Starting phenix.real_space_refine on Thu Jul 2 03:11:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wl7_66048/07_2026/9wl7_66048.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wl7_66048/07_2026/9wl7_66048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wl7_66048/07_2026/9wl7_66048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wl7_66048/07_2026/9wl7_66048.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wl7_66048/07_2026/9wl7_66048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wl7_66048/07_2026/9wl7_66048.map" } resolution = 2.93 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= 0.003 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 3846 2.51 5 N 1116 2.21 5 O 1122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6132 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1022 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 123} Restraints were copied for chains: A, C, D, E, F Time building chain proxies: 0.95, per 1000 atoms: 0.15 Number of scatterers: 6132 At special positions: 0 Unit cell: (155.31, 132.99, 39.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1122 8.00 N 1116 7.00 C 3846 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS B 42 " distance=2.04 Simple disulfide: pdb=" SG CYS B 18 " - pdb=" SG CYS B 23 " distance=2.03 Simple disulfide: pdb=" SG CYS B 81 " - pdb=" SG CYS B 124 " distance=2.03 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS A 42 " distance=2.04 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 42 " distance=2.04 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 42 " distance=2.04 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS E 42 " distance=2.04 Simple disulfide: pdb=" SG CYS F 7 " - pdb=" SG CYS F 42 " distance=2.04 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 23 " distance=2.03 Simple disulfide: pdb=" SG CYS C 18 " - pdb=" SG CYS C 23 " distance=2.03 Simple disulfide: pdb=" SG CYS D 18 " - pdb=" SG CYS D 23 " distance=2.03 Simple disulfide: pdb=" SG CYS E 18 " - pdb=" SG CYS E 23 " distance=2.03 Simple disulfide: pdb=" SG CYS F 18 " - pdb=" SG CYS F 23 " distance=2.03 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 124 " distance=2.03 Simple disulfide: pdb=" SG CYS D 81 " - pdb=" SG CYS D 124 " distance=2.03 Simple disulfide: pdb=" SG CYS E 81 " - pdb=" SG CYS E 124 " distance=2.03 Simple disulfide: pdb=" SG CYS F 81 " - pdb=" SG CYS F 124 " 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: 0.39 Conformation dependent library (CDL) restraints added in 219.2 milliseconds 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1416 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 26 sheets defined 0.0% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 6 removed outlier: 8.978A pdb=" N TRP B 3 " --> pdb=" O ALA C 4 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ILE C 6 " --> pdb=" O TRP B 3 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ASN B 5 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ALA B 4 " --> pdb=" O TRP E 3 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ASN E 5 " --> pdb=" O ALA B 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 12 through 19 removed outlier: 6.136A pdb=" N SER B 12 " --> pdb=" O ASN C 13 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE C 15 " --> pdb=" O SER B 12 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N GLU B 14 " --> pdb=" O ILE C 15 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N THR C 17 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG B 16 " --> pdb=" O THR C 17 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASP C 19 " --> pdb=" O ARG B 16 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N CYS B 18 " --> pdb=" O ASP C 19 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASP B 19 " --> pdb=" O CYS E 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 26 through 29 removed outlier: 6.319A pdb=" N TYR B 26 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N GLN E 29 " --> pdb=" O TYR B 26 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA B 28 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 40 through 41 removed outlier: 6.486A pdb=" N VAL B 40 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 47 through 49 removed outlier: 6.556A pdb=" N VAL B 48 " --> pdb=" O TYR C 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 52 through 60 removed outlier: 6.915A pdb=" N THR B 53 " --> pdb=" O PHE C 52 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLY C 54 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N MET B 55 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE C 56 " --> pdb=" O MET B 55 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLN B 59 " --> pdb=" O GLY C 58 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLU C 60 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N PHE B 52 " --> pdb=" O THR E 53 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N MET E 55 " --> pdb=" O PHE B 52 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N GLY B 54 " --> pdb=" O MET E 55 " (cutoff:3.500A) removed outlier: 9.831A pdb=" N VAL E 57 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ILE B 56 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLN E 59 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLY B 58 " --> pdb=" O GLN E 59 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 66 through 71 removed outlier: 6.320A pdb=" N ASN B 67 " --> pdb=" O ALA E 68 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ASN E 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE B 69 " --> pdb=" O ASN E 70 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 83 through 87 removed outlier: 6.079A pdb=" N MET B 84 " --> pdb=" O PHE E 85 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ILE E 87 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TYR B 86 " --> pdb=" O ILE E 87 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 98 removed outlier: 6.162A pdb=" N ILE B 96 " --> pdb=" O LYS C 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 104 through 105 removed outlier: 6.626A pdb=" N THR B 104 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 108 through 111 removed outlier: 5.993A pdb=" N LEU B 108 " --> pdb=" O GLN C 109 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N VAL C 111 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LYS B 110 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 111 " --> pdb=" O LYS E 110 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 114 through 115 removed outlier: 6.803A pdb=" N GLY B 114 " --> pdb=" O ILE E 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 119 through 123 removed outlier: 6.410A pdb=" N HIS B 120 " --> pdb=" O ILE E 121 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ASN E 123 " --> pdb=" O HIS B 120 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLU B 122 " --> pdb=" O ASN E 123 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 3 through 6 removed outlier: 8.979A pdb=" N TRP A 3 " --> pdb=" O ALA D 4 " (cutoff:3.500A) removed outlier: 9.200A pdb=" N ILE D 6 " --> pdb=" O TRP A 3 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ASN A 5 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ALA A 4 " --> pdb=" O TRP F 3 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASN F 5 " --> pdb=" O ALA A 4 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 12 through 19 removed outlier: 6.137A pdb=" N SER A 12 " --> pdb=" O ASN D 13 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE D 15 " --> pdb=" O SER A 12 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLU A 14 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N THR D 17 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG A 16 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASP D 19 " --> pdb=" O ARG A 16 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N CYS A 18 " --> pdb=" O ASP D 19 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASP A 19 " --> pdb=" O CYS F 18 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 26 through 29 removed outlier: 6.318A pdb=" N TYR A 26 " --> pdb=" O SER F 27 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N GLN F 29 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ALA A 28 " --> pdb=" O GLN F 29 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 40 through 41 removed outlier: 6.486A pdb=" N VAL A 40 " --> pdb=" O LEU D 41 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 47 through 49 removed outlier: 6.556A pdb=" N VAL A 48 " --> pdb=" O TYR D 49 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 52 through 60 removed outlier: 6.915A pdb=" N THR A 53 " --> pdb=" O PHE D 52 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLY D 54 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N MET A 55 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE D 56 " --> pdb=" O MET A 55 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLN A 59 " --> pdb=" O GLY D 58 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLU D 60 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N PHE A 52 " --> pdb=" O THR F 53 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N MET F 55 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N GLY A 54 " --> pdb=" O MET F 55 " (cutoff:3.500A) removed outlier: 9.830A pdb=" N VAL F 57 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ILE A 56 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLN F 59 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLY A 58 " --> pdb=" O GLN F 59 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 66 through 71 removed outlier: 6.321A pdb=" N ASN A 67 " --> pdb=" O ALA F 68 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ASN F 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE A 69 " --> pdb=" O ASN F 70 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 83 through 87 removed outlier: 6.080A pdb=" N MET A 84 " --> pdb=" O PHE F 85 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ILE F 87 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TYR A 86 " --> pdb=" O ILE F 87 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 96 through 98 removed outlier: 6.162A pdb=" N ILE A 96 " --> pdb=" O LYS D 97 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 104 through 105 removed outlier: 6.627A pdb=" N THR A 104 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 108 through 111 removed outlier: 5.994A pdb=" N LEU A 108 " --> pdb=" O GLN D 109 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N VAL D 111 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LYS A 110 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A 111 " --> pdb=" O LYS F 110 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 114 through 115 removed outlier: 6.802A pdb=" N GLY A 114 " --> pdb=" O ILE F 115 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 119 through 123 removed outlier: 6.411A pdb=" N HIS A 120 " --> pdb=" O ILE F 121 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ASN F 123 " --> pdb=" O HIS A 120 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLU A 122 " --> pdb=" O ASN F 123 " (cutoff:3.500A) 68 hydrogen bonds defined for protein. 204 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: 0.95 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2027 1.34 - 1.46: 1274 1.46 - 1.58: 2915 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 6276 Sorted by residual: bond pdb=" CA ARG E 20 " pdb=" C ARG E 20 " ideal model delta sigma weight residual 1.532 1.511 0.021 9.60e-03 1.09e+04 4.79e+00 bond pdb=" CA ARG D 20 " pdb=" C ARG D 20 " ideal model delta sigma weight residual 1.532 1.512 0.021 9.60e-03 1.09e+04 4.67e+00 bond pdb=" CA ARG C 20 " pdb=" C ARG C 20 " ideal model delta sigma weight residual 1.532 1.512 0.020 9.60e-03 1.09e+04 4.54e+00 bond pdb=" CA ARG B 20 " pdb=" C ARG B 20 " ideal model delta sigma weight residual 1.532 1.512 0.020 9.60e-03 1.09e+04 4.53e+00 bond pdb=" CA ARG F 20 " pdb=" C ARG F 20 " ideal model delta sigma weight residual 1.532 1.512 0.020 9.60e-03 1.09e+04 4.36e+00 ... (remaining 6271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 8007 2.06 - 4.12: 387 4.12 - 6.17: 30 6.17 - 8.23: 42 8.23 - 10.29: 6 Bond angle restraints: 8472 Sorted by residual: angle pdb=" CA TYR D 86 " pdb=" CB TYR D 86 " pdb=" CG TYR D 86 " ideal model delta sigma weight residual 113.90 120.54 -6.64 1.80e+00 3.09e-01 1.36e+01 angle pdb=" CA TYR A 86 " pdb=" CB TYR A 86 " pdb=" CG TYR A 86 " ideal model delta sigma weight residual 113.90 120.52 -6.62 1.80e+00 3.09e-01 1.35e+01 angle pdb=" CA TYR C 86 " pdb=" CB TYR C 86 " pdb=" CG TYR C 86 " ideal model delta sigma weight residual 113.90 120.52 -6.62 1.80e+00 3.09e-01 1.35e+01 angle pdb=" CA TYR E 86 " pdb=" CB TYR E 86 " pdb=" CG TYR E 86 " ideal model delta sigma weight residual 113.90 120.52 -6.62 1.80e+00 3.09e-01 1.35e+01 angle pdb=" CA TYR B 86 " pdb=" CB TYR B 86 " pdb=" CG TYR B 86 " ideal model delta sigma weight residual 113.90 120.51 -6.61 1.80e+00 3.09e-01 1.35e+01 ... (remaining 8467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 3341 16.75 - 33.50: 349 33.50 - 50.26: 120 50.26 - 67.01: 30 67.01 - 83.76: 6 Dihedral angle restraints: 3846 sinusoidal: 1596 harmonic: 2250 Sorted by residual: dihedral pdb=" CA VAL E 119 " pdb=" C VAL E 119 " pdb=" N HIS E 120 " pdb=" CA HIS E 120 " ideal model delta harmonic sigma weight residual 180.00 -159.43 -20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA VAL C 119 " pdb=" C VAL C 119 " pdb=" N HIS C 120 " pdb=" CA HIS C 120 " ideal model delta harmonic sigma weight residual -180.00 -159.44 -20.56 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA VAL B 119 " pdb=" C VAL B 119 " pdb=" N HIS B 120 " pdb=" CA HIS B 120 " ideal model delta harmonic sigma weight residual -180.00 -159.45 -20.55 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 3843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 676 0.071 - 0.141: 188 0.141 - 0.212: 10 0.212 - 0.283: 2 0.283 - 0.353: 6 Chirality restraints: 882 Sorted by residual: chirality pdb=" CB VAL B 38 " pdb=" CA VAL B 38 " pdb=" CG1 VAL B 38 " pdb=" CG2 VAL B 38 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CB VAL C 38 " pdb=" CA VAL C 38 " pdb=" CG1 VAL C 38 " pdb=" CG2 VAL C 38 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CB VAL F 38 " pdb=" CA VAL F 38 " pdb=" CG1 VAL F 38 " pdb=" CG2 VAL F 38 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.07e+00 ... (remaining 879 not shown) Planarity restraints: 1116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 86 " 0.018 2.00e-02 2.50e+03 1.93e-02 7.47e+00 pdb=" CG TYR E 86 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR E 86 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR E 86 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR E 86 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR E 86 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR E 86 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 86 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 86 " 0.019 2.00e-02 2.50e+03 1.93e-02 7.45e+00 pdb=" CG TYR C 86 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR C 86 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR C 86 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR C 86 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 86 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 86 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 86 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 86 " 0.019 2.00e-02 2.50e+03 1.93e-02 7.42e+00 pdb=" CG TYR F 86 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR F 86 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR F 86 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR F 86 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR F 86 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR F 86 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR F 86 " 0.001 2.00e-02 2.50e+03 ... (remaining 1113 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 2428 2.91 - 3.41: 5201 3.41 - 3.90: 11166 3.90 - 4.40: 11580 4.40 - 4.90: 21317 Nonbonded interactions: 51692 Sorted by model distance: nonbonded pdb=" OD1 ASP E 125 " pdb=" OG SER E 127 " model vdw 2.412 3.040 nonbonded pdb=" OD1 ASP D 125 " pdb=" OG SER D 127 " model vdw 2.413 3.040 nonbonded pdb=" OD1 ASP F 125 " pdb=" OG SER F 127 " model vdw 2.413 3.040 nonbonded pdb=" OD1 ASP B 125 " pdb=" OG SER B 127 " model vdw 2.413 3.040 nonbonded pdb=" OD1 ASP A 125 " pdb=" OG SER A 127 " model vdw 2.413 3.040 ... (remaining 51687 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: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.270 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.420 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:5.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 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 : 0.005 0.059 6294 Z= 0.252 Angle : 1.056 10.290 8508 Z= 0.570 Chirality : 0.068 0.353 882 Planarity : 0.006 0.039 1116 Dihedral : 16.145 83.761 2376 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 0.00 % Allowed : 16.22 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -4.27 (0.19), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.15), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 20 TYR 0.048 0.003 TYR E 86 PHE 0.016 0.003 PHE E 85 TRP 0.006 0.002 TRP C 3 HIS 0.016 0.007 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.25 ( 6276) covalent geometry : angle 1.05414 / 0.57 ( 8472) SS BOND : bond 0.00513 / 0.38 ( 18) SS BOND : angle 1.34476 / 0.91 ( 36) hydrogen bonds : bond 0.13013 / 8.75 ( 68) hydrogen bonds : angle 8.35809 / 6.07 ( 204) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.243 Fit side-chains REVERT: B 98 LYS cc_start: 0.7960 (mttt) cc_final: 0.7185 (mttp) REVERT: A 98 LYS cc_start: 0.7960 (mttt) cc_final: 0.7186 (mttp) REVERT: C 55 MET cc_start: 0.8954 (ttp) cc_final: 0.8654 (ttm) REVERT: C 98 LYS cc_start: 0.8292 (mttt) cc_final: 0.7476 (mptt) REVERT: C 127 SER cc_start: 0.8797 (p) cc_final: 0.8586 (m) REVERT: D 55 MET cc_start: 0.8953 (ttp) cc_final: 0.8653 (ttm) REVERT: D 98 LYS cc_start: 0.8290 (mttt) cc_final: 0.7476 (mptt) REVERT: D 127 SER cc_start: 0.8796 (p) cc_final: 0.8586 (m) REVERT: E 55 MET cc_start: 0.8900 (ttp) cc_final: 0.8523 (ttp) REVERT: E 98 LYS cc_start: 0.7996 (mttt) cc_final: 0.7132 (mmpt) REVERT: E 127 SER cc_start: 0.8955 (p) cc_final: 0.8629 (m) REVERT: F 55 MET cc_start: 0.8900 (ttp) cc_final: 0.8521 (ttp) REVERT: F 98 LYS cc_start: 0.7998 (mttt) cc_final: 0.7134 (mmpt) REVERT: F 127 SER cc_start: 0.8954 (p) cc_final: 0.8631 (m) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.5715 time to fit residues: 91.6797 Evaluate side-chains 103 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 21 HIS B 64 GLN B 123 ASN A 21 HIS A 64 GLN A 123 ASN C 21 HIS ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN D 21 HIS ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 ASN E 21 HIS E 64 GLN E 123 ASN F 21 HIS F 64 GLN F 123 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.163968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.139781 restraints weight = 7225.852| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 1.91 r_work: 0.3830 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 6294 Z= 0.240 Angle : 0.795 8.934 8508 Z= 0.404 Chirality : 0.053 0.146 882 Planarity : 0.004 0.028 1116 Dihedral : 7.247 47.160 876 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.20 % Allowed : 22.52 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -4.24 (0.19), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.15), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 20 TYR 0.018 0.003 TYR D 86 PHE 0.008 0.002 PHE E 85 TRP 0.004 0.001 TRP D 3 HIS 0.008 0.003 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.24 ( 6276) covalent geometry : angle 0.79255 / 0.40 ( 8472) SS BOND : bond 0.00460 / 0.28 ( 18) SS BOND : angle 1.23889 / 0.85 ( 36) hydrogen bonds : bond 0.02384 / 1.58 ( 68) hydrogen bonds : angle 5.77751 / 4.09 ( 204) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.185 Fit side-chains REVERT: B 36 GLN cc_start: 0.7918 (tt0) cc_final: 0.7654 (tt0) REVERT: B 98 LYS cc_start: 0.8067 (mttt) cc_final: 0.7367 (mttp) REVERT: A 36 GLN cc_start: 0.7922 (tt0) cc_final: 0.7597 (tt0) REVERT: A 98 LYS cc_start: 0.8078 (mttt) cc_final: 0.7380 (mttp) REVERT: C 23 CYS cc_start: 0.7559 (m) cc_final: 0.7346 (m) REVERT: C 36 GLN cc_start: 0.7677 (tt0) cc_final: 0.7310 (tt0) REVERT: C 98 LYS cc_start: 0.8445 (mttt) cc_final: 0.7648 (mppt) REVERT: D 10 LYS cc_start: 0.7988 (mttt) cc_final: 0.6534 (pttp) REVERT: D 23 CYS cc_start: 0.7572 (m) cc_final: 0.7342 (m) REVERT: D 36 GLN cc_start: 0.7672 (tt0) cc_final: 0.7294 (tt0) REVERT: D 66 LYS cc_start: 0.8517 (mttt) cc_final: 0.8182 (mtpp) REVERT: D 98 LYS cc_start: 0.8431 (mttt) cc_final: 0.7640 (mppt) REVERT: E 10 LYS cc_start: 0.8070 (mttt) cc_final: 0.6791 (mmpt) REVERT: E 55 MET cc_start: 0.9016 (ttp) cc_final: 0.8707 (ttp) REVERT: E 84 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.7850 (tpp) REVERT: E 97 LYS cc_start: 0.8820 (mtmt) cc_final: 0.8519 (mtpp) REVERT: E 98 LYS cc_start: 0.8094 (mttt) cc_final: 0.7400 (mmmt) REVERT: F 10 LYS cc_start: 0.8069 (mttt) cc_final: 0.6778 (mmpt) REVERT: F 55 MET cc_start: 0.9032 (ttp) cc_final: 0.8720 (ttp) REVERT: F 84 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.7821 (tpp) REVERT: F 97 LYS cc_start: 0.8833 (mtmt) cc_final: 0.8525 (mtpp) REVERT: F 98 LYS cc_start: 0.8085 (mttt) cc_final: 0.7384 (mmmt) outliers start: 28 outliers final: 16 residues processed: 135 average time/residue: 0.6163 time to fit residues: 86.2996 Evaluate side-chains 130 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 0.0980 chunk 14 optimal weight: 40.0000 chunk 52 optimal weight: 0.7980 chunk 26 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 21 HIS A 21 HIS ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 HIS F 21 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.163090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.140226 restraints weight = 7273.234| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 1.85 r_work: 0.3860 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3762 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6294 Z= 0.163 Angle : 0.724 8.673 8508 Z= 0.366 Chirality : 0.051 0.145 882 Planarity : 0.003 0.027 1116 Dihedral : 6.971 45.277 876 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 4.95 % Allowed : 22.22 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -4.15 (0.20), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.15), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 20 TYR 0.017 0.002 TYR C 86 PHE 0.007 0.001 PHE C 85 TRP 0.003 0.001 TRP D 3 HIS 0.007 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 6276) covalent geometry : angle 0.72274 / 0.36 ( 8472) SS BOND : bond 0.00409 / 0.25 ( 18) SS BOND : angle 1.05533 / 0.76 ( 36) hydrogen bonds : bond 0.02353 / 1.58 ( 68) hydrogen bonds : angle 5.22270 / 3.65 ( 204) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 0.264 Fit side-chains REVERT: B 36 GLN cc_start: 0.7883 (tt0) cc_final: 0.7562 (tt0) REVERT: B 98 LYS cc_start: 0.8049 (mttt) cc_final: 0.7371 (mttp) REVERT: A 36 GLN cc_start: 0.7886 (tt0) cc_final: 0.7569 (tt0) REVERT: A 98 LYS cc_start: 0.8037 (mttt) cc_final: 0.7342 (mttp) REVERT: C 23 CYS cc_start: 0.7472 (m) cc_final: 0.7247 (m) REVERT: C 25 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: C 36 GLN cc_start: 0.7754 (tt0) cc_final: 0.7401 (tt0) REVERT: C 66 LYS cc_start: 0.8505 (mttt) cc_final: 0.8203 (mtpp) REVERT: C 98 LYS cc_start: 0.8444 (mttt) cc_final: 0.7643 (mppt) REVERT: D 23 CYS cc_start: 0.7502 (m) cc_final: 0.7271 (m) REVERT: D 36 GLN cc_start: 0.7752 (tt0) cc_final: 0.7399 (tt0) REVERT: D 66 LYS cc_start: 0.8501 (mttt) cc_final: 0.8195 (mtpp) REVERT: D 98 LYS cc_start: 0.8388 (mttt) cc_final: 0.7617 (mptt) REVERT: E 10 LYS cc_start: 0.8155 (mttt) cc_final: 0.6757 (tptm) REVERT: E 55 MET cc_start: 0.8981 (ttp) cc_final: 0.8684 (ttp) REVERT: E 60 GLU cc_start: 0.8193 (tt0) cc_final: 0.7991 (mm-30) REVERT: E 83 LYS cc_start: 0.7591 (ttmt) cc_final: 0.7012 (tttm) REVERT: E 84 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7656 (tpp) REVERT: E 98 LYS cc_start: 0.8154 (mttt) cc_final: 0.7441 (mmmt) REVERT: E 127 SER cc_start: 0.9120 (p) cc_final: 0.8849 (m) REVERT: F 10 LYS cc_start: 0.8148 (mttt) cc_final: 0.6744 (tptm) REVERT: F 55 MET cc_start: 0.8978 (ttp) cc_final: 0.8677 (ttp) REVERT: F 83 LYS cc_start: 0.7595 (ttmt) cc_final: 0.7010 (tttm) REVERT: F 84 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7631 (tpp) REVERT: F 98 LYS cc_start: 0.8139 (mttt) cc_final: 0.7412 (mmmt) REVERT: F 127 SER cc_start: 0.9117 (p) cc_final: 0.8840 (m) outliers start: 33 outliers final: 20 residues processed: 137 average time/residue: 0.6313 time to fit residues: 89.9989 Evaluate side-chains 136 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain C residue 25 GLN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 22 optimal weight: 20.0000 chunk 62 optimal weight: 0.0980 chunk 44 optimal weight: 0.1980 chunk 17 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN ** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN ** D 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 HIS ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 HIS ** F 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.168653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.145684 restraints weight = 7206.157| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 1.86 r_work: 0.3942 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3846 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6294 Z= 0.097 Angle : 0.635 7.007 8508 Z= 0.322 Chirality : 0.050 0.140 882 Planarity : 0.003 0.024 1116 Dihedral : 6.511 43.744 876 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.90 % Allowed : 23.12 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -4.05 (0.20), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.15), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 20 TYR 0.016 0.001 TYR D 86 PHE 0.006 0.001 PHE C 85 TRP 0.001 0.000 TRP B 3 HIS 0.005 0.001 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 6276) covalent geometry : angle 0.63436 / 0.32 ( 8472) SS BOND : bond 0.00250 / 0.16 ( 18) SS BOND : angle 0.82926 / 0.60 ( 36) hydrogen bonds : bond 0.01767 / 1.18 ( 68) hydrogen bonds : angle 5.00287 / 3.49 ( 204) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.238 Fit side-chains REVERT: B 36 GLN cc_start: 0.7717 (tt0) cc_final: 0.7447 (tt0) REVERT: B 98 LYS cc_start: 0.8057 (mttt) cc_final: 0.7317 (mptp) REVERT: A 36 GLN cc_start: 0.7725 (tt0) cc_final: 0.7457 (tt0) REVERT: A 98 LYS cc_start: 0.8052 (mttt) cc_final: 0.7328 (mptp) REVERT: C 36 GLN cc_start: 0.7747 (tt0) cc_final: 0.7382 (tt0) REVERT: C 65 ASN cc_start: 0.7995 (m110) cc_final: 0.7762 (m110) REVERT: C 98 LYS cc_start: 0.8410 (mttt) cc_final: 0.7635 (mptt) REVERT: D 36 GLN cc_start: 0.7761 (tt0) cc_final: 0.7396 (tt0) REVERT: D 65 ASN cc_start: 0.7990 (m110) cc_final: 0.7758 (m110) REVERT: D 98 LYS cc_start: 0.8421 (mttt) cc_final: 0.7658 (mttp) REVERT: E 10 LYS cc_start: 0.8143 (mttt) cc_final: 0.6800 (tptm) REVERT: E 55 MET cc_start: 0.8901 (ttp) cc_final: 0.8648 (ttp) REVERT: E 60 GLU cc_start: 0.8194 (tt0) cc_final: 0.7989 (mm-30) REVERT: E 83 LYS cc_start: 0.7652 (ttmt) cc_final: 0.7040 (tttm) REVERT: E 98 LYS cc_start: 0.8204 (mttt) cc_final: 0.7417 (mmmt) REVERT: F 10 LYS cc_start: 0.8142 (mttt) cc_final: 0.6796 (tptm) REVERT: F 55 MET cc_start: 0.8887 (ttp) cc_final: 0.8626 (ttp) REVERT: F 83 LYS cc_start: 0.7637 (ttmt) cc_final: 0.7045 (tttm) REVERT: F 98 LYS cc_start: 0.8190 (mttt) cc_final: 0.7434 (mmmt) outliers start: 26 outliers final: 12 residues processed: 119 average time/residue: 0.6175 time to fit residues: 76.4752 Evaluate side-chains 116 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 20.0000 chunk 61 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 HIS F 21 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.159693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.137037 restraints weight = 7442.415| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.87 r_work: 0.3812 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3713 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6294 Z= 0.222 Angle : 0.755 7.387 8508 Z= 0.385 Chirality : 0.052 0.143 882 Planarity : 0.003 0.024 1116 Dihedral : 6.824 48.480 876 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.20 % Allowed : 23.12 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -4.03 (0.20), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.15), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 20 TYR 0.015 0.003 TYR D 86 PHE 0.009 0.002 PHE A 80 TRP 0.005 0.002 TRP F 3 HIS 0.007 0.002 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.22 ( 6276) covalent geometry : angle 0.75261 / 0.38 ( 8472) SS BOND : bond 0.00487 / 0.29 ( 18) SS BOND : angle 1.17202 / 0.83 ( 36) hydrogen bonds : bond 0.02131 / 1.44 ( 68) hydrogen bonds : angle 4.89604 / 3.40 ( 204) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.238 Fit side-chains REVERT: B 36 GLN cc_start: 0.8129 (tt0) cc_final: 0.7860 (tt0) REVERT: B 98 LYS cc_start: 0.8090 (mttt) cc_final: 0.7398 (mttp) REVERT: A 36 GLN cc_start: 0.8139 (tt0) cc_final: 0.7876 (tt0) REVERT: A 98 LYS cc_start: 0.8053 (mttt) cc_final: 0.7362 (mttp) REVERT: C 36 GLN cc_start: 0.7990 (tt0) cc_final: 0.7636 (tt0) REVERT: C 84 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7861 (ttp) REVERT: C 98 LYS cc_start: 0.8408 (mttt) cc_final: 0.7636 (mttp) REVERT: D 36 GLN cc_start: 0.7993 (tt0) cc_final: 0.7646 (tt0) REVERT: D 84 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7803 (ttp) REVERT: D 98 LYS cc_start: 0.8387 (mttt) cc_final: 0.7623 (mttp) REVERT: E 10 LYS cc_start: 0.8226 (mttt) cc_final: 0.6870 (tptm) REVERT: E 55 MET cc_start: 0.9035 (ttp) cc_final: 0.8719 (ttp) REVERT: E 83 LYS cc_start: 0.7632 (ttmt) cc_final: 0.7052 (tttp) REVERT: E 98 LYS cc_start: 0.8246 (mttt) cc_final: 0.7410 (mmmt) REVERT: E 127 SER cc_start: 0.9105 (p) cc_final: 0.8792 (m) REVERT: F 10 LYS cc_start: 0.8224 (mttt) cc_final: 0.6861 (tptm) REVERT: F 55 MET cc_start: 0.9026 (ttp) cc_final: 0.8694 (ttp) REVERT: F 83 LYS cc_start: 0.7645 (ttmt) cc_final: 0.7073 (tttp) REVERT: F 98 LYS cc_start: 0.8210 (mttt) cc_final: 0.7407 (mmmt) REVERT: F 127 SER cc_start: 0.9142 (p) cc_final: 0.8820 (m) outliers start: 28 outliers final: 10 residues processed: 123 average time/residue: 0.6796 time to fit residues: 86.7034 Evaluate side-chains 114 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 108 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 52 optimal weight: 30.0000 chunk 66 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 72 optimal weight: 0.9980 chunk 1 optimal weight: 20.0000 chunk 74 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 HIS ** 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 = 0.4192 r_free = 0.4192 target = 0.163057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.140436 restraints weight = 7316.483| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 1.83 r_work: 0.3865 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3768 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6294 Z= 0.136 Angle : 0.681 6.458 8508 Z= 0.348 Chirality : 0.050 0.146 882 Planarity : 0.003 0.024 1116 Dihedral : 6.649 49.089 876 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.15 % Allowed : 25.38 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -3.95 (0.20), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.16), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 20 TYR 0.015 0.002 TYR C 86 PHE 0.006 0.001 PHE A 85 TRP 0.002 0.001 TRP F 3 HIS 0.006 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 6276) covalent geometry : angle 0.67788 / 0.35 ( 8472) SS BOND : bond 0.00408 / 0.24 ( 18) SS BOND : angle 1.14712 / 0.82 ( 36) hydrogen bonds : bond 0.01872 / 1.26 ( 68) hydrogen bonds : angle 4.84468 / 3.39 ( 204) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.153 Fit side-chains REVERT: B 36 GLN cc_start: 0.7911 (tt0) cc_final: 0.7637 (tt0) REVERT: B 98 LYS cc_start: 0.8047 (mttt) cc_final: 0.7356 (mttp) REVERT: A 36 GLN cc_start: 0.7922 (tt0) cc_final: 0.7648 (tt0) REVERT: A 98 LYS cc_start: 0.8046 (mttt) cc_final: 0.7353 (mttp) REVERT: C 36 GLN cc_start: 0.7966 (tt0) cc_final: 0.7643 (tt0) REVERT: C 84 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7892 (ttp) REVERT: C 98 LYS cc_start: 0.8373 (mttt) cc_final: 0.7594 (mttp) REVERT: D 36 GLN cc_start: 0.7969 (tt0) cc_final: 0.7651 (tt0) REVERT: D 84 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7842 (ttp) REVERT: D 98 LYS cc_start: 0.8401 (mttt) cc_final: 0.7628 (mttp) REVERT: E 10 LYS cc_start: 0.8221 (mttt) cc_final: 0.6844 (tptm) REVERT: E 55 MET cc_start: 0.8928 (ttp) cc_final: 0.8626 (ttp) REVERT: E 83 LYS cc_start: 0.7643 (ttmt) cc_final: 0.7028 (tttp) REVERT: E 98 LYS cc_start: 0.8233 (mttt) cc_final: 0.7418 (mmmt) REVERT: E 127 SER cc_start: 0.9046 (p) cc_final: 0.8770 (m) REVERT: F 10 LYS cc_start: 0.8220 (mttt) cc_final: 0.6840 (tptm) REVERT: F 55 MET cc_start: 0.8938 (ttp) cc_final: 0.8631 (ttp) REVERT: F 83 LYS cc_start: 0.7633 (ttmt) cc_final: 0.7039 (tttp) REVERT: F 98 LYS cc_start: 0.8236 (mttt) cc_final: 0.7435 (mmmt) REVERT: F 127 SER cc_start: 0.9108 (p) cc_final: 0.8823 (m) outliers start: 21 outliers final: 10 residues processed: 107 average time/residue: 0.7504 time to fit residues: 82.9911 Evaluate side-chains 110 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 108 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 6.9990 chunk 41 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 37 optimal weight: 0.1980 chunk 40 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 HIS ** 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 = 0.4177 r_free = 0.4177 target = 0.161545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.138797 restraints weight = 7325.151| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 1.86 r_work: 0.3847 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3750 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6294 Z= 0.170 Angle : 0.713 6.515 8508 Z= 0.364 Chirality : 0.051 0.143 882 Planarity : 0.003 0.032 1116 Dihedral : 6.686 52.529 876 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.70 % Allowed : 26.43 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -3.91 (0.20), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.16), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 20 TYR 0.014 0.002 TYR C 86 PHE 0.006 0.001 PHE B 85 TRP 0.003 0.001 TRP F 3 HIS 0.007 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 ( 6276) covalent geometry : angle 0.71066 / 0.36 ( 8472) SS BOND : bond 0.00424 / 0.25 ( 18) SS BOND : angle 1.11656 / 0.80 ( 36) hydrogen bonds : bond 0.01932 / 1.30 ( 68) hydrogen bonds : angle 4.82681 / 3.36 ( 204) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.279 Fit side-chains REVERT: B 36 GLN cc_start: 0.8048 (tt0) cc_final: 0.7803 (tt0) REVERT: B 98 LYS cc_start: 0.8031 (mttt) cc_final: 0.7345 (mttp) REVERT: A 36 GLN cc_start: 0.8053 (tt0) cc_final: 0.7807 (tt0) REVERT: A 98 LYS cc_start: 0.8033 (mttt) cc_final: 0.7349 (mttp) REVERT: C 36 GLN cc_start: 0.7932 (tt0) cc_final: 0.7616 (tt0) REVERT: C 84 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7918 (ttp) REVERT: C 98 LYS cc_start: 0.8443 (mttt) cc_final: 0.7673 (mttp) REVERT: D 36 GLN cc_start: 0.8052 (tt0) cc_final: 0.7748 (tt0) REVERT: D 84 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7905 (ttp) REVERT: D 98 LYS cc_start: 0.8424 (mttt) cc_final: 0.7614 (mttm) REVERT: E 10 LYS cc_start: 0.8244 (mttt) cc_final: 0.6849 (tptm) REVERT: E 55 MET cc_start: 0.8966 (ttp) cc_final: 0.8648 (ttp) REVERT: E 83 LYS cc_start: 0.7561 (ttmt) cc_final: 0.7064 (tttm) REVERT: E 84 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8236 (ttp) REVERT: E 98 LYS cc_start: 0.8223 (mttt) cc_final: 0.7399 (mmmt) REVERT: E 127 SER cc_start: 0.9085 (p) cc_final: 0.8804 (m) REVERT: F 10 LYS cc_start: 0.8235 (mttt) cc_final: 0.6838 (tptm) REVERT: F 55 MET cc_start: 0.8976 (ttp) cc_final: 0.8651 (ttp) REVERT: F 83 LYS cc_start: 0.7574 (ttmt) cc_final: 0.7079 (tttm) REVERT: F 98 LYS cc_start: 0.8232 (mttt) cc_final: 0.7415 (mmmt) REVERT: F 127 SER cc_start: 0.9133 (p) cc_final: 0.8823 (m) outliers start: 18 outliers final: 11 residues processed: 111 average time/residue: 0.7594 time to fit residues: 87.2281 Evaluate side-chains 113 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 108 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 68 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 0.4980 chunk 14 optimal weight: 30.0000 chunk 70 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 HIS ** 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 = 0.4214 r_free = 0.4214 target = 0.165172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.142498 restraints weight = 7311.971| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 1.86 r_work: 0.3895 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3799 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6294 Z= 0.113 Angle : 0.654 5.792 8508 Z= 0.335 Chirality : 0.050 0.141 882 Planarity : 0.003 0.022 1116 Dihedral : 6.457 52.564 876 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.70 % Allowed : 25.98 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -3.88 (0.21), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.16), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 20 TYR 0.014 0.002 TYR C 86 PHE 0.004 0.001 PHE B 85 TRP 0.001 0.001 TRP F 3 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 ( 6276) covalent geometry : angle 0.65211 / 0.33 ( 8472) SS BOND : bond 0.00451 / 0.26 ( 18) SS BOND : angle 1.05378 / 0.76 ( 36) hydrogen bonds : bond 0.01778 / 1.19 ( 68) hydrogen bonds : angle 4.82253 / 3.36 ( 204) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.234 Fit side-chains REVERT: B 36 GLN cc_start: 0.7869 (tt0) cc_final: 0.7570 (tt0) REVERT: B 66 LYS cc_start: 0.7897 (mttt) cc_final: 0.7618 (mtpp) REVERT: B 98 LYS cc_start: 0.8126 (mttt) cc_final: 0.7324 (mttp) REVERT: A 36 GLN cc_start: 0.7883 (tt0) cc_final: 0.7585 (tt0) REVERT: A 66 LYS cc_start: 0.7888 (mttt) cc_final: 0.7602 (mtpp) REVERT: A 98 LYS cc_start: 0.8060 (mttt) cc_final: 0.7326 (mttp) REVERT: C 36 GLN cc_start: 0.7814 (tt0) cc_final: 0.7508 (tt0) REVERT: C 84 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7920 (ttp) REVERT: C 98 LYS cc_start: 0.8386 (mttt) cc_final: 0.7634 (mttp) REVERT: D 36 GLN cc_start: 0.7821 (tt0) cc_final: 0.7520 (tt0) REVERT: D 84 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7909 (ttp) REVERT: D 98 LYS cc_start: 0.8399 (mttt) cc_final: 0.7625 (mttp) REVERT: E 10 LYS cc_start: 0.8264 (mttt) cc_final: 0.6855 (tptm) REVERT: E 55 MET cc_start: 0.8968 (ttp) cc_final: 0.8658 (ttp) REVERT: E 83 LYS cc_start: 0.7560 (ttmt) cc_final: 0.7089 (tttm) REVERT: E 84 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8255 (ttp) REVERT: E 98 LYS cc_start: 0.8223 (mttt) cc_final: 0.7424 (mmmt) REVERT: F 10 LYS cc_start: 0.8252 (mttt) cc_final: 0.6832 (tptm) REVERT: F 55 MET cc_start: 0.8991 (ttp) cc_final: 0.8681 (ttp) REVERT: F 83 LYS cc_start: 0.7577 (ttmt) cc_final: 0.7103 (tttm) REVERT: F 84 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8225 (ttp) REVERT: F 98 LYS cc_start: 0.8231 (mttt) cc_final: 0.7419 (mmmt) outliers start: 18 outliers final: 10 residues processed: 109 average time/residue: 0.7163 time to fit residues: 80.9403 Evaluate side-chains 109 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 108 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 26 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 67 optimal weight: 0.0570 chunk 11 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 55 optimal weight: 0.0050 chunk 3 optimal weight: 1.9990 overall best weight: 3.0118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 HIS ** 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 = 0.4205 r_free = 0.4205 target = 0.164261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.141524 restraints weight = 7272.873| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 1.86 r_work: 0.3887 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3791 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6294 Z= 0.138 Angle : 0.679 6.041 8508 Z= 0.348 Chirality : 0.050 0.139 882 Planarity : 0.003 0.035 1116 Dihedral : 6.460 54.357 876 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.10 % Allowed : 26.73 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -3.85 (0.21), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.16), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 20 TYR 0.014 0.002 TYR D 86 PHE 0.004 0.001 PHE A 80 TRP 0.002 0.001 TRP E 3 HIS 0.008 0.002 HIS B 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 6276) covalent geometry : angle 0.67744 / 0.35 ( 8472) SS BOND : bond 0.00371 / 0.22 ( 18) SS BOND : angle 1.02279 / 0.73 ( 36) hydrogen bonds : bond 0.01864 / 1.24 ( 68) hydrogen bonds : angle 4.79547 / 3.34 ( 204) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.206 Fit side-chains REVERT: B 36 GLN cc_start: 0.7950 (tt0) cc_final: 0.7649 (tt0) REVERT: B 66 LYS cc_start: 0.7891 (mttt) cc_final: 0.7598 (mtpp) REVERT: B 98 LYS cc_start: 0.8055 (mttt) cc_final: 0.7343 (mttp) REVERT: A 36 GLN cc_start: 0.7990 (tt0) cc_final: 0.7705 (tt0) REVERT: A 66 LYS cc_start: 0.7886 (mttt) cc_final: 0.7587 (mtpp) REVERT: A 98 LYS cc_start: 0.8024 (mttt) cc_final: 0.7304 (mttp) REVERT: C 36 GLN cc_start: 0.7936 (tt0) cc_final: 0.7633 (tt0) REVERT: C 84 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7929 (ttp) REVERT: C 98 LYS cc_start: 0.8435 (mttt) cc_final: 0.7675 (mttp) REVERT: D 36 GLN cc_start: 0.7947 (tt0) cc_final: 0.7652 (tt0) REVERT: D 84 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7925 (ttp) REVERT: D 98 LYS cc_start: 0.8385 (mttt) cc_final: 0.7597 (mttm) REVERT: E 10 LYS cc_start: 0.8250 (mttt) cc_final: 0.6824 (tptm) REVERT: E 55 MET cc_start: 0.8940 (ttp) cc_final: 0.8605 (ttp) REVERT: E 83 LYS cc_start: 0.7554 (ttmt) cc_final: 0.7082 (tttm) REVERT: E 98 LYS cc_start: 0.8228 (mttt) cc_final: 0.7414 (mmmt) REVERT: F 10 LYS cc_start: 0.8242 (mttt) cc_final: 0.6811 (tptm) REVERT: F 55 MET cc_start: 0.8939 (ttp) cc_final: 0.8606 (ttp) REVERT: F 83 LYS cc_start: 0.7552 (ttmt) cc_final: 0.7084 (tttm) REVERT: F 98 LYS cc_start: 0.8226 (mttt) cc_final: 0.7407 (mmmt) outliers start: 14 outliers final: 10 residues processed: 102 average time/residue: 0.7632 time to fit residues: 80.5505 Evaluate side-chains 110 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 HIS ** 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 = 0.4162 r_free = 0.4162 target = 0.160083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.137412 restraints weight = 7293.545| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 1.85 r_work: 0.3824 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6294 Z= 0.210 Angle : 0.750 6.391 8508 Z= 0.385 Chirality : 0.052 0.145 882 Planarity : 0.003 0.022 1116 Dihedral : 6.745 59.824 876 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.10 % Allowed : 26.73 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -3.91 (0.21), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.16), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 20 TYR 0.014 0.002 TYR D 86 PHE 0.006 0.002 PHE E 52 TRP 0.004 0.001 TRP E 3 HIS 0.008 0.002 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 ( 6276) covalent geometry : angle 0.74815 / 0.38 ( 8472) SS BOND : bond 0.00480 / 0.28 ( 18) SS BOND : angle 1.17533 / 0.82 ( 36) hydrogen bonds : bond 0.01988 / 1.33 ( 68) hydrogen bonds : angle 4.89723 / 3.40 ( 204) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.219 Fit side-chains REVERT: B 36 GLN cc_start: 0.8172 (tt0) cc_final: 0.7953 (tt0) REVERT: B 66 LYS cc_start: 0.7903 (mttt) cc_final: 0.7594 (mtpp) REVERT: B 98 LYS cc_start: 0.8021 (mttt) cc_final: 0.7321 (mttp) REVERT: A 36 GLN cc_start: 0.8171 (tt0) cc_final: 0.7937 (tt0) REVERT: A 98 LYS cc_start: 0.8044 (mttt) cc_final: 0.7350 (mttp) REVERT: C 36 GLN cc_start: 0.7941 (tt0) cc_final: 0.7627 (tt0) REVERT: C 84 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7962 (ttp) REVERT: C 98 LYS cc_start: 0.8425 (mttt) cc_final: 0.7668 (mttp) REVERT: D 36 GLN cc_start: 0.7967 (tt0) cc_final: 0.7660 (tt0) REVERT: D 84 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7960 (ttp) REVERT: D 98 LYS cc_start: 0.8364 (mttt) cc_final: 0.7582 (mttp) REVERT: E 10 LYS cc_start: 0.8233 (mttt) cc_final: 0.6819 (tptm) REVERT: E 55 MET cc_start: 0.8990 (ttp) cc_final: 0.8661 (ttp) REVERT: E 83 LYS cc_start: 0.7558 (ttmt) cc_final: 0.7117 (tttp) REVERT: E 98 LYS cc_start: 0.8224 (mttt) cc_final: 0.7393 (mmmt) REVERT: F 10 LYS cc_start: 0.8262 (mttt) cc_final: 0.6818 (tptm) REVERT: F 55 MET cc_start: 0.8992 (ttp) cc_final: 0.8663 (ttp) REVERT: F 83 LYS cc_start: 0.7557 (ttmt) cc_final: 0.7123 (tttp) REVERT: F 98 LYS cc_start: 0.8237 (mttt) cc_final: 0.7416 (mmmt) outliers start: 14 outliers final: 8 residues processed: 108 average time/residue: 0.7643 time to fit residues: 85.3297 Evaluate side-chains 109 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 69 optimal weight: 30.0000 chunk 28 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 HIS ** 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 = 0.4132 r_free = 0.4132 target = 0.157254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.134660 restraints weight = 7363.595| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 1.86 r_work: 0.3791 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 6294 Z= 0.276 Angle : 0.810 7.265 8508 Z= 0.419 Chirality : 0.054 0.150 882 Planarity : 0.004 0.032 1116 Dihedral : 7.165 68.142 876 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 2.40 % Allowed : 27.03 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -4.03 (0.21), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.16), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 20 TYR 0.016 0.003 TYR E 49 PHE 0.008 0.002 PHE B 80 TRP 0.005 0.002 TRP E 3 HIS 0.009 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.28 ( 6276) covalent geometry : angle 0.80762 / 0.42 ( 8472) SS BOND : bond 0.00576 / 0.34 ( 18) SS BOND : angle 1.27563 / 0.90 ( 36) hydrogen bonds : bond 0.02237 / 1.50 ( 68) hydrogen bonds : angle 5.04952 / 3.49 ( 204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2462.89 seconds wall clock time: 42 minutes 41.91 seconds (2561.91 seconds total)