Starting phenix.real_space_refine on Sat Aug 23 02:26:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i0n_35104/08_2025/8i0n_35104.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i0n_35104/08_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_35104/08_2025/8i0n_35104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i0n_35104/08_2025/8i0n_35104.map" model { file = "/net/cci-nas-00/data/ceres_data/8i0n_35104/08_2025/8i0n_35104.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i0n_35104/08_2025/8i0n_35104.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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, 'ARG:plan': 5, 'GLU:plan': 6, '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, 'ARG:plan': 5, 'ASP:plan': 1, 'GLU:plan': 8, 'ASN:plan1': 2} 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: 2.03, per 1000 atoms: 0.22 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: 0.80 Conformation dependent library (CDL) restraints added in 342.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.24 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: 1.44 Time building geometry restraints manager: 1.02 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: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.070 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.760 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG A 363 TYR 0.012 0.001 TYR M 92 PHE 0.013 0.002 PHE A 349 TRP 0.010 0.002 TRP H 39 HIS 0.005 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00595 ( 9347) covalent geometry : angle 0.71421 (12733) SS BOND : bond 0.00210 ( 4) SS BOND : angle 0.36433 ( 8) hydrogen bonds : bond 0.22026 ( 345) hydrogen bonds : angle 8.89481 ( 1035) *********************** 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 : 0.427 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: 0.1085 time to fit residues: 14.3659 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 : 0.330 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.0030 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.0870 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.0970 overall best weight: 0.3766 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.144671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.115340 restraints weight = 12956.185| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.62 r_work: 0.3207 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1117 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= 0.110 Angle : 0.541 4.848 12741 Z= 0.283 Chirality : 0.044 0.138 1450 Planarity : 0.004 0.030 1622 Dihedral : 5.816 66.625 1320 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.16 % Allowed : 11.10 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.25), residues: 1160 helix: 0.11 (1.15), residues: 20 sheet: 0.77 (0.23), residues: 532 loop : -0.16 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 25 TYR 0.014 0.001 TYR A 21 PHE 0.014 0.002 PHE M 84 TRP 0.005 0.001 TRP I 50 HIS 0.003 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9347) covalent geometry : angle 0.54085 (12733) SS BOND : bond 0.00341 ( 4) SS BOND : angle 0.31807 ( 8) hydrogen bonds : bond 0.03567 ( 345) hydrogen bonds : angle 5.27089 ( 1035) *********************** 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 118 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.351 Fit side-chains REVERT: B 204 ASP cc_start: 0.8229 (m-30) cc_final: 0.7962 (m-30) REVERT: H 120 THR cc_start: 0.8333 (OUTLIER) cc_final: 0.7985 (p) REVERT: I 120 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.7957 (p) REVERT: L 6 THR cc_start: 0.8325 (m) cc_final: 0.8121 (t) REVERT: L 43 LYS cc_start: 0.8659 (mmmm) cc_final: 0.8409 (mmtp) REVERT: L 82 GLU cc_start: 0.7321 (pm20) cc_final: 0.7037 (pm20) REVERT: M 43 LYS cc_start: 0.8589 (mmmm) cc_final: 0.8371 (mmtp) outliers start: 21 outliers final: 13 residues processed: 109 average time/residue: 0.0896 time to fit residues: 13.6957 Evaluate side-chains 104 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 40 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- 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 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS B 189 GLN I 85 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.137692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.107164 restraints weight = 13021.549| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.88 r_work: 0.3124 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 9351 Z= 0.263 Angle : 0.636 7.773 12741 Z= 0.332 Chirality : 0.048 0.166 1450 Planarity : 0.005 0.032 1622 Dihedral : 5.803 60.573 1314 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.49 % Allowed : 12.13 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.25), residues: 1160 helix: -0.08 (1.07), residues: 20 sheet: 0.64 (0.24), residues: 514 loop : -0.24 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 169 TYR 0.022 0.002 TYR L 92 PHE 0.015 0.002 PHE L 99 TRP 0.012 0.003 TRP H 50 HIS 0.009 0.002 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00646 ( 9347) covalent geometry : angle 0.63581 (12733) SS BOND : bond 0.00188 ( 4) SS BOND : angle 0.37614 ( 8) hydrogen bonds : bond 0.03821 ( 345) hydrogen bonds : angle 5.12689 ( 1035) *********************** 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 131 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 0.367 Fit side-chains REVERT: A 48 LEU cc_start: 0.6164 (OUTLIER) cc_final: 0.5851 (tp) REVERT: B 204 ASP cc_start: 0.8484 (m-30) cc_final: 0.8272 (m-30) REVERT: B 206 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7976 (tp30) REVERT: H 83 TYR cc_start: 0.8565 (m-80) cc_final: 0.8298 (m-80) REVERT: H 120 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.8106 (p) REVERT: I 83 TYR cc_start: 0.8639 (m-80) cc_final: 0.8424 (m-80) REVERT: I 120 THR cc_start: 0.8338 (OUTLIER) cc_final: 0.8072 (p) REVERT: L 82 GLU cc_start: 0.7418 (pm20) cc_final: 0.7167 (pm20) REVERT: M 82 GLU cc_start: 0.7856 (pp20) cc_final: 0.7387 (pm20) REVERT: V 335 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7664 (m-10) outliers start: 34 outliers final: 19 residues processed: 119 average time/residue: 0.0917 time to fit residues: 15.3072 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 : 0.346 ------------------------------------------------------------------------------- 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 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 B residue 245 ASN 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 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 Chi-restraints excluded: chain V residue 335 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 39 optimal weight: 0.7980 chunk 35 optimal weight: 0.0670 chunk 93 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 66 optimal weight: 0.0010 chunk 79 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.4124 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.143086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.113532 restraints weight = 13105.931| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.65 r_work: 0.3162 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9351 Z= 0.105 Angle : 0.512 6.311 12741 Z= 0.265 Chirality : 0.043 0.141 1450 Planarity : 0.003 0.027 1622 Dihedral : 5.202 57.189 1312 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.36 % Allowed : 14.59 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.26), residues: 1160 helix: 0.57 (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 ARG 0.003 0.000 ARG A 169 TYR 0.011 0.001 TYR L 92 PHE 0.009 0.001 PHE A 349 TRP 0.007 0.001 TRP H 50 HIS 0.005 0.001 HIS I 38 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9347) covalent geometry : angle 0.51264 (12733) SS BOND : bond 0.00302 ( 4) SS BOND : angle 0.13031 ( 8) hydrogen bonds : bond 0.02778 ( 345) hydrogen bonds : angle 4.62433 ( 1035) *********************** 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 115 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.256 Fit side-chains REVERT: A 48 LEU cc_start: 0.6021 (OUTLIER) cc_final: 0.5687 (tp) REVERT: B 44 ASP cc_start: 0.7276 (t0) cc_final: 0.6948 (t0) REVERT: B 204 ASP cc_start: 0.8516 (m-30) cc_final: 0.8238 (m-30) REVERT: B 248 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8340 (tp40) REVERT: L 43 LYS cc_start: 0.8821 (mmmm) cc_final: 0.8592 (mmtp) REVERT: L 82 GLU cc_start: 0.7425 (pm20) cc_final: 0.7153 (pm20) REVERT: M 2 ASP cc_start: 0.7379 (p0) cc_final: 0.7178 (p0) REVERT: M 83 ASP cc_start: 0.8079 (m-30) cc_final: 0.7529 (m-30) REVERT: V 335 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7576 (m-10) outliers start: 23 outliers final: 14 residues processed: 108 average time/residue: 0.0727 time to fit residues: 11.2429 Evaluate side-chains 103 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 297 ASP 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 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 75 THR Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain V residue 335 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 70 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.139766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.110182 restraints weight = 13147.974| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.65 r_work: 0.3112 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 9351 Z= 0.226 Angle : 0.583 5.720 12741 Z= 0.303 Chirality : 0.046 0.145 1450 Planarity : 0.004 0.031 1622 Dihedral : 5.361 56.755 1312 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.49 % Allowed : 15.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.25), residues: 1160 helix: 0.36 (1.01), residues: 24 sheet: 0.61 (0.23), residues: 528 loop : -0.21 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 90 TYR 0.018 0.002 TYR L 92 PHE 0.015 0.002 PHE L 99 TRP 0.011 0.002 TRP H 50 HIS 0.007 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00551 ( 9347) covalent geometry : angle 0.58279 (12733) SS BOND : bond 0.00196 ( 4) SS BOND : angle 0.27525 ( 8) hydrogen bonds : bond 0.03150 ( 345) hydrogen bonds : angle 4.76732 ( 1035) *********************** 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 119 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 85 time to evaluate : 0.337 Fit side-chains REVERT: A 48 LEU cc_start: 0.6235 (OUTLIER) cc_final: 0.5945 (tp) REVERT: B 75 PHE cc_start: 0.6846 (OUTLIER) cc_final: 0.6178 (p90) REVERT: B 189 GLN cc_start: 0.7073 (tp-100) cc_final: 0.6836 (tp40) REVERT: B 204 ASP cc_start: 0.8530 (m-30) cc_final: 0.8289 (m-30) REVERT: B 206 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8189 (tp30) REVERT: B 248 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8329 (tp40) REVERT: L 43 LYS cc_start: 0.8863 (mmmm) cc_final: 0.8628 (mmtp) REVERT: M 83 ASP cc_start: 0.7915 (m-30) cc_final: 0.7649 (m-30) REVERT: V 335 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7628 (m-10) outliers start: 34 outliers final: 24 residues processed: 108 average time/residue: 0.0808 time to fit residues: 12.3888 Evaluate side-chains 114 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 116 THR 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 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 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 Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain V residue 335 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 50 optimal weight: 0.0980 chunk 57 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 108 optimal weight: 0.0070 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.140531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.110606 restraints weight = 12939.832| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.64 r_work: 0.3194 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9351 Z= 0.105 Angle : 0.509 7.574 12741 Z= 0.261 Chirality : 0.043 0.139 1450 Planarity : 0.003 0.026 1622 Dihedral : 5.071 58.627 1312 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.57 % Allowed : 16.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.25), residues: 1160 helix: 0.73 (1.05), residues: 24 sheet: 0.71 (0.23), residues: 534 loop : -0.14 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 90 TYR 0.012 0.001 TYR M 92 PHE 0.009 0.001 PHE M 84 TRP 0.007 0.001 TRP I 50 HIS 0.005 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9347) covalent geometry : angle 0.50904 (12733) SS BOND : bond 0.00282 ( 4) SS BOND : angle 0.09481 ( 8) hydrogen bonds : bond 0.02577 ( 345) hydrogen bonds : angle 4.44864 ( 1035) *********************** 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 111 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.374 Fit side-chains REVERT: A 48 LEU cc_start: 0.5993 (OUTLIER) cc_final: 0.5690 (tp) REVERT: B 44 ASP cc_start: 0.7263 (t0) cc_final: 0.6957 (t0) REVERT: B 75 PHE cc_start: 0.6757 (OUTLIER) cc_final: 0.6126 (p90) REVERT: B 248 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8323 (tp40) REVERT: H 90 ARG cc_start: 0.7456 (ttm110) cc_final: 0.7215 (ttm110) REVERT: H 92 GLU cc_start: 0.8068 (mm-30) cc_final: 0.6678 (pm20) REVERT: I 90 ARG cc_start: 0.7291 (ttm110) cc_final: 0.7045 (ttm110) REVERT: I 92 GLU cc_start: 0.8065 (mm-30) cc_final: 0.6701 (pm20) REVERT: L 43 LYS cc_start: 0.8688 (mmmm) cc_final: 0.8452 (mmtp) REVERT: M 43 LYS cc_start: 0.8487 (mmmm) cc_final: 0.8285 (mmtp) REVERT: M 83 ASP cc_start: 0.7604 (m-30) cc_final: 0.7379 (m-30) REVERT: V 335 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.7468 (m-10) outliers start: 25 outliers final: 19 residues processed: 104 average time/residue: 0.0881 time to fit residues: 13.0438 Evaluate side-chains 105 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 12 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 Chi-restraints excluded: chain V residue 335 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 78 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 109 optimal weight: 0.0060 overall best weight: 1.1400 ------------------------------------------------------------------------------- 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** ** 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 = 0.3700 r_free = 0.3700 target = 0.138402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.108325 restraints weight = 13069.888| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.64 r_work: 0.3172 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9351 Z= 0.183 Angle : 0.548 6.728 12741 Z= 0.283 Chirality : 0.044 0.143 1450 Planarity : 0.004 0.030 1622 Dihedral : 5.124 57.254 1312 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.80 % Allowed : 15.62 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.25), residues: 1160 helix: 0.50 (1.00), residues: 24 sheet: 0.69 (0.23), residues: 532 loop : -0.17 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 90 TYR 0.016 0.002 TYR L 92 PHE 0.012 0.002 PHE L 99 TRP 0.011 0.002 TRP I 50 HIS 0.005 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 9347) covalent geometry : angle 0.54838 (12733) SS BOND : bond 0.00238 ( 4) SS BOND : angle 0.29729 ( 8) hydrogen bonds : bond 0.02847 ( 345) hydrogen bonds : angle 4.55999 ( 1035) *********************** 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 118 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 81 time to evaluate : 0.254 Fit side-chains REVERT: A 48 LEU cc_start: 0.6124 (OUTLIER) cc_final: 0.5867 (tp) REVERT: A 242 CYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8800 (m) REVERT: B 75 PHE cc_start: 0.6710 (OUTLIER) cc_final: 0.6018 (p90) REVERT: B 248 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8320 (tp40) REVERT: H 92 GLU cc_start: 0.8159 (mm-30) cc_final: 0.6789 (pm20) REVERT: I 90 ARG cc_start: 0.7580 (ttm110) cc_final: 0.7307 (ttm110) REVERT: I 92 GLU cc_start: 0.8143 (mm-30) cc_final: 0.6769 (pm20) REVERT: I 120 THR cc_start: 0.8312 (OUTLIER) cc_final: 0.8068 (p) REVERT: L 43 LYS cc_start: 0.8732 (mmmm) cc_final: 0.8510 (mmtp) REVERT: M 43 LYS cc_start: 0.8595 (mmmm) cc_final: 0.8388 (mmtp) REVERT: M 83 ASP cc_start: 0.7747 (m-30) cc_final: 0.7466 (m-30) REVERT: V 335 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.7497 (m-10) outliers start: 37 outliers final: 22 residues processed: 109 average time/residue: 0.0896 time to fit residues: 13.7902 Evaluate side-chains 108 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 116 THR Chi-restraints excluded: chain A residue 242 CYS 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 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 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 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 V residue 335 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 95 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 chunk 29 optimal weight: 0.0980 chunk 27 optimal weight: 0.0980 chunk 107 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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** L 4 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 = 0.142201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.111409 restraints weight = 12905.421| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.77 r_work: 0.3152 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2576 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= 0.104 Angle : 0.498 6.220 12741 Z= 0.256 Chirality : 0.043 0.139 1450 Planarity : 0.003 0.028 1622 Dihedral : 4.874 53.936 1312 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.36 % Allowed : 17.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.25), residues: 1160 helix: 0.71 (1.02), residues: 24 sheet: 0.76 (0.23), residues: 534 loop : -0.13 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 90 TYR 0.012 0.001 TYR M 92 PHE 0.008 0.001 PHE A 349 TRP 0.007 0.001 TRP I 50 HIS 0.004 0.001 HIS I 38 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9347) covalent geometry : angle 0.49834 (12733) SS BOND : bond 0.00287 ( 4) SS BOND : angle 0.19809 ( 8) hydrogen bonds : bond 0.02495 ( 345) hydrogen bonds : angle 4.34195 ( 1035) *********************** 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 113 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.318 Fit side-chains REVERT: A 48 LEU cc_start: 0.6155 (OUTLIER) cc_final: 0.5889 (tp) REVERT: B 44 ASP cc_start: 0.7334 (t0) cc_final: 0.7043 (t0) REVERT: B 75 PHE cc_start: 0.6787 (OUTLIER) cc_final: 0.6093 (p90) REVERT: B 238 TYR cc_start: 0.8830 (m-80) cc_final: 0.8588 (m-80) REVERT: B 248 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8358 (tp40) REVERT: H 90 ARG cc_start: 0.7562 (ttm110) cc_final: 0.7320 (ttm110) REVERT: H 92 GLU cc_start: 0.8156 (mm-30) cc_final: 0.6875 (pm20) REVERT: I 90 ARG cc_start: 0.7532 (ttm110) cc_final: 0.7278 (ttm110) REVERT: I 92 GLU cc_start: 0.8088 (mm-30) cc_final: 0.6801 (pm20) REVERT: M 43 LYS cc_start: 0.8693 (mmmm) cc_final: 0.8475 (mmtp) REVERT: M 83 ASP cc_start: 0.7663 (m-30) cc_final: 0.7423 (m-30) REVERT: V 335 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.7516 (m-10) outliers start: 23 outliers final: 19 residues processed: 106 average time/residue: 0.0971 time to fit residues: 14.2465 Evaluate side-chains 107 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 328 VAL 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 297 ASP 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 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 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 V residue 335 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 81 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 105 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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** ** 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 = 0.139194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.110781 restraints weight = 12754.205| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.47 r_work: 0.3149 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9351 Z= 0.179 Angle : 0.546 6.671 12741 Z= 0.282 Chirality : 0.044 0.143 1450 Planarity : 0.004 0.029 1622 Dihedral : 4.970 53.321 1312 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.77 % Allowed : 17.06 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.25), residues: 1160 helix: 0.58 (0.99), residues: 24 sheet: 0.68 (0.23), residues: 530 loop : -0.19 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 90 TYR 0.013 0.002 TYR M 92 PHE 0.012 0.002 PHE L 99 TRP 0.012 0.002 TRP I 50 HIS 0.005 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 9347) covalent geometry : angle 0.54630 (12733) SS BOND : bond 0.00262 ( 4) SS BOND : angle 0.26263 ( 8) hydrogen bonds : bond 0.02807 ( 345) hydrogen bonds : angle 4.50393 ( 1035) *********************** 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 108 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.384 Fit side-chains REVERT: A 48 LEU cc_start: 0.6170 (OUTLIER) cc_final: 0.5915 (tp) REVERT: A 242 CYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8766 (m) REVERT: B 44 ASP cc_start: 0.7312 (t0) cc_final: 0.7037 (t0) REVERT: B 75 PHE cc_start: 0.6818 (OUTLIER) cc_final: 0.6129 (p90) REVERT: B 248 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8346 (tp40) REVERT: H 90 ARG cc_start: 0.7657 (ttm110) cc_final: 0.7409 (ttm110) REVERT: H 92 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7085 (pm20) REVERT: I 90 ARG cc_start: 0.7637 (ttm110) cc_final: 0.7383 (ttm110) REVERT: I 92 GLU cc_start: 0.8073 (mm-30) cc_final: 0.6817 (pm20) REVERT: L 18 ASP cc_start: 0.8925 (t0) cc_final: 0.8685 (t0) REVERT: M 43 LYS cc_start: 0.8715 (mmmm) cc_final: 0.8487 (mmtp) REVERT: M 83 ASP cc_start: 0.7751 (m-30) cc_final: 0.7466 (m-30) REVERT: V 335 PHE cc_start: 0.7774 (OUTLIER) cc_final: 0.7532 (m-10) outliers start: 27 outliers final: 21 residues processed: 100 average time/residue: 0.1011 time to fit residues: 14.2044 Evaluate side-chains 105 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 242 CYS Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 8 VAL 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 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 L residue 12 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 75 THR 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 73 THR Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain V residue 335 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 39 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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** ** 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 = 0.3709 r_free = 0.3709 target = 0.139125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.109199 restraints weight = 12902.255| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.62 r_work: 0.3166 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9351 Z= 0.154 Angle : 0.529 6.267 12741 Z= 0.273 Chirality : 0.044 0.143 1450 Planarity : 0.004 0.029 1622 Dihedral : 4.921 51.467 1312 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.77 % Allowed : 16.96 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.25), residues: 1160 helix: 0.67 (1.01), residues: 24 sheet: 0.71 (0.24), residues: 522 loop : -0.23 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 90 TYR 0.018 0.001 TYR B 238 PHE 0.010 0.001 PHE L 99 TRP 0.010 0.001 TRP I 50 HIS 0.005 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 9347) covalent geometry : angle 0.52928 (12733) SS BOND : bond 0.00287 ( 4) SS BOND : angle 0.17410 ( 8) hydrogen bonds : bond 0.02703 ( 345) hydrogen bonds : angle 4.47212 ( 1035) ********************** 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 110 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.281 Fit side-chains REVERT: A 48 LEU cc_start: 0.6174 (OUTLIER) cc_final: 0.5912 (tp) REVERT: B 44 ASP cc_start: 0.7298 (t0) cc_final: 0.7045 (t0) REVERT: B 75 PHE cc_start: 0.6825 (OUTLIER) cc_final: 0.6212 (p90) REVERT: B 248 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8425 (tp40) REVERT: H 90 ARG cc_start: 0.7595 (ttm110) cc_final: 0.7336 (ttm110) REVERT: H 92 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7076 (pm20) REVERT: I 90 ARG cc_start: 0.7577 (ttm110) cc_final: 0.7333 (ttm110) REVERT: I 92 GLU cc_start: 0.8076 (mm-30) cc_final: 0.6885 (pm20) REVERT: M 43 LYS cc_start: 0.8668 (mmmm) cc_final: 0.8427 (mmtp) REVERT: M 83 ASP cc_start: 0.7585 (m-30) cc_final: 0.7308 (m-30) REVERT: V 335 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.7502 (m-10) outliers start: 27 outliers final: 22 residues processed: 101 average time/residue: 0.1057 time to fit residues: 14.8818 Evaluate side-chains 107 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 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 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 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 107 ILE Chi-restraints excluded: chain M residue 12 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 Chi-restraints excluded: chain V residue 335 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 54 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 84 optimal weight: 0.0970 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 0.0870 chunk 73 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 overall best weight: 0.5756 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.142232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.111037 restraints weight = 12969.469| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.70 r_work: 0.3185 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9351 Z= 0.112 Angle : 0.502 5.934 12741 Z= 0.258 Chirality : 0.043 0.140 1450 Planarity : 0.003 0.027 1622 Dihedral : 4.718 47.927 1312 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.77 % Allowed : 16.75 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.26), residues: 1160 helix: 0.84 (1.04), residues: 24 sheet: 0.74 (0.23), residues: 534 loop : -0.12 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 90 TYR 0.016 0.001 TYR B 249 PHE 0.009 0.001 PHE L 84 TRP 0.008 0.001 TRP H 50 HIS 0.004 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9347) covalent geometry : angle 0.50245 (12733) SS BOND : bond 0.00318 ( 4) SS BOND : angle 0.15693 ( 8) hydrogen bonds : bond 0.02505 ( 345) hydrogen bonds : angle 4.30895 ( 1035) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1959.73 seconds wall clock time: 34 minutes 26.33 seconds (2066.33 seconds total)