Starting phenix.real_space_refine on Sat Aug 23 11:26:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c9x_45375/08_2025/9c9x_45375_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c9x_45375/08_2025/9c9x_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_2025/9c9x_45375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c9x_45375/08_2025/9c9x_45375.map" model { file = "/net/cci-nas-00/data/ceres_data/9c9x_45375/08_2025/9c9x_45375_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c9x_45375/08_2025/9c9x_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-2.0-5787/lib/python3.9/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: 2.57, per 1000 atoms: 0.22 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: 0.79 Conformation dependent library (CDL) restraints added in 244.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.62 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: 2.17 Time building geometry restraints manager: 1.09 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=" C3' DT I -17 " pdb=" O3' DT I -17 " ideal model delta sigma weight residual 1.422 1.490 -0.068 3.00e-02 1.11e+03 5.16e+00 bond pdb=" CB ASP F 25 " pdb=" CG ASP F 25 " ideal model delta sigma weight residual 1.516 1.571 -0.055 2.50e-02 1.60e+03 4.90e+00 bond pdb=" CB ARG A 130 " pdb=" CG ARG A 130 " ideal model delta sigma weight residual 1.520 1.585 -0.065 3.00e-02 1.11e+03 4.66e+00 bond pdb=" CB ASP H 66 " pdb=" CG ASP H 66 " ideal model delta sigma weight residual 1.516 1.567 -0.051 2.50e-02 1.60e+03 4.17e+00 bond pdb=" CB ASN G 39 " pdb=" CG ASN G 39 " ideal model delta sigma weight residual 1.516 1.567 -0.051 2.50e-02 1.60e+03 4.16e+00 ... (remaining 12593 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 17968 3.29 - 6.58: 244 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=" 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 angle pdb=" C THR E 81 " pdb=" N ASP E 82 " pdb=" CA ASP E 82 " ideal model delta sigma weight residual 121.54 131.48 -9.94 1.91e+00 2.74e-01 2.71e+01 angle pdb=" CG ARG D 31 " pdb=" CD ARG D 31 " pdb=" NE ARG D 31 " ideal model delta sigma weight residual 112.00 123.17 -11.17 2.20e+00 2.07e-01 2.58e+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: 1671 0.057 - 0.115: 332 0.115 - 0.172: 61 0.172 - 0.230: 14 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: 0.850 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.580 Find NCS groups from input model: 0.080 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:5.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 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 0.068 12598 Z= 0.240 Angle : 1.032 16.438 18268 Z= 0.561 Chirality : 0.051 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 aren 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 covalent geometry : bond 0.00531 (12598) covalent geometry : angle 1.03222 (18268) hydrogen bonds : bond 0.09181 ( 735) hydrogen bonds : angle 4.50698 ( 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 : 0.233 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: 0.6076 time to fit residues: 202.5234 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 : 0.278 ------------------------------------------------------------------------------- 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: 8.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 overall best weight: 0.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 113 GLN D 61 ASN D 65 ASN E 56 GLN F 26 ASN H 61 ASN H 107 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.090306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.065682 restraints weight = 28681.463| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.94 r_work: 0.2957 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12598 Z= 0.154 Angle : 0.616 7.763 18268 Z= 0.361 Chirality : 0.035 0.156 2084 Planarity : 0.005 0.055 1311 Dihedral : 30.949 177.731 3993 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 6.08 % Allowed : 41.54 % 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 aren not related in a simple way. whole: -0.48 (0.29), residues: 728 helix: 0.23 (0.22), residues: 511 sheet: None (None), residues: 0 loop : -1.45 (0.37), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 93 TYR 0.018 0.001 TYR F 89 PHE 0.009 0.001 PHE D 68 HIS 0.004 0.001 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00329 (12598) covalent geometry : angle 0.61640 (18268) hydrogen bonds : bond 0.03205 ( 735) hydrogen bonds : angle 3.07337 ( 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 335 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 298 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: C 105 GLN cc_start: 0.8805 (mm110) cc_final: 0.8600 (mm-40) REVERT: D 61 ASN cc_start: 0.9136 (OUTLIER) cc_final: 0.8685 (t0) REVERT: D 65 ASN cc_start: 0.9144 (OUTLIER) cc_final: 0.8781 (m110) REVERT: D 74 GLU cc_start: 0.9270 (tp30) cc_final: 0.9030 (tp30) REVERT: D 103 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8117 (tp30) REVERT: F 96 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8398 (ptp90) REVERT: G 91 ASP cc_start: 0.8794 (t0) cc_final: 0.8322 (t0) outliers start: 37 outliers final: 11 residues processed: 313 average time/residue: 0.5672 time to fit residues: 191.4316 Evaluate side-chains 291 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 277 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 F residue 96 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain G residue 20 SER 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: 9.9990 chunk 26 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN D 61 ASN F 65 ASN G 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.086834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.061380 restraints weight = 28894.639| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.95 r_work: 0.2857 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12598 Z= 0.211 Angle : 0.635 8.771 18268 Z= 0.370 Chirality : 0.037 0.180 2084 Planarity : 0.004 0.043 1311 Dihedral : 31.118 179.639 3991 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 8.05 % Allowed : 37.44 % Favored : 54.52 % 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 aren not related in a simple way. whole: 0.33 (0.30), residues: 728 helix: 0.86 (0.23), residues: 523 sheet: None (None), residues: 0 loop : -1.36 (0.39), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 31 TYR 0.016 0.002 TYR H 81 PHE 0.007 0.001 PHE D 68 HIS 0.007 0.001 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00476 (12598) covalent geometry : angle 0.63539 (18268) hydrogen bonds : bond 0.03342 ( 735) hydrogen bonds : angle 2.87953 ( 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 343 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 294 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8634 (mtp) REVERT: B 78 LYS cc_start: 0.9442 (OUTLIER) cc_final: 0.8985 (mmtm) REVERT: C 86 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9351 (mm) REVERT: C 105 GLN cc_start: 0.8827 (mm110) cc_final: 0.8617 (mm-40) REVERT: F 96 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.8475 (ptp90) REVERT: H 77 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.8759 (ptp90) REVERT: H 82 ASN cc_start: 0.9250 (m-40) cc_final: 0.9043 (m-40) REVERT: G 25 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8330 (mm-40) REVERT: G 74 ASN cc_start: 0.8928 (OUTLIER) cc_final: 0.8453 (t0) REVERT: G 91 ASP cc_start: 0.8787 (t0) cc_final: 0.8327 (t0) outliers start: 49 outliers final: 21 residues processed: 317 average time/residue: 0.6436 time to fit residues: 219.9584 Evaluate side-chains 299 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 271 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 121 MET 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 B residue 98 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 34 SER 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 H residue 46 VAL Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 25 GLN Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 74 ASN 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: 0.7980 chunk 97 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 ASN E 114 HIS F 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.088394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.063216 restraints weight = 28702.183| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.94 r_work: 0.2900 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12598 Z= 0.162 Angle : 0.618 8.724 18268 Z= 0.359 Chirality : 0.035 0.154 2084 Planarity : 0.004 0.043 1311 Dihedral : 30.913 179.061 3991 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 7.06 % Allowed : 40.39 % 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 aren not related in a simple way. whole: 0.76 (0.31), residues: 728 helix: 1.20 (0.23), residues: 519 sheet: None (None), residues: 0 loop : -1.19 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 33 TYR 0.020 0.002 TYR F 52 PHE 0.006 0.001 PHE D 68 HIS 0.003 0.001 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00356 (12598) covalent geometry : angle 0.61758 (18268) hydrogen bonds : bond 0.03052 ( 735) hydrogen bonds : angle 2.78543 ( 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 336 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 293 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: B 60 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.9009 (ttmt) REVERT: C 43 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8813 (ptm-80) REVERT: C 86 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9314 (mm) REVERT: C 90 ASN cc_start: 0.9093 (m-40) cc_final: 0.8850 (m110) REVERT: D 103 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8509 (mm-30) REVERT: E 91 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8900 (mmm) REVERT: F 96 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8381 (ptp90) REVERT: H 57 MET cc_start: 0.9481 (tpp) cc_final: 0.9173 (tpp) REVERT: H 77 ARG cc_start: 0.9169 (ptp90) cc_final: 0.8732 (ptp90) REVERT: G 25 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8096 (mm-40) REVERT: G 74 ASN cc_start: 0.8822 (t0) cc_final: 0.8477 (t0) REVERT: G 91 ASP cc_start: 0.8872 (t0) cc_final: 0.8387 (t0) outliers start: 43 outliers final: 22 residues processed: 312 average time/residue: 0.6205 time to fit residues: 208.6802 Evaluate side-chains 308 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 280 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 91 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 102 THR 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 58 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 52 LEU Chi-restraints excluded: chain G residue 102 THR 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: 10.0000 chunk 65 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.2980 chunk 82 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 92 optimal weight: 0.6980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 GLN F 65 ASN G 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.088313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.062742 restraints weight = 28614.189| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.95 r_work: 0.2895 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12598 Z= 0.171 Angle : 0.626 9.119 18268 Z= 0.362 Chirality : 0.036 0.161 2084 Planarity : 0.004 0.042 1311 Dihedral : 30.897 178.929 3991 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 7.55 % Allowed : 41.05 % Favored : 51.40 % 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 aren not related in a simple way. whole: 1.01 (0.31), residues: 728 helix: 1.37 (0.23), residues: 519 sheet: None (None), residues: 0 loop : -1.06 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 31 TYR 0.022 0.002 TYR G 58 PHE 0.006 0.001 PHE D 68 HIS 0.004 0.001 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00383 (12598) covalent geometry : angle 0.62569 (18268) hydrogen bonds : bond 0.03067 ( 735) hydrogen bonds : angle 2.72181 ( 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 337 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 291 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: B 60 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.9022 (ttmt) REVERT: B 78 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.8887 (mmtm) REVERT: B 93 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8936 (mmm-85) REVERT: C 86 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9278 (mm) REVERT: D 32 LYS cc_start: 0.8139 (mmtt) cc_final: 0.7684 (mppt) REVERT: D 55 LYS cc_start: 0.9092 (tppp) cc_final: 0.8866 (mmmm) REVERT: D 106 LYS cc_start: 0.9032 (mtmm) cc_final: 0.8784 (mtmm) REVERT: E 91 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.8924 (mmm) REVERT: E 95 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8863 (mm-30) REVERT: F 96 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8375 (ptp90) REVERT: G 74 ASN cc_start: 0.8918 (OUTLIER) cc_final: 0.8417 (t0) REVERT: G 91 ASP cc_start: 0.8870 (t0) cc_final: 0.8491 (t0) outliers start: 46 outliers final: 28 residues processed: 311 average time/residue: 0.6442 time to fit residues: 216.0912 Evaluate side-chains 310 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 275 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 98 LEU 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 98 LEU 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 78 LEU 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 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 121 SER Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 102 THR 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: 0.9990 chunk 21 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 95 optimal weight: 0.3980 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN G 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.087988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.062308 restraints weight = 28616.506| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.94 r_work: 0.2890 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12598 Z= 0.179 Angle : 0.638 9.314 18268 Z= 0.366 Chirality : 0.036 0.169 2084 Planarity : 0.004 0.041 1311 Dihedral : 30.899 178.884 3991 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 8.05 % Allowed : 42.04 % Favored : 49.92 % 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 aren not related in a simple way. whole: 1.05 (0.31), residues: 728 helix: 1.41 (0.23), residues: 519 sheet: None (None), residues: 0 loop : -1.07 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 31 TYR 0.025 0.002 TYR G 58 PHE 0.005 0.001 PHE D 68 HIS 0.003 0.001 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00401 (12598) covalent geometry : angle 0.63813 (18268) hydrogen bonds : bond 0.03101 ( 735) hydrogen bonds : angle 2.74469 ( 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 334 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 285 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 60 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.9025 (ttmt) REVERT: B 78 LYS cc_start: 0.9414 (OUTLIER) cc_final: 0.8884 (mmtm) REVERT: B 93 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8919 (mmm-85) REVERT: C 43 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.8826 (ptm-80) REVERT: C 86 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9266 (mm) REVERT: D 32 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7724 (mppt) REVERT: D 55 LYS cc_start: 0.9100 (tppp) cc_final: 0.8865 (mmmm) REVERT: E 91 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8911 (mmm) REVERT: F 96 ARG cc_start: 0.9178 (OUTLIER) cc_final: 0.8436 (ptp90) REVERT: G 74 ASN cc_start: 0.8953 (OUTLIER) cc_final: 0.8424 (t0) REVERT: G 91 ASP cc_start: 0.8899 (t0) cc_final: 0.8404 (t0) outliers start: 49 outliers final: 33 residues processed: 304 average time/residue: 0.6398 time to fit residues: 209.4641 Evaluate side-chains 318 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 277 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 78 LYS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 43 ARG 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 98 LEU 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 78 LEU 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 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 121 SER Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 74 ASN 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: 0.6980 chunk 78 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.088188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.063062 restraints weight = 28755.329| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.93 r_work: 0.2892 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12598 Z= 0.175 Angle : 0.647 10.299 18268 Z= 0.370 Chirality : 0.036 0.178 2084 Planarity : 0.004 0.041 1311 Dihedral : 30.877 178.841 3991 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 8.21 % Allowed : 42.86 % Favored : 48.93 % 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 aren not related in a simple way. whole: 1.11 (0.31), residues: 728 helix: 1.46 (0.23), residues: 519 sheet: None (None), residues: 0 loop : -1.07 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 31 TYR 0.026 0.002 TYR F 89 PHE 0.004 0.001 PHE D 68 HIS 0.003 0.001 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00395 (12598) covalent geometry : angle 0.64726 (18268) hydrogen bonds : bond 0.03110 ( 735) hydrogen bonds : angle 2.73851 ( 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 338 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 288 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 60 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.8995 (ttmt) REVERT: B 78 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.8845 (mmtm) REVERT: C 43 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.8847 (ptm-80) REVERT: C 86 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9289 (mm) REVERT: D 32 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7757 (mppt) REVERT: D 55 LYS cc_start: 0.9100 (tppp) cc_final: 0.8876 (mmmm) REVERT: D 66 ASP cc_start: 0.9222 (t0) cc_final: 0.9022 (t0) REVERT: E 91 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8890 (mmm) REVERT: F 96 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.8359 (ptp90) REVERT: G 74 ASN cc_start: 0.9146 (OUTLIER) cc_final: 0.8547 (t0) REVERT: G 91 ASP cc_start: 0.8734 (t0) cc_final: 0.8485 (t0) outliers start: 50 outliers final: 36 residues processed: 306 average time/residue: 0.6262 time to fit residues: 206.7553 Evaluate side-chains 324 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 281 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 98 LEU Chi-restraints excluded: chain C residue 43 ARG 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 98 LEU 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 78 LEU 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 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 106 LYS Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 80 ILE 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: 3.9990 chunk 82 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN G 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.089266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.064080 restraints weight = 28550.110| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.94 r_work: 0.2919 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12598 Z= 0.159 Angle : 0.647 10.250 18268 Z= 0.368 Chirality : 0.035 0.182 2084 Planarity : 0.004 0.042 1311 Dihedral : 30.804 178.748 3991 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 7.55 % Allowed : 44.01 % 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 aren not related in a simple way. whole: 1.15 (0.31), residues: 728 helix: 1.49 (0.23), residues: 517 sheet: None (None), residues: 0 loop : -1.02 (0.39), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 31 TYR 0.030 0.002 TYR F 89 PHE 0.004 0.001 PHE B 62 HIS 0.002 0.001 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00353 (12598) covalent geometry : angle 0.64691 (18268) hydrogen bonds : bond 0.03071 ( 735) hydrogen bonds : angle 2.73124 ( 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 345 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 299 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.9085 (tppp) cc_final: 0.8692 (mmtp) REVERT: B 60 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8987 (ttmt) REVERT: B 78 LYS cc_start: 0.9387 (OUTLIER) cc_final: 0.8850 (mmtm) REVERT: C 43 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8862 (ptm-80) REVERT: C 65 GLU cc_start: 0.8714 (tp30) cc_final: 0.8436 (tp30) REVERT: C 86 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9268 (mm) REVERT: D 32 LYS cc_start: 0.8153 (mmtt) cc_final: 0.7772 (mppt) REVERT: D 47 HIS cc_start: 0.8935 (OUTLIER) cc_final: 0.8672 (m-70) REVERT: D 55 LYS cc_start: 0.9072 (tppp) cc_final: 0.8844 (mmmm) REVERT: D 66 ASP cc_start: 0.9243 (t0) cc_final: 0.9008 (t0) REVERT: E 91 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8890 (mmm) REVERT: F 96 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8375 (ptp90) REVERT: G 74 ASN cc_start: 0.8963 (OUTLIER) cc_final: 0.8420 (t0) REVERT: G 91 ASP cc_start: 0.8765 (t0) cc_final: 0.8478 (t0) outliers start: 46 outliers final: 28 residues processed: 319 average time/residue: 0.6109 time to fit residues: 210.3695 Evaluate side-chains 319 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 283 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 78 LYS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 43 ARG 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 98 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 78 LEU 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 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 G residue 17 THR Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 74 ASN 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: 10.0000 chunk 4 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN C 111 ASN G 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.089107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.063334 restraints weight = 28442.841| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.95 r_work: 0.2910 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12598 Z= 0.172 Angle : 0.666 10.919 18268 Z= 0.378 Chirality : 0.036 0.190 2084 Planarity : 0.004 0.048 1311 Dihedral : 30.817 178.693 3991 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 7.06 % Allowed : 45.48 % Favored : 47.45 % 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 aren not related in a simple way. whole: 1.19 (0.31), residues: 728 helix: 1.51 (0.23), residues: 517 sheet: None (None), residues: 0 loop : -0.99 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 31 TYR 0.036 0.002 TYR F 89 PHE 0.005 0.001 PHE B 62 HIS 0.003 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00387 (12598) covalent geometry : angle 0.66599 (18268) hydrogen bonds : bond 0.03137 ( 735) hydrogen bonds : angle 2.76283 ( 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 330 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 287 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.9497 (ttmm) cc_final: 0.9280 (ttpp) REVERT: A 65 LYS cc_start: 0.9086 (tppp) cc_final: 0.8701 (mmtp) REVERT: B 60 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.9009 (ttmt) REVERT: B 78 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.8821 (mmtm) REVERT: C 43 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8894 (ptm-80) REVERT: C 65 GLU cc_start: 0.8719 (tp30) cc_final: 0.8452 (tp30) REVERT: C 76 LYS cc_start: 0.9549 (OUTLIER) cc_final: 0.9117 (mtmm) REVERT: C 86 LEU cc_start: 0.9599 (OUTLIER) cc_final: 0.9293 (mm) REVERT: D 32 LYS cc_start: 0.8236 (mmtt) cc_final: 0.7826 (mppt) REVERT: D 47 HIS cc_start: 0.8942 (OUTLIER) cc_final: 0.8702 (m-70) REVERT: D 55 LYS cc_start: 0.9096 (tppp) cc_final: 0.8881 (mmmm) REVERT: D 66 ASP cc_start: 0.9204 (t0) cc_final: 0.8967 (t0) REVERT: E 91 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8913 (mmm) REVERT: F 96 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8365 (ptp90) REVERT: H 40 TYR cc_start: 0.8646 (t80) cc_final: 0.8286 (t80) REVERT: G 74 ASN cc_start: 0.9153 (OUTLIER) cc_final: 0.8530 (t0) outliers start: 43 outliers final: 32 residues processed: 306 average time/residue: 0.6315 time to fit residues: 208.6152 Evaluate side-chains 323 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 282 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 78 LYS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 98 LEU 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 44 LYS Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 78 LEU 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 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 106 LYS Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 74 ASN 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: 10.0000 chunk 90 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN F 65 ASN G 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.089628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.063808 restraints weight = 28716.204| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.98 r_work: 0.2919 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12598 Z= 0.165 Angle : 0.666 11.392 18268 Z= 0.378 Chirality : 0.036 0.190 2084 Planarity : 0.004 0.042 1311 Dihedral : 30.792 178.639 3991 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 6.90 % Allowed : 46.63 % Favored : 46.47 % 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 aren not related in a simple way. whole: 1.16 (0.31), residues: 728 helix: 1.49 (0.23), residues: 517 sheet: None (None), residues: 0 loop : -1.00 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 31 TYR 0.038 0.002 TYR F 89 PHE 0.005 0.001 PHE B 62 HIS 0.003 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00370 (12598) covalent geometry : angle 0.66606 (18268) hydrogen bonds : bond 0.03124 ( 735) hydrogen bonds : angle 2.75295 ( 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 331 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 289 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.9092 (tppp) cc_final: 0.8707 (mmtp) REVERT: B 78 LYS cc_start: 0.9390 (OUTLIER) cc_final: 0.8861 (mmtm) REVERT: C 37 LYS cc_start: 0.9355 (mtpp) cc_final: 0.9014 (mmmt) REVERT: C 43 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8880 (ptm-80) REVERT: C 65 GLU cc_start: 0.8731 (tp30) cc_final: 0.8455 (tp30) REVERT: C 76 LYS cc_start: 0.9427 (OUTLIER) cc_final: 0.9064 (mtmm) REVERT: C 86 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9266 (mm) REVERT: D 32 LYS cc_start: 0.8211 (mmtt) cc_final: 0.7881 (mppt) REVERT: D 47 HIS cc_start: 0.8935 (OUTLIER) cc_final: 0.8683 (m-70) REVERT: D 55 LYS cc_start: 0.9095 (tppp) cc_final: 0.8879 (mmmm) REVERT: D 66 ASP cc_start: 0.9229 (t0) cc_final: 0.8983 (t0) REVERT: E 91 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8929 (mmm) REVERT: F 96 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8381 (ptp90) REVERT: H 40 TYR cc_start: 0.8607 (t80) cc_final: 0.8356 (t80) REVERT: G 74 ASN cc_start: 0.9253 (OUTLIER) cc_final: 0.8604 (t0) REVERT: G 93 GLU cc_start: 0.8582 (pm20) cc_final: 0.8345 (pm20) outliers start: 42 outliers final: 33 residues processed: 306 average time/residue: 0.6223 time to fit residues: 205.5710 Evaluate side-chains 326 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 285 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 88 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 98 LEU 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 44 LYS Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 78 LEU 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 27 ILE 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 106 LYS Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 80 ILE 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: 8.9990 chunk 17 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN C 111 ASN F 65 ASN G 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.089169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.063511 restraints weight = 28989.053| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.97 r_work: 0.2905 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12598 Z= 0.180 Angle : 0.686 11.377 18268 Z= 0.385 Chirality : 0.036 0.191 2084 Planarity : 0.004 0.048 1311 Dihedral : 30.809 178.608 3991 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 6.57 % Allowed : 46.96 % Favored : 46.47 % 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 aren not related in a simple way. whole: 1.13 (0.31), residues: 728 helix: 1.46 (0.23), residues: 517 sheet: None (None), residues: 0 loop : -1.00 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 31 TYR 0.040 0.003 TYR F 89 PHE 0.005 0.001 PHE B 62 HIS 0.004 0.001 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00409 (12598) covalent geometry : angle 0.68551 (18268) hydrogen bonds : bond 0.03179 ( 735) hydrogen bonds : angle 2.79044 ( 1825) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4955.59 seconds wall clock time: 84 minutes 58.69 seconds (5098.69 seconds total)