Starting phenix.real_space_refine on Wed Aug 5 20:56:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c9x_45375/08_2026/9c9x_45375_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c9x_45375/08_2026/9c9x_45375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c9x_45375/08_2026/9c9x_45375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c9x_45375/08_2026/9c9x_45375.map" model { file = "/net/cci-nas-00/data/ceres_data/9c9x_45375/08_2026/9c9x_45375_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c9x_45375/08_2026/9c9x_45375_neut.cif" } resolution = 2.83 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= 0.029 sd= 0.311 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 10 5.16 5 C 6511 2.51 5 N 2204 2.21 5 O 2786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11799 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 753 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 89} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 624 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 781 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 92} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 620 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 739 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 2954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2954 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2985 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "G" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 804 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Time building chain proxies: 2.52, per 1000 atoms: 0.21 Number of scatterers: 11799 At special positions: 0 Unit cell: (116.284, 101.544, 122.016, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 288 15.00 O 2786 8.00 N 2204 7.00 C 6511 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.93 Conformation dependent library (CDL) restraints added in 235.5 milliseconds 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1392 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 72.7% alpha, 3.2% beta 143 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 removed outlier: 4.347A pdb=" N LEU A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.597A pdb=" N PHE A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 115 removed outlier: 3.556A pdb=" N VAL A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 95 " --> pdb=" O MET A 91 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 removed outlier: 3.726A pdb=" N ILE A 125 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 Processing helix chain 'B' and resid 31 through 42 removed outlier: 3.592A pdb=" N ILE B 35 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 77 removed outlier: 4.460A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP B 69 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B 77 " --> pdb=" O TYR B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 94 removed outlier: 3.674A pdb=" N GLN B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 4.297A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 removed outlier: 4.048A pdb=" N ASP C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 98 Processing helix chain 'C' and resid 113 through 117 removed outlier: 3.797A pdb=" N LEU C 117 " --> pdb=" O SER C 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 47 removed outlier: 3.817A pdb=" N VAL D 39 " --> pdb=" O TYR D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 82 removed outlier: 3.576A pdb=" N ASN D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 100 removed outlier: 3.513A pdb=" N ILE D 92 " --> pdb=" O THR D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.685A pdb=" N LYS D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 removed outlier: 3.961A pdb=" N ARG E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG E 54 " --> pdb=" O ARG E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 78 removed outlier: 3.591A pdb=" N PHE E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 removed outlier: 3.589A pdb=" N ALA E 96 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP E 107 " --> pdb=" O ALA E 103 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS E 114 " --> pdb=" O LEU E 110 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA E 115 " --> pdb=" O ALA E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 132 removed outlier: 3.661A pdb=" N ILE E 125 " --> pdb=" O MET E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 30 removed outlier: 3.816A pdb=" N ILE F 30 " --> pdb=" O ILE F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 51 through 77 removed outlier: 3.901A pdb=" N ASP F 69 " --> pdb=" O ASN F 65 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR F 72 " --> pdb=" O ARG F 68 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA F 77 " --> pdb=" O TYR F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 4.095A pdb=" N VAL F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 47 Processing helix chain 'H' and resid 53 through 82 Processing helix chain 'H' and resid 88 through 100 removed outlier: 3.704A pdb=" N ILE H 92 " --> pdb=" O THR H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 122 Processing helix chain 'G' and resid 17 through 23 removed outlier: 3.668A pdb=" N ARG G 21 " --> pdb=" O THR G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 37 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.389A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU G 66 " --> pdb=" O GLU G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 90 Processing helix chain 'G' and resid 91 through 98 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.287A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 99 removed outlier: 6.564A pdb=" N THR B 97 " --> pdb=" O THR G 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.188A pdb=" N ARG C 43 " --> pdb=" O ILE D 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103 removed outlier: 7.154A pdb=" N THR C 102 " --> pdb=" O TYR F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.785A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'H' and resid 51 through 52 removed outlier: 7.508A pdb=" N GLY H 51 " --> pdb=" O ILE G 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 86 through 87 367 hydrogen bonds defined for protein. 1089 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2419 1.34 - 1.46: 4340 1.46 - 1.58: 5242 1.58 - 1.70: 577 1.70 - 1.82: 20 Bond restraints: 12598 Sorted by residual: bond pdb=" C5' DG I 47 " pdb=" C4' DG I 47 " ideal model delta sigma weight residual 1.512 1.544 -0.032 7.00e-03 2.04e+04 2.03e+01 bond pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " ideal model delta sigma weight residual 1.435 1.490 -0.055 1.30e-02 5.92e+03 1.80e+01 bond pdb=" C3' DG J 23 " pdb=" C2' DG J 23 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.35e+01 bond pdb=" C3' DG I -58 " pdb=" O3' DG I -58 " ideal model delta sigma weight residual 1.435 1.483 -0.048 1.30e-02 5.92e+03 1.35e+01 bond pdb=" C3' DC I -38 " pdb=" O3' DC I -38 " ideal model delta sigma weight residual 1.435 1.482 -0.047 1.30e-02 5.92e+03 1.31e+01 ... (remaining 12593 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 17948 3.29 - 6.58: 264 6.58 - 9.86: 44 9.86 - 13.15: 7 13.15 - 16.44: 5 Bond angle restraints: 18268 Sorted by residual: angle pdb=" CB MET A 91 " pdb=" CG MET A 91 " pdb=" SD MET A 91 " ideal model delta sigma weight residual 112.70 129.14 -16.44 3.00e+00 1.11e-01 3.00e+01 angle pdb=" O5' DG I 47 " pdb=" C5' DG I 47 " pdb=" C4' DG I 47 " ideal model delta sigma weight residual 109.40 113.74 -4.34 8.00e-01 1.56e+00 2.95e+01 angle pdb=" O4' DG I 26 " pdb=" C4' DG I 26 " pdb=" C3' DG I 26 " ideal model delta sigma weight residual 106.00 102.79 3.21 6.00e-01 2.78e+00 2.87e+01 angle pdb=" CB MET H 60 " pdb=" CG MET H 60 " pdb=" SD MET H 60 " ideal model delta sigma weight residual 112.70 128.54 -15.84 3.00e+00 1.11e-01 2.79e+01 angle pdb=" C THR A 81 " pdb=" N ASP A 82 " pdb=" CA ASP A 82 " ideal model delta sigma weight residual 121.54 131.57 -10.03 1.91e+00 2.74e-01 2.76e+01 ... (remaining 18263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 5277 35.32 - 70.63: 1514 70.63 - 105.94: 25 105.94 - 141.26: 4 141.26 - 176.57: 1 Dihedral angle restraints: 6821 sinusoidal: 4663 harmonic: 2158 Sorted by residual: dihedral pdb=" CA ILE F 30 " pdb=" C ILE F 30 " pdb=" N THR F 31 " pdb=" CA THR F 31 " ideal model delta harmonic sigma weight residual 180.00 -152.05 -27.95 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ILE B 30 " pdb=" C ILE B 30 " pdb=" N THR B 31 " pdb=" CA THR B 31 " ideal model delta harmonic sigma weight residual 180.00 -154.58 -25.42 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ILE F 51 " pdb=" C ILE F 51 " pdb=" N TYR F 52 " pdb=" CA TYR F 52 " ideal model delta harmonic sigma weight residual -180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 6818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1553 0.057 - 0.115: 445 0.115 - 0.172: 63 0.172 - 0.230: 17 0.230 - 0.287: 6 Chirality restraints: 2084 Sorted by residual: chirality pdb=" CG LEU A 127 " pdb=" CB LEU A 127 " pdb=" CD1 LEU A 127 " pdb=" CD2 LEU A 127 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA ASN G 39 " pdb=" N ASN G 39 " pdb=" C ASN G 39 " pdb=" CB ASN G 39 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB VAL H 64 " pdb=" CA VAL H 64 " pdb=" CG1 VAL H 64 " pdb=" CG2 VAL H 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 2081 not shown) Planarity restraints: 1311 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 109 " -0.020 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" CG ASN E 109 " 0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN E 109 " -0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN E 109 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 66 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" CG ASP D 66 " 0.060 2.00e-02 2.50e+03 pdb=" OD1 ASP D 66 " -0.022 2.00e-02 2.50e+03 pdb=" OD2 ASP D 66 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 51 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" CD GLU E 51 " 0.056 2.00e-02 2.50e+03 pdb=" OE1 GLU E 51 " -0.020 2.00e-02 2.50e+03 pdb=" OE2 GLU E 51 " -0.019 2.00e-02 2.50e+03 ... (remaining 1308 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 286 2.66 - 3.22: 9170 3.22 - 3.78: 23335 3.78 - 4.34: 28757 4.34 - 4.90: 40387 Nonbonded interactions: 101935 Sorted by model distance: nonbonded pdb=" O ASN D 61 " pdb=" ND2 ASN D 65 " model vdw 2.101 3.120 nonbonded pdb=" O ILE A 120 " pdb=" OG SER B 48 " model vdw 2.289 3.040 nonbonded pdb=" O VAL H 109 " pdb=" OG1 THR H 113 " model vdw 2.297 3.040 nonbonded pdb=" OG SER E 87 " pdb=" OP2 DG I -24 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR E 100 " pdb=" OE1 GLU E 134 " model vdw 2.326 3.040 ... (remaining 101930 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 42 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB )) or resid 51 through 100 or (resid 101 and (name N or n \ ame CA or name C or name O or name CB )) or resid 102 through 134)) selection = (chain 'E' and (resid 42 through 61 or (resid 62 and (name N or name CA or name \ C or name O or name CB )) or resid 63 through 83 or (resid 84 and (name N or nam \ e CA or name C or name O or name CB )) or resid 85 through 134)) } ncs_group { reference = (chain 'B' and (resid 25 through 91 or (resid 92 and (name N or name CA or name \ C or name O or name CB )) or resid 93 through 103)) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 16 through 119) selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 31 through 96 or (resid 97 and (name N or name CA or name \ C or name O or name CB )) or resid 98 through 122)) selection = (chain 'H' and resid 31 through 122) } 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.910 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 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 : 0.007 0.065 12598 Z= 0.575 Angle : 1.148 16.438 18268 Z= 0.830 Chirality : 0.056 0.287 2084 Planarity : 0.008 0.072 1311 Dihedral : 29.426 176.574 5429 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 49.92 % Favored : 50.08 % 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: -2.49 (0.25), residues: 728 helix: -1.44 (0.19), residues: 507 sheet: None (None), residues: 0 loop : -1.75 (0.36), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 93 TYR 0.049 0.003 TYR H 81 PHE 0.036 0.002 PHE D 68 HIS 0.006 0.001 HIS H 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00702 / 0.58 (12598) covalent geometry : angle 1.14832 / 0.83 (18268) hydrogen bonds : bond 0.09181 / 6.24 ( 735) hydrogen bonds : angle 4.50698 / 3.20 ( 1825) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8693 (tt0) cc_final: 0.8378 (mt-10) REVERT: D 74 GLU cc_start: 0.9224 (tp30) cc_final: 0.8900 (tp30) REVERT: D 110 SER cc_start: 0.9263 (p) cc_final: 0.8993 (p) REVERT: E 46 THR cc_start: 0.8848 (t) cc_final: 0.8613 (p) outliers start: 0 outliers final: 1 residues processed: 310 average time/residue: 0.4968 time to fit residues: 166.2724 Evaluate side-chains 287 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 286 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 113 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.0170 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 30.0000 chunk 45 optimal weight: 0.7980 overall best weight: 0.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 113 GLN D 61 ASN D 65 ASN E 56 GLN H 61 ASN H 107 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.089937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.065371 restraints weight = 28671.842| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.84 r_work: 0.2965 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12598 Z= 0.148 Angle : 0.712 9.473 18268 Z= 0.410 Chirality : 0.048 0.262 2084 Planarity : 0.005 0.054 1311 Dihedral : 31.368 178.040 3993 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 6.24 % Allowed : 41.22 % Favored : 52.55 % 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: -0.77 (0.29), residues: 728 helix: -0.03 (0.22), residues: 518 sheet: None (None), residues: 0 loop : -1.47 (0.38), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 36 TYR 0.019 0.002 TYR B 89 PHE 0.009 0.001 PHE D 68 HIS 0.008 0.001 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.15 (12598) covalent geometry : angle 0.71167 / 0.41 (18268) hydrogen bonds : bond 0.04240 / 2.85 ( 735) hydrogen bonds : angle 3.28172 / 2.30 ( 1825) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 293 time to evaluate : 0.283 Fit side-chains REVERT: A 107 ASP cc_start: 0.8705 (m-30) cc_final: 0.8428 (m-30) REVERT: D 61 ASN cc_start: 0.9181 (OUTLIER) cc_final: 0.8705 (t0) REVERT: D 65 ASN cc_start: 0.9135 (OUTLIER) cc_final: 0.8765 (m110) REVERT: D 74 GLU cc_start: 0.9216 (tp30) cc_final: 0.8941 (tp30) REVERT: D 103 GLU cc_start: 0.8621 (mm-30) cc_final: 0.7968 (tp30) REVERT: F 94 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8099 (mt0) REVERT: F 96 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8391 (ptp90) REVERT: G 91 ASP cc_start: 0.8917 (t0) cc_final: 0.8368 (t0) outliers start: 38 outliers final: 12 residues processed: 310 average time/residue: 0.4903 time to fit residues: 164.7140 Evaluate side-chains 293 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 277 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 94 GLN Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 50 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 22 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 63 optimal weight: 30.0000 chunk 16 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 64 optimal weight: 30.0000 chunk 7 optimal weight: 0.0970 chunk 59 optimal weight: 0.8980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 56 GLN E 109 ASN F 26 ASN F 65 ASN H 61 ASN G 74 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.088775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.063376 restraints weight = 28554.467| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.96 r_work: 0.2920 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12598 Z= 0.154 Angle : 0.673 8.712 18268 Z= 0.391 Chirality : 0.046 0.266 2084 Planarity : 0.004 0.048 1311 Dihedral : 31.419 179.372 3991 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 6.57 % Allowed : 40.39 % Favored : 53.04 % 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: 0.10 (0.30), residues: 728 helix: 0.68 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.36 (0.38), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 93 TYR 0.015 0.001 TYR G 58 PHE 0.008 0.001 PHE D 68 HIS 0.004 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.15 (12598) covalent geometry : angle 0.67271 / 0.39 (18268) hydrogen bonds : bond 0.03872 / 2.61 ( 735) hydrogen bonds : angle 3.07141 / 2.14 ( 1825) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 299 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 80 LYS cc_start: 0.9029 (ttmm) cc_final: 0.8689 (mtpp) REVERT: C 43 ARG cc_start: 0.9078 (ptm160) cc_final: 0.8802 (ptm-80) REVERT: D 74 GLU cc_start: 0.9307 (tp30) cc_final: 0.9033 (tp30) REVERT: D 103 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8335 (tp30) REVERT: E 56 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8991 (tt0) REVERT: F 96 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8460 (ptp90) REVERT: G 25 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8296 (mm-40) REVERT: G 91 ASP cc_start: 0.8775 (t0) cc_final: 0.8280 (t0) outliers start: 40 outliers final: 17 residues processed: 315 average time/residue: 0.5179 time to fit residues: 176.5309 Evaluate side-chains 301 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 281 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 25 GLN Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 115 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 32 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 86 optimal weight: 30.0000 chunk 89 optimal weight: 4.9990 chunk 69 optimal weight: 30.0000 chunk 92 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 62 optimal weight: 30.0000 chunk 87 optimal weight: 40.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN D 61 ASN E 56 GLN F 26 ASN F 65 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.087783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.062331 restraints weight = 28693.094| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.96 r_work: 0.2887 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12598 Z= 0.171 Angle : 0.678 8.609 18268 Z= 0.389 Chirality : 0.046 0.267 2084 Planarity : 0.005 0.044 1311 Dihedral : 31.461 178.715 3991 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 7.72 % Allowed : 39.90 % Favored : 52.38 % 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: 0.55 (0.31), residues: 728 helix: 1.05 (0.23), residues: 517 sheet: None (None), residues: 0 loop : -1.27 (0.39), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 93 TYR 0.019 0.002 TYR G 58 PHE 0.007 0.001 PHE D 68 HIS 0.004 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.17 (12598) covalent geometry : angle 0.67776 / 0.39 (18268) hydrogen bonds : bond 0.03739 / 2.51 ( 735) hydrogen bonds : angle 2.97006 / 2.08 ( 1825) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 292 time to evaluate : 0.296 Fit side-chains REVERT: A 80 LYS cc_start: 0.9045 (ttmm) cc_final: 0.8663 (mtpp) REVERT: B 78 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.8897 (mmtm) REVERT: C 43 ARG cc_start: 0.9125 (ptm160) cc_final: 0.8819 (ptm-80) REVERT: C 65 GLU cc_start: 0.8631 (tp30) cc_final: 0.8397 (tp30) REVERT: C 105 GLN cc_start: 0.8845 (mm110) cc_final: 0.8632 (mm-40) REVERT: D 47 HIS cc_start: 0.8929 (OUTLIER) cc_final: 0.8671 (m-70) REVERT: D 66 ASP cc_start: 0.9238 (t0) cc_final: 0.9001 (t0) REVERT: D 74 GLU cc_start: 0.9337 (tp30) cc_final: 0.9085 (tp30) REVERT: F 96 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.8457 (ptp90) REVERT: G 25 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8341 (mm-40) REVERT: G 91 ASP cc_start: 0.8788 (t0) cc_final: 0.8190 (t0) outliers start: 47 outliers final: 25 residues processed: 317 average time/residue: 0.5193 time to fit residues: 177.9159 Evaluate side-chains 301 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 272 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 25 GLN Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 115 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 66 optimal weight: 30.0000 chunk 65 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 42 optimal weight: 0.0980 chunk 52 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.0770 chunk 82 optimal weight: 20.0000 chunk 60 optimal weight: 30.0000 chunk 92 optimal weight: 1.9990 overall best weight: 2.6344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN E 56 GLN F 65 ASN G 74 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.087285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.061926 restraints weight = 28792.029| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.92 r_work: 0.2874 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12598 Z= 0.177 Angle : 0.693 8.795 18268 Z= 0.393 Chirality : 0.046 0.270 2084 Planarity : 0.005 0.058 1311 Dihedral : 31.470 178.539 3991 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 8.21 % Allowed : 41.38 % Favored : 50.41 % 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: 0.68 (0.31), residues: 728 helix: 1.18 (0.23), residues: 520 sheet: None (None), residues: 0 loop : -1.36 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 93 TYR 0.025 0.002 TYR G 58 PHE 0.007 0.001 PHE D 68 HIS 0.004 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.18 (12598) covalent geometry : angle 0.69252 / 0.39 (18268) hydrogen bonds : bond 0.03746 / 2.50 ( 735) hydrogen bonds : angle 2.95713 / 2.08 ( 1825) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 284 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 78 LYS cc_start: 0.9414 (OUTLIER) cc_final: 0.8887 (mmtm) REVERT: C 43 ARG cc_start: 0.9145 (ptm160) cc_final: 0.8863 (ptm-80) REVERT: C 65 GLU cc_start: 0.8667 (tp30) cc_final: 0.8383 (tp30) REVERT: D 47 HIS cc_start: 0.8931 (OUTLIER) cc_final: 0.8667 (m-70) REVERT: D 66 ASP cc_start: 0.9213 (t0) cc_final: 0.8982 (t0) REVERT: D 74 GLU cc_start: 0.9322 (tp30) cc_final: 0.9073 (tp30) REVERT: E 60 GLU cc_start: 0.8863 (pm20) cc_final: 0.8606 (pm20) REVERT: F 96 ARG cc_start: 0.9204 (OUTLIER) cc_final: 0.8478 (ptp90) REVERT: G 25 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8331 (mm-40) REVERT: G 74 ASN cc_start: 0.8921 (OUTLIER) cc_final: 0.8575 (t0) REVERT: G 91 ASP cc_start: 0.8767 (t0) cc_final: 0.8240 (t0) outliers start: 50 outliers final: 28 residues processed: 304 average time/residue: 0.4924 time to fit residues: 161.6933 Evaluate side-chains 304 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 271 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 25 GLN Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 115 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 6 optimal weight: 0.6980 chunk 21 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 2 optimal weight: 0.0470 chunk 70 optimal weight: 30.0000 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 65 optimal weight: 30.0000 chunk 95 optimal weight: 1.9990 overall best weight: 1.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN D 61 ASN D 65 ASN E 56 GLN F 65 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.087914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.062634 restraints weight = 28650.431| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.92 r_work: 0.2890 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12598 Z= 0.149 Angle : 0.686 9.354 18268 Z= 0.391 Chirality : 0.046 0.269 2084 Planarity : 0.005 0.043 1311 Dihedral : 31.419 178.542 3991 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 7.06 % Allowed : 42.69 % Favored : 50.25 % 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: 0.78 (0.31), residues: 728 helix: 1.26 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.33 (0.38), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 93 TYR 0.030 0.002 TYR G 58 PHE 0.006 0.001 PHE D 68 HIS 0.003 0.001 HIS H 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 (12598) covalent geometry : angle 0.68616 / 0.39 (18268) hydrogen bonds : bond 0.03594 / 2.39 ( 735) hydrogen bonds : angle 2.93113 / 2.07 ( 1825) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 286 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 60 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.9028 (ttmt) REVERT: C 65 GLU cc_start: 0.8678 (tp30) cc_final: 0.8329 (tp30) REVERT: D 47 HIS cc_start: 0.8890 (OUTLIER) cc_final: 0.8610 (m-70) REVERT: D 61 ASN cc_start: 0.9331 (OUTLIER) cc_final: 0.8876 (t0) REVERT: D 65 ASN cc_start: 0.9169 (OUTLIER) cc_final: 0.8777 (m110) REVERT: D 66 ASP cc_start: 0.9229 (t0) cc_final: 0.8985 (t0) REVERT: F 96 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8446 (ptp90) REVERT: H 106 LYS cc_start: 0.8816 (pptt) cc_final: 0.8486 (pttt) REVERT: G 25 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8290 (mm-40) REVERT: G 91 ASP cc_start: 0.8675 (t0) cc_final: 0.8192 (t0) outliers start: 43 outliers final: 25 residues processed: 304 average time/residue: 0.5010 time to fit residues: 165.0315 Evaluate side-chains 306 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 275 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 61 ASN Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 25 GLN Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 115 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 11 optimal weight: 1.9990 chunk 78 optimal weight: 30.0000 chunk 77 optimal weight: 30.0000 chunk 73 optimal weight: 50.0000 chunk 30 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 69 optimal weight: 30.0000 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN E 56 GLN F 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.086906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.061545 restraints weight = 28605.572| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.91 r_work: 0.2865 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12598 Z= 0.198 Angle : 0.718 10.480 18268 Z= 0.403 Chirality : 0.047 0.272 2084 Planarity : 0.005 0.046 1311 Dihedral : 31.447 178.486 3991 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 8.21 % Allowed : 42.69 % Favored : 49.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.76 (0.31), residues: 728 helix: 1.26 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.42 (0.39), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 31 TYR 0.025 0.002 TYR F 89 PHE 0.006 0.001 PHE D 68 HIS 0.005 0.001 HIS H 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.20 (12598) covalent geometry : angle 0.71779 / 0.40 (18268) hydrogen bonds : bond 0.03715 / 2.48 ( 735) hydrogen bonds : angle 2.94913 / 2.09 ( 1825) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 279 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: B 60 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.9048 (ttmt) REVERT: B 78 LYS cc_start: 0.9446 (OUTLIER) cc_final: 0.8927 (mmtm) REVERT: C 37 LYS cc_start: 0.9391 (mtpp) cc_final: 0.9041 (mmmt) REVERT: C 65 GLU cc_start: 0.8724 (tp30) cc_final: 0.8388 (tp30) REVERT: C 86 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9374 (mm) REVERT: C 105 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8656 (mm-40) REVERT: D 47 HIS cc_start: 0.8959 (OUTLIER) cc_final: 0.8668 (m-70) REVERT: D 66 ASP cc_start: 0.9250 (t0) cc_final: 0.8996 (t0) REVERT: E 91 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8934 (mmm) REVERT: F 96 ARG cc_start: 0.9214 (OUTLIER) cc_final: 0.8499 (ptp90) REVERT: G 25 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8401 (mm-40) REVERT: G 91 ASP cc_start: 0.8709 (t0) cc_final: 0.8253 (t0) outliers start: 50 outliers final: 31 residues processed: 300 average time/residue: 0.5553 time to fit residues: 180.2333 Evaluate side-chains 310 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 272 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 66 ASP Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 25 GLN Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 115 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 97 optimal weight: 8.9990 chunk 82 optimal weight: 20.0000 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 0.0470 chunk 57 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 67 optimal weight: 30.0000 chunk 48 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN E 56 GLN E 114 HIS F 65 ASN ** H 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.088236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.062888 restraints weight = 28604.441| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.93 r_work: 0.2896 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12598 Z= 0.145 Angle : 0.700 10.267 18268 Z= 0.396 Chirality : 0.045 0.269 2084 Planarity : 0.004 0.050 1311 Dihedral : 31.385 178.568 3991 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 6.57 % Allowed : 45.32 % Favored : 48.11 % 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: 0.86 (0.31), residues: 728 helix: 1.35 (0.23), residues: 517 sheet: None (None), residues: 0 loop : -1.35 (0.38), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 31 TYR 0.031 0.002 TYR G 58 PHE 0.007 0.001 PHE D 68 HIS 0.007 0.001 HIS H 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 (12598) covalent geometry : angle 0.70030 / 0.40 (18268) hydrogen bonds : bond 0.03549 / 2.36 ( 735) hydrogen bonds : angle 2.90808 / 2.07 ( 1825) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 291 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: B 60 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.9013 (ttmt) REVERT: C 37 LYS cc_start: 0.9375 (mtpp) cc_final: 0.9018 (mmmt) REVERT: C 65 GLU cc_start: 0.8721 (tp30) cc_final: 0.8349 (tp30) REVERT: C 86 LEU cc_start: 0.9625 (OUTLIER) cc_final: 0.9315 (mm) REVERT: D 47 HIS cc_start: 0.8902 (OUTLIER) cc_final: 0.8612 (m-70) REVERT: D 66 ASP cc_start: 0.9250 (t0) cc_final: 0.8997 (t0) REVERT: E 91 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8923 (mmm) REVERT: F 96 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.8403 (ptp90) REVERT: H 106 LYS cc_start: 0.8756 (pptt) cc_final: 0.8465 (pttt) REVERT: G 25 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8241 (mm-40) REVERT: G 91 ASP cc_start: 0.8734 (t0) cc_final: 0.8212 (t0) REVERT: G 94 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9160 (mt) outliers start: 40 outliers final: 25 residues processed: 305 average time/residue: 0.5481 time to fit residues: 180.9110 Evaluate side-chains 310 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 278 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 66 ASP Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 25 GLN Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 115 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 30.0000 chunk 4 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 60 optimal weight: 30.0000 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN D 61 ASN E 56 GLN F 65 ASN H 107 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.088031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.062711 restraints weight = 28457.580| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.92 r_work: 0.2892 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 12598 Z= 0.159 Angle : 0.721 11.904 18268 Z= 0.403 Chirality : 0.046 0.272 2084 Planarity : 0.004 0.052 1311 Dihedral : 31.371 178.668 3991 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 6.57 % Allowed : 44.83 % Favored : 48.60 % 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: 0.88 (0.31), residues: 728 helix: 1.32 (0.23), residues: 519 sheet: None (None), residues: 0 loop : -1.26 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 93 TYR 0.033 0.002 TYR F 89 PHE 0.006 0.001 PHE D 68 HIS 0.008 0.001 HIS H 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 (12598) covalent geometry : angle 0.72073 / 0.40 (18268) hydrogen bonds : bond 0.03582 / 2.40 ( 735) hydrogen bonds : angle 2.89129 / 2.05 ( 1825) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 279 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: B 60 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.9013 (ttmt) REVERT: C 37 LYS cc_start: 0.9361 (mtpp) cc_final: 0.9028 (mmmt) REVERT: C 65 GLU cc_start: 0.8715 (tp30) cc_final: 0.8366 (tp30) REVERT: C 86 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9319 (mm) REVERT: D 47 HIS cc_start: 0.8921 (OUTLIER) cc_final: 0.8628 (m-70) REVERT: D 66 ASP cc_start: 0.9223 (t0) cc_final: 0.8968 (t0) REVERT: E 91 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8902 (mmm) REVERT: F 96 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8440 (ptp90) REVERT: H 103 GLU cc_start: 0.7946 (pm20) cc_final: 0.7733 (pm20) REVERT: H 106 LYS cc_start: 0.8725 (pptt) cc_final: 0.8445 (pttt) REVERT: G 25 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8256 (mm-40) REVERT: G 91 ASP cc_start: 0.8672 (t0) cc_final: 0.8297 (t0) REVERT: G 94 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9103 (mt) outliers start: 40 outliers final: 28 residues processed: 293 average time/residue: 0.5557 time to fit residues: 176.3449 Evaluate side-chains 307 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 272 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 66 ASP Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 25 GLN Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 115 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 60 optimal weight: 40.0000 chunk 90 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 62 optimal weight: 30.0000 chunk 22 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN F 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.087454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.062105 restraints weight = 28775.636| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.92 r_work: 0.2877 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12598 Z= 0.181 Angle : 0.725 12.342 18268 Z= 0.406 Chirality : 0.046 0.273 2084 Planarity : 0.005 0.054 1311 Dihedral : 31.392 178.633 3991 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 5.91 % Allowed : 45.98 % Favored : 48.11 % 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: 0.85 (0.31), residues: 728 helix: 1.30 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.30 (0.39), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 31 TYR 0.042 0.003 TYR F 89 PHE 0.006 0.001 PHE D 68 HIS 0.007 0.001 HIS H 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 (12598) covalent geometry : angle 0.72514 / 0.41 (18268) hydrogen bonds : bond 0.03623 / 2.42 ( 735) hydrogen bonds : angle 2.91595 / 2.08 ( 1825) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 275 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: B 60 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.9008 (ttmt) REVERT: C 37 LYS cc_start: 0.9360 (mtpp) cc_final: 0.9036 (mmmt) REVERT: C 65 GLU cc_start: 0.8736 (tp30) cc_final: 0.8350 (tp30) REVERT: C 86 LEU cc_start: 0.9625 (OUTLIER) cc_final: 0.9322 (mm) REVERT: D 47 HIS cc_start: 0.8943 (OUTLIER) cc_final: 0.8623 (m-70) REVERT: D 66 ASP cc_start: 0.9217 (t0) cc_final: 0.8961 (t0) REVERT: E 91 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8910 (mmm) REVERT: F 96 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.8460 (ptp90) REVERT: H 106 LYS cc_start: 0.8757 (pptt) cc_final: 0.8472 (pttt) REVERT: G 25 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8313 (mm-40) REVERT: G 91 ASP cc_start: 0.8704 (t0) cc_final: 0.8350 (t70) REVERT: G 94 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9143 (mt) outliers start: 36 outliers final: 28 residues processed: 289 average time/residue: 0.5760 time to fit residues: 179.9849 Evaluate side-chains 306 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 271 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 106 LYS Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 66 ASP Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 25 GLN Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 115 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 69 optimal weight: 30.0000 chunk 17 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 80 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.088332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.062985 restraints weight = 28667.932| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.92 r_work: 0.2899 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12598 Z= 0.148 Angle : 0.714 12.335 18268 Z= 0.401 Chirality : 0.045 0.271 2084 Planarity : 0.004 0.041 1311 Dihedral : 31.358 178.676 3991 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.58 % Allowed : 45.98 % Favored : 48.44 % 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: 0.88 (0.31), residues: 728 helix: 1.31 (0.23), residues: 519 sheet: None (None), residues: 0 loop : -1.23 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 36 TYR 0.043 0.003 TYR F 89 PHE 0.007 0.001 PHE D 68 HIS 0.007 0.001 HIS H 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (12598) covalent geometry : angle 0.71392 / 0.40 (18268) hydrogen bonds : bond 0.03540 / 2.35 ( 735) hydrogen bonds : angle 2.88017 / 2.05 ( 1825) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4222.45 seconds wall clock time: 72 minutes 22.08 seconds (4342.08 seconds total)