent geometry : bond 0.00269 ( 9347) covalent geometry : angle 0.54642 (12733) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 1.064 Fit side-chains REVERT: B 204 ASP cc_start: 0.8230 (m-30) cc_final: 0.7958 (m-30) REVERT: H 120 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.7990 (p) REVERT: I 120 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.7967 (p) REVERT: L 43 LYS cc_start: 0.8683 (mmmm) cc_final: 0.8435 (mmtp) REVERT: L 82 GLU cc_start: 0.7374 (pm20) cc_final: 0.7027 (pm20) REVERT: M 43 LYS cc_start: 0.8595 (mmmm) cc_final: 0.8375 (mmtp) outliers start: 22 outliers final: 14 residues processed: 108 average time/residue: 0.2207 time to fit residues: 33.2793 Evaluate side-chains 104 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain U residue 335 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS B 111 HIS B 189 GLN I 85 GLN L 7 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.140995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.112599 restraints weight = 12984.055| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.58 r_work: 0.3177 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9351 Z= 0.174 Angle : 0.560 8.030 12741 Z= 0.291 Chirality : 0.045 0.200 1450 Planarity : 0.004 0.026 1622 Dihedral : 5.516 61.632 1314 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.29 % Allowed : 11.51 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.18 % 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: 0.41 (0.25), residues: 1160 helix: 0.38 (1.05), residues: 24 sheet: 0.77 (0.23), residues: 534 loop : -0.11 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 50 HIS 0.006 0.001 HIS A 353 PHE 0.013 0.002 PHE B 27 TYR 0.019 0.002 TYR M 92 ARG 0.007 0.001 ARG V 337 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 345) hydrogen bonds : angle 4.86502 ( 1035) SS BOND : bond 0.00262 ( 4) SS BOND : angle 0.42910 ( 8) covalent geometry : bond 0.00420 ( 9347) covalent geometry : angle 0.56011 (12733) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 1.061 Fit side-chains REVERT: A 48 LEU cc_start: 0.5956 (OUTLIER) cc_final: 0.5616 (tp) REVERT: B 29 ASP cc_start: 0.8273 (t0) cc_final: 0.8019 (t0) REVERT: B 204 ASP cc_start: 0.8426 (m-30) cc_final: 0.8178 (m-30) REVERT: B 206 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7936 (tp30) REVERT: H 120 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.8036 (p) REVERT: I 120 THR cc_start: 0.8276 (OUTLIER) cc_final: 0.7944 (p) REVERT: L 43 LYS cc_start: 0.8694 (mmmm) cc_final: 0.8457 (mmtp) REVERT: L 82 GLU cc_start: 0.7406 (pm20) cc_final: 0.7163 (pm20) REVERT: M 82 GLU cc_start: 0.7615 (pp20) cc_final: 0.7316 (pm20) outliers start: 32 outliers final: 19 residues processed: 119 average time/residue: 0.2170 time to fit residues: 36.3246 Evaluate side-chains 111 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 61 THR Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 59 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.140704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.112263 restraints weight = 12791.454| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.50 r_work: 0.3158 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9351 Z= 0.148 Angle : 0.526 7.545 12741 Z= 0.271 Chirality : 0.044 0.142 1450 Planarity : 0.004 0.029 1622 Dihedral : 5.199 56.509 1312 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.60 % Allowed : 13.57 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.18 % 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: 0.44 (0.26), residues: 1160 helix: 0.51 (1.05), residues: 24 sheet: 0.82 (0.23), residues: 532 loop : -0.13 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 50 HIS 0.005 0.001 HIS A 353 PHE 0.010 0.001 PHE A 349 TYR 0.015 0.001 TYR L 92 ARG 0.003 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.02943 ( 345) hydrogen bonds : angle 4.61305 ( 1035) SS BOND : bond 0.00418 ( 4) SS BOND : angle 0.66062 ( 8) covalent geometry : bond 0.00358 ( 9347) covalent geometry : angle 0.52555 (12733) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 1.098 Fit side-chains REVERT: A 48 LEU cc_start: 0.6059 (OUTLIER) cc_final: 0.5691 (tp) REVERT: A 189 GLN cc_start: 0.7040 (tp-100) cc_final: 0.6763 (tp40) REVERT: B 44 ASP cc_start: 0.7306 (t0) cc_final: 0.6999 (t0) REVERT: B 204 ASP cc_start: 0.8513 (m-30) cc_final: 0.8232 (m-30) REVERT: B 206 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.8011 (tp30) REVERT: B 248 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8345 (tp40) REVERT: I 120 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.8067 (p) REVERT: L 43 LYS cc_start: 0.8844 (mmmm) cc_final: 0.8618 (mmtp) REVERT: L 79 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7435 (tp) REVERT: L 82 GLU cc_start: 0.7448 (pm20) cc_final: 0.7180 (pm20) outliers start: 35 outliers final: 21 residues processed: 119 average time/residue: 0.2101 time to fit residues: 35.2102 Evaluate side-chains 112 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 248 GLN Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 75 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 95 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.137212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.107180 restraints weight = 12807.903| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.60 r_work: 0.3150 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 9351 Z= 0.213 Angle : 0.577 6.014 12741 Z= 0.299 Chirality : 0.045 0.146 1450 Planarity : 0.004 0.031 1622 Dihedral : 5.312 58.704 1312 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.32 % Allowed : 14.39 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.18 % 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: 0.29 (0.25), residues: 1160 helix: 0.37 (1.04), residues: 24 sheet: 0.68 (0.23), residues: 528 loop : -0.18 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 50 HIS 0.007 0.001 HIS A 353 PHE 0.013 0.002 PHE L 99 TYR 0.015 0.002 TYR L 92 ARG 0.004 0.001 ARG I 90 Details of bonding type rmsd hydrogen bonds : bond 0.03129 ( 345) hydrogen bonds : angle 4.72292 ( 1035) SS BOND : bond 0.00241 ( 4) SS BOND : angle 0.93407 ( 8) covalent geometry : bond 0.00522 ( 9347) covalent geometry : angle 0.57630 (12733) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 85 time to evaluate : 0.969 Fit side-chains REVERT: A 48 LEU cc_start: 0.6210 (OUTLIER) cc_final: 0.5917 (tp) REVERT: B 44 ASP cc_start: 0.7311 (t0) cc_final: 0.7024 (t0) REVERT: B 75 PHE cc_start: 0.6788 (OUTLIER) cc_final: 0.6133 (p90) REVERT: B 206 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8086 (tp30) REVERT: B 248 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8323 (tp40) REVERT: I 120 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.8131 (p) REVERT: L 43 LYS cc_start: 0.8847 (mmmm) cc_final: 0.8618 (mmtp) REVERT: L 79 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7538 (tp) REVERT: L 82 GLU cc_start: 0.7387 (pm20) cc_final: 0.7130 (pm20) outliers start: 42 outliers final: 31 residues processed: 114 average time/residue: 0.2091 time to fit residues: 33.6101 Evaluate side-chains 120 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 83 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 248 GLN Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 107 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 93 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 57 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 0.0270 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.139940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.110109 restraints weight = 12810.444| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.66 r_work: 0.3153 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9351 Z= 0.118 Angle : 0.517 7.590 12741 Z= 0.265 Chirality : 0.043 0.142 1450 Planarity : 0.004 0.028 1622 Dihedral : 5.081 58.289 1312 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.98 % Allowed : 16.34 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.18 % 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: 0.37 (0.25), residues: 1160 helix: 0.65 (1.06), residues: 24 sheet: 0.73 (0.23), residues: 532 loop : -0.14 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 50 HIS 0.004 0.001 HIS H 38 PHE 0.009 0.001 PHE M 99 TYR 0.014 0.001 TYR L 92 ARG 0.007 0.000 ARG H 90 Details of bonding type rmsd hydrogen bonds : bond 0.02671 ( 345) hydrogen bonds : angle 4.50946 ( 1035) SS BOND : bond 0.00286 ( 4) SS BOND : angle 0.60622 ( 8) covalent geometry : bond 0.00286 ( 9347) covalent geometry : angle 0.51694 (12733) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.902 Fit side-chains REVERT: A 48 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5759 (tp) REVERT: B 44 ASP cc_start: 0.7294 (t0) cc_final: 0.6999 (t0) REVERT: B 75 PHE cc_start: 0.6798 (OUTLIER) cc_final: 0.6168 (p90) REVERT: B 206 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8102 (tp30) REVERT: B 248 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8370 (tp40) REVERT: H 92 GLU cc_start: 0.8064 (mm-30) cc_final: 0.6703 (pm20) REVERT: I 90 ARG cc_start: 0.7547 (ttm110) cc_final: 0.7289 (ttm110) REVERT: I 92 GLU cc_start: 0.8069 (mm-30) cc_final: 0.6732 (pm20) REVERT: L 43 LYS cc_start: 0.8750 (mmmm) cc_final: 0.8534 (mmtp) REVERT: L 79 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7462 (tp) REVERT: M 43 LYS cc_start: 0.8604 (mmmm) cc_final: 0.8393 (mmtp) outliers start: 29 outliers final: 21 residues processed: 106 average time/residue: 0.2259 time to fit residues: 33.5796 Evaluate side-chains 106 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 248 GLN Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 100 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 9 optimal weight: 0.0870 chunk 42 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 GLN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.139242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.109316 restraints weight = 12780.833| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.61 r_work: 0.3197 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9351 Z= 0.119 Angle : 0.513 6.329 12741 Z= 0.263 Chirality : 0.043 0.143 1450 Planarity : 0.004 0.028 1622 Dihedral : 4.905 55.450 1312 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.19 % Allowed : 16.34 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.18 % 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: 0.45 (0.25), residues: 1160 helix: 0.64 (1.03), residues: 24 sheet: 0.80 (0.23), residues: 534 loop : -0.11 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 50 HIS 0.004 0.001 HIS A 353 PHE 0.009 0.001 PHE A 115 TYR 0.012 0.001 TYR B 249 ARG 0.008 0.000 ARG M 25 Details of bonding type rmsd hydrogen bonds : bond 0.02588 ( 345) hydrogen bonds : angle 4.38293 ( 1035) SS BOND : bond 0.00401 ( 4) SS BOND : angle 0.68587 ( 8) covalent geometry : bond 0.00287 ( 9347) covalent geometry : angle 0.51306 (12733) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 1.033 Fit side-chains REVERT: A 48 LEU cc_start: 0.6051 (OUTLIER) cc_final: 0.5814 (tp) REVERT: B 44 ASP cc_start: 0.7292 (t0) cc_final: 0.6994 (t0) REVERT: B 75 PHE cc_start: 0.6684 (OUTLIER) cc_final: 0.6030 (p90) REVERT: B 206 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7998 (tp30) REVERT: B 248 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8375 (tp40) REVERT: H 90 ARG cc_start: 0.7489 (ttm110) cc_final: 0.7228 (ttm110) REVERT: H 92 GLU cc_start: 0.8097 (mm-30) cc_final: 0.6741 (pm20) REVERT: I 90 ARG cc_start: 0.7481 (ttm110) cc_final: 0.7194 (ttm110) REVERT: I 92 GLU cc_start: 0.8082 (mm-30) cc_final: 0.6730 (pm20) REVERT: L 43 LYS cc_start: 0.8704 (mmmm) cc_final: 0.8477 (mmtp) REVERT: L 79 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7390 (tp) REVERT: M 43 LYS cc_start: 0.8577 (mmmm) cc_final: 0.8362 (mmtp) outliers start: 31 outliers final: 22 residues processed: 107 average time/residue: 0.2208 time to fit residues: 32.8404 Evaluate side-chains 107 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 248 GLN Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 85 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 chunk 96 optimal weight: 0.4980 chunk 101 optimal weight: 0.5980 chunk 30 optimal weight: 0.1980 chunk 57 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.142303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.110339 restraints weight = 13208.556| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.98 r_work: 0.3176 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9351 Z= 0.108 Angle : 0.504 6.469 12741 Z= 0.258 Chirality : 0.043 0.139 1450 Planarity : 0.003 0.031 1622 Dihedral : 4.728 52.236 1312 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.67 % Allowed : 16.96 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.18 % 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: 0.48 (0.26), residues: 1160 helix: 0.72 (1.03), residues: 24 sheet: 0.86 (0.24), residues: 528 loop : -0.13 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 50 HIS 0.004 0.001 HIS I 38 PHE 0.012 0.001 PHE L 84 TYR 0.014 0.001 TYR A 249 ARG 0.007 0.000 ARG M 25 Details of bonding type rmsd hydrogen bonds : bond 0.02467 ( 345) hydrogen bonds : angle 4.27531 ( 1035) SS BOND : bond 0.00308 ( 4) SS BOND : angle 0.72333 ( 8) covalent geometry : bond 0.00258 ( 9347) covalent geometry : angle 0.50350 (12733) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 1.099 Fit side-chains REVERT: A 48 LEU cc_start: 0.6186 (OUTLIER) cc_final: 0.5963 (tp) REVERT: B 44 ASP cc_start: 0.7411 (t0) cc_final: 0.7163 (t0) REVERT: B 75 PHE cc_start: 0.6878 (OUTLIER) cc_final: 0.6239 (p90) REVERT: B 238 TYR cc_start: 0.8804 (m-80) cc_final: 0.8561 (m-80) REVERT: B 248 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8375 (tp40) REVERT: H 90 ARG cc_start: 0.7522 (ttm110) cc_final: 0.7287 (ttm110) REVERT: H 92 GLU cc_start: 0.8100 (mm-30) cc_final: 0.6805 (pm20) REVERT: I 90 ARG cc_start: 0.7499 (ttm110) cc_final: 0.7236 (ttm110) REVERT: I 92 GLU cc_start: 0.8087 (mm-30) cc_final: 0.6775 (pm20) REVERT: I 120 THR cc_start: 0.8308 (OUTLIER) cc_final: 0.8078 (p) REVERT: M 25 ARG cc_start: 0.7965 (ttm110) cc_final: 0.7713 (ttm110) REVERT: M 43 LYS cc_start: 0.8685 (mmmm) cc_final: 0.8454 (mmtp) outliers start: 26 outliers final: 20 residues processed: 111 average time/residue: 0.2201 time to fit residues: 34.1091 Evaluate side-chains 110 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 248 GLN Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 50 optimal weight: 2.9990 chunk 95 optimal weight: 0.0980 chunk 45 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 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 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.140755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.110257 restraints weight = 12803.920| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.79 r_work: 0.3182 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9351 Z= 0.121 Angle : 0.504 6.024 12741 Z= 0.257 Chirality : 0.043 0.141 1450 Planarity : 0.004 0.028 1622 Dihedral : 4.677 50.539 1312 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.88 % Allowed : 16.65 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.18 % 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: 0.51 (0.26), residues: 1160 helix: 0.70 (1.02), residues: 24 sheet: 0.87 (0.23), residues: 534 loop : -0.10 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 50 HIS 0.004 0.001 HIS A 353 PHE 0.009 0.001 PHE L 99 TYR 0.012 0.001 TYR B 249 ARG 0.006 0.000 ARG M 25 Details of bonding type rmsd hydrogen bonds : bond 0.02514 ( 345) hydrogen bonds : angle 4.28707 ( 1035) SS BOND : bond 0.00286 ( 4) SS BOND : angle 0.83291 ( 8) covalent geometry : bond 0.00294 ( 9347) covalent geometry : angle 0.50370 (12733) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 1.125 Fit side-chains REVERT: A 48 LEU cc_start: 0.6109 (OUTLIER) cc_final: 0.5887 (tp) REVERT: B 44 ASP cc_start: 0.7375 (t0) cc_final: 0.7143 (t0) REVERT: B 75 PHE cc_start: 0.6732 (OUTLIER) cc_final: 0.6071 (p90) REVERT: B 238 TYR cc_start: 0.8803 (m-80) cc_final: 0.8558 (m-80) REVERT: B 248 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8397 (tp40) REVERT: H 90 ARG cc_start: 0.7507 (ttm110) cc_final: 0.7247 (ttm110) REVERT: H 92 GLU cc_start: 0.8126 (mm-30) cc_final: 0.6963 (pm20) REVERT: I 90 ARG cc_start: 0.7506 (ttm110) cc_final: 0.7224 (ttm110) REVERT: I 92 GLU cc_start: 0.8088 (mm-30) cc_final: 0.6783 (pm20) REVERT: I 120 THR cc_start: 0.8297 (OUTLIER) cc_final: 0.8065 (p) REVERT: M 43 LYS cc_start: 0.8649 (mmmm) cc_final: 0.8410 (mmtp) outliers start: 28 outliers final: 22 residues processed: 109 average time/residue: 0.2338 time to fit residues: 35.6426 Evaluate side-chains 112 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 248 GLN Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.139477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.109538 restraints weight = 13050.066| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.62 r_work: 0.3184 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9351 Z= 0.150 Angle : 0.531 6.865 12741 Z= 0.272 Chirality : 0.043 0.142 1450 Planarity : 0.004 0.034 1622 Dihedral : 4.724 49.582 1312 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.98 % Allowed : 16.55 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.18 % 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: 0.44 (0.25), residues: 1160 helix: 0.64 (1.01), residues: 24 sheet: 0.82 (0.23), residues: 534 loop : -0.15 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.005 0.001 HIS A 353 PHE 0.010 0.001 PHE M 99 TYR 0.013 0.001 TYR L 92 ARG 0.008 0.001 ARG M 25 Details of bonding type rmsd hydrogen bonds : bond 0.02655 ( 345) hydrogen bonds : angle 4.38696 ( 1035) SS BOND : bond 0.00286 ( 4) SS BOND : angle 1.01540 ( 8) covalent geometry : bond 0.00366 ( 9347) covalent geometry : angle 0.53052 (12733) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 1.064 Fit side-chains REVERT: A 48 LEU cc_start: 0.6131 (OUTLIER) cc_final: 0.5879 (tp) REVERT: B 44 ASP cc_start: 0.7365 (t0) cc_final: 0.7097 (t0) REVERT: B 75 PHE cc_start: 0.6647 (OUTLIER) cc_final: 0.5989 (p90) REVERT: B 238 TYR cc_start: 0.8814 (m-80) cc_final: 0.8613 (m-80) REVERT: B 248 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8399 (tp40) REVERT: H 90 ARG cc_start: 0.7525 (ttm110) cc_final: 0.7235 (ttm110) REVERT: H 92 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7005 (pm20) REVERT: I 90 ARG cc_start: 0.7521 (ttm110) cc_final: 0.7209 (ttm110) REVERT: I 92 GLU cc_start: 0.8078 (mm-30) cc_final: 0.6731 (pm20) REVERT: I 120 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.8059 (p) REVERT: M 43 LYS cc_start: 0.8659 (mmmm) cc_final: 0.8427 (mmtp) outliers start: 29 outliers final: 24 residues processed: 103 average time/residue: 0.2320 time to fit residues: 33.1816 Evaluate side-chains 111 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 248 GLN Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 0.0020 chunk 6 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 44 optimal weight: 0.0570 chunk 48 optimal weight: 0.8980 chunk 69 optimal weight: 0.0870 chunk 94 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 overall best weight: 0.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.140813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.111041 restraints weight = 12711.580| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.60 r_work: 0.3199 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9351 Z= 0.090 Angle : 0.490 6.687 12741 Z= 0.249 Chirality : 0.042 0.137 1450 Planarity : 0.003 0.030 1622 Dihedral : 4.462 45.472 1312 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.16 % Allowed : 17.37 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.18 % 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: 0.53 (0.26), residues: 1160 helix: 0.84 (1.04), residues: 24 sheet: 0.92 (0.24), residues: 528 loop : -0.12 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 50 HIS 0.004 0.001 HIS I 38 PHE 0.009 0.001 PHE M 84 TYR 0.013 0.001 TYR B 249 ARG 0.008 0.000 ARG L 25 Details of bonding type rmsd hydrogen bonds : bond 0.02336 ( 345) hydrogen bonds : angle 4.16071 ( 1035) SS BOND : bond 0.00372 ( 4) SS BOND : angle 0.84612 ( 8) covalent geometry : bond 0.00212 ( 9347) covalent geometry : angle 0.48926 (12733) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4163.21 seconds wall clock time: 73 minutes 17.52 seconds (4397.52 seconds total)