Starting phenix.real_space_refine on Tue Jul 29 22:34:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c9x_45375/07_2025/9c9x_45375_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c9x_45375/07_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_45375/07_2025/9c9x_45375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c9x_45375/07_2025/9c9x_45375.map" model { file = "/net/cci-nas-00/data/ceres_data/9c9x_45375/07_2025/9c9x_45375_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c9x_45375/07_2025/9c9x_45375_neut.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.029 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.68, per 1000 atoms: 0.57 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: 2.64 Conformation dependent library (CDL) restraints added in 831.7 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: 5.64 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: 4.89 Time building geometry restraints manager: 3.19 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: 0.580 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.250 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.020 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.006 0.001 HIS H 47 PHE 0.036 0.002 PHE D 68 TYR 0.049 0.003 TYR H 81 ARG 0.017 0.001 ARG F 93 Details of bonding type rmsd hydrogen bonds : bond 0.09181 ( 735) hydrogen bonds : angle 4.50698 ( 1825) covalent geometry : bond 0.00531 (12598) covalent geometry : angle 1.03222 (18268) *********************** 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 : 0.862 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: 1.2065 time to fit residues: 402.9789 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 : 0.849 ------------------------------------------------------------------------------- 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 82 optimal weight: 8.9990 chunk 74 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN C 113 GLN D 61 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 = 0.3538 r_free = 0.3538 target = 0.086416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.061054 restraints weight = 28478.807| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.92 r_work: 0.2853 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12598 Z= 0.233 Angle : 0.655 8.856 18268 Z= 0.381 Chirality : 0.038 0.190 2084 Planarity : 0.005 0.053 1311 Dihedral : 31.143 178.061 3993 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 7.72 % Allowed : 38.92 % Favored : 53.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.29), residues: 728 helix: 0.26 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -1.46 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 76 PHE 0.010 0.001 PHE D 68 TYR 0.019 0.002 TYR F 89 ARG 0.006 0.001 ARG F 93 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 735) hydrogen bonds : angle 3.04959 ( 1825) covalent geometry : bond 0.00522 (12598) covalent geometry : angle 0.65463 (18268) *********************** 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 329 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 282 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: B 78 LYS cc_start: 0.9442 (OUTLIER) cc_final: 0.8930 (mmtm) REVERT: C 105 GLN cc_start: 0.8880 (mm110) cc_final: 0.8622 (mm-40) REVERT: D 74 GLU cc_start: 0.9338 (tp30) cc_final: 0.8965 (tp30) REVERT: D 103 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8222 (mm-30) REVERT: E 132 ARG cc_start: 0.9298 (OUTLIER) cc_final: 0.9028 (mtp85) REVERT: F 96 ARG cc_start: 0.9232 (OUTLIER) cc_final: 0.8525 (ptp90) REVERT: G 74 ASN cc_start: 0.8629 (m110) cc_final: 0.8410 (t0) REVERT: G 91 ASP cc_start: 0.8788 (t0) cc_final: 0.8267 (t0) outliers start: 47 outliers final: 16 residues processed: 302 average time/residue: 1.2961 time to fit residues: 422.1710 Evaluate side-chains 283 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 264 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 B residue 66 VAL 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 C residue 102 THR Chi-restraints excluded: chain D residue 110 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 E residue 132 ARG 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 50 VAL Chi-restraints excluded: chain G residue 115 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 75 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 ASN F 65 ASN H 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.087695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.062420 restraints weight = 28491.666| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.90 r_work: 0.2888 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12598 Z= 0.168 Angle : 0.620 8.366 18268 Z= 0.362 Chirality : 0.036 0.152 2084 Planarity : 0.004 0.048 1311 Dihedral : 31.019 179.388 3991 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 6.73 % Allowed : 38.92 % Favored : 54.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.30), residues: 728 helix: 0.89 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.26 (0.39), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 76 PHE 0.008 0.001 PHE D 68 TYR 0.017 0.002 TYR F 52 ARG 0.008 0.001 ARG D 31 Details of bonding type rmsd hydrogen bonds : bond 0.03156 ( 735) hydrogen bonds : angle 2.86639 ( 1825) covalent geometry : bond 0.00371 (12598) covalent geometry : angle 0.62037 (18268) *********************** 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 342 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 301 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 98 GLU cc_start: 0.8859 (pt0) cc_final: 0.8638 (pt0) REVERT: B 60 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8997 (ttmt) REVERT: C 43 ARG cc_start: 0.9130 (ptm160) cc_final: 0.8837 (ptm-80) REVERT: C 75 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.9122 (mppt) REVERT: D 74 GLU cc_start: 0.9299 (tp30) cc_final: 0.9091 (tp30) REVERT: D 103 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8470 (mm-30) REVERT: D 106 LYS cc_start: 0.9083 (mtpp) cc_final: 0.8751 (mtmm) REVERT: F 96 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.8414 (ptp90) REVERT: H 57 MET cc_start: 0.9449 (tpp) cc_final: 0.9158 (tpp) REVERT: H 77 ARG cc_start: 0.9160 (ptp90) cc_final: 0.8754 (ptp90) REVERT: G 25 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8322 (mm-40) REVERT: G 74 ASN cc_start: 0.8638 (m110) cc_final: 0.8437 (t0) REVERT: G 91 ASP cc_start: 0.8716 (t0) cc_final: 0.8224 (t0) outliers start: 41 outliers final: 22 residues processed: 319 average time/residue: 1.6184 time to fit residues: 557.4980 Evaluate side-chains 303 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 277 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL 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 B residue 98 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 91 ASP 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 27 ILE 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 G residue 20 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 11 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN D 61 ASN E 114 HIS F 65 ASN G 105 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.089014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.063970 restraints weight = 28685.977| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.94 r_work: 0.2914 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12598 Z= 0.155 Angle : 0.613 8.620 18268 Z= 0.357 Chirality : 0.035 0.154 2084 Planarity : 0.004 0.043 1311 Dihedral : 30.899 178.966 3991 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 7.22 % Allowed : 39.24 % Favored : 53.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.31), residues: 728 helix: 1.22 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.05 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 47 PHE 0.008 0.001 PHE D 68 TYR 0.019 0.002 TYR G 58 ARG 0.008 0.000 ARG C 33 Details of bonding type rmsd hydrogen bonds : bond 0.03026 ( 735) hydrogen bonds : angle 2.76488 ( 1825) covalent geometry : bond 0.00339 (12598) covalent geometry : angle 0.61251 (18268) *********************** 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 342 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 298 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 98 GLU cc_start: 0.8743 (pt0) cc_final: 0.8371 (pt0) REVERT: B 60 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.8956 (ttmt) REVERT: B 78 LYS cc_start: 0.9390 (OUTLIER) cc_final: 0.8862 (mmtm) REVERT: B 93 ARG cc_start: 0.9026 (mmm-85) cc_final: 0.8817 (ttp80) REVERT: C 75 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.9097 (mppt) REVERT: C 86 LEU cc_start: 0.9617 (OUTLIER) cc_final: 0.9301 (mm) REVERT: D 74 GLU cc_start: 0.9278 (tp30) cc_final: 0.9015 (tp30) REVERT: D 103 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8227 (mm-30) REVERT: D 106 LYS cc_start: 0.9055 (mtpp) cc_final: 0.8615 (mtpt) REVERT: F 96 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8374 (ptp90) REVERT: G 91 ASP cc_start: 0.8705 (t0) cc_final: 0.7996 (t0) outliers start: 44 outliers final: 19 residues processed: 318 average time/residue: 1.3249 time to fit residues: 456.0155 Evaluate side-chains 302 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 278 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 97 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 102 THR 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 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 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 19 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN E 69 GLN F 65 ASN H 82 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 = 0.3588 r_free = 0.3588 target = 0.089370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.063840 restraints weight = 28433.022| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.96 r_work: 0.2921 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12598 Z= 0.158 Angle : 0.619 9.217 18268 Z= 0.359 Chirality : 0.035 0.162 2084 Planarity : 0.004 0.042 1311 Dihedral : 30.847 178.987 3991 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 6.90 % Allowed : 41.22 % Favored : 51.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.31), residues: 728 helix: 1.39 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -0.98 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 76 PHE 0.007 0.001 PHE D 68 TYR 0.023 0.002 TYR G 58 ARG 0.009 0.001 ARG D 31 Details of bonding type rmsd hydrogen bonds : bond 0.03012 ( 735) hydrogen bonds : angle 2.70116 ( 1825) covalent geometry : bond 0.00350 (12598) covalent geometry : angle 0.61885 (18268) *********************** 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 343 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 301 time to evaluate : 1.314 Fit side-chains revert: symmetry clash REVERT: A 98 GLU cc_start: 0.8747 (pt0) cc_final: 0.8459 (pt0) REVERT: B 60 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8950 (ttmt) REVERT: B 78 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.8869 (mmtm) REVERT: C 43 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8902 (ptm-80) REVERT: C 75 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.9095 (mppt) REVERT: C 86 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9263 (mm) REVERT: D 32 LYS cc_start: 0.8111 (mmtt) cc_final: 0.7660 (mppt) REVERT: D 55 LYS cc_start: 0.9102 (tppp) cc_final: 0.8887 (mmmm) REVERT: D 103 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8235 (mm-30) REVERT: D 106 LYS cc_start: 0.9047 (mtpp) cc_final: 0.8626 (mtpt) REVERT: F 32 LYS cc_start: 0.9238 (tptp) cc_final: 0.9037 (tptp) REVERT: F 96 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8333 (ptp90) REVERT: G 25 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8054 (mm-40) REVERT: G 74 ASN cc_start: 0.8790 (OUTLIER) cc_final: 0.8512 (t0) REVERT: G 91 ASP cc_start: 0.8759 (t0) cc_final: 0.8374 (t0) outliers start: 42 outliers final: 20 residues processed: 316 average time/residue: 1.7128 time to fit residues: 583.3621 Evaluate side-chains 307 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 279 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 97 THR Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 44 LYS Chi-restraints excluded: chain E residue 52 ILE 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 66 ASP Chi-restraints excluded: chain H residue 83 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 25 GLN Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 75 LYS 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 36 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 19 optimal weight: 0.2980 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 F 65 ASN G 39 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 = 0.3573 r_free = 0.3573 target = 0.088590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.063346 restraints weight = 28865.317| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.94 r_work: 0.2897 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 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 0.038 12598 Z= 0.177 Angle : 0.631 9.351 18268 Z= 0.364 Chirality : 0.036 0.171 2084 Planarity : 0.004 0.041 1311 Dihedral : 30.874 178.963 3991 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 5.75 % Allowed : 44.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.31), residues: 728 helix: 1.45 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -1.04 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 76 PHE 0.006 0.001 PHE D 68 TYR 0.025 0.002 TYR F 89 ARG 0.008 0.001 ARG D 31 Details of bonding type rmsd hydrogen bonds : bond 0.03083 ( 735) hydrogen bonds : angle 2.71939 ( 1825) covalent geometry : bond 0.00396 (12598) covalent geometry : angle 0.63080 (18268) *********************** 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 323 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 288 time to evaluate : 2.541 Fit side-chains revert: symmetry clash REVERT: A 98 GLU cc_start: 0.8759 (pt0) cc_final: 0.8465 (pt0) REVERT: B 78 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.8903 (mmtm) REVERT: C 75 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.9096 (mppt) REVERT: C 86 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9288 (mm) REVERT: D 32 LYS cc_start: 0.8126 (mmtt) cc_final: 0.7713 (mppt) REVERT: D 55 LYS cc_start: 0.9131 (tppp) cc_final: 0.8908 (mmmm) REVERT: D 103 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8288 (mm-30) REVERT: D 106 LYS cc_start: 0.9048 (mtpp) cc_final: 0.8625 (mtpt) REVERT: F 96 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8415 (ptp90) REVERT: G 74 ASN cc_start: 0.9026 (OUTLIER) cc_final: 0.8664 (t0) REVERT: G 91 ASP cc_start: 0.8833 (t0) cc_final: 0.8174 (t70) outliers start: 35 outliers final: 23 residues processed: 301 average time/residue: 1.4914 time to fit residues: 485.5229 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 : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 93 ARG Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 75 LYS 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 44 LYS 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 66 ASP Chi-restraints excluded: chain H residue 83 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 39 ASN Chi-restraints excluded: chain G residue 74 ASN 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 34 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- 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 E 69 GLN G 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.088038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.062564 restraints weight = 28841.594| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.97 r_work: 0.2887 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12598 Z= 0.185 Angle : 0.649 10.222 18268 Z= 0.371 Chirality : 0.037 0.177 2084 Planarity : 0.004 0.044 1311 Dihedral : 30.878 178.926 3991 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 6.40 % Allowed : 44.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.31), residues: 728 helix: 1.46 (0.23), residues: 517 sheet: None (None), residues: 0 loop : -1.04 (0.39), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 76 PHE 0.006 0.001 PHE D 68 TYR 0.028 0.002 TYR F 89 ARG 0.011 0.001 ARG D 31 Details of bonding type rmsd hydrogen bonds : bond 0.03131 ( 735) hydrogen bonds : angle 2.74406 ( 1825) covalent geometry : bond 0.00418 (12598) covalent geometry : angle 0.64853 (18268) *********************** 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 324 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 285 time to evaluate : 2.127 Fit side-chains revert: symmetry clash REVERT: A 98 GLU cc_start: 0.8766 (pt0) cc_final: 0.8429 (pt0) REVERT: B 60 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.8955 (ttmt) REVERT: B 78 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.8887 (mmtm) REVERT: C 43 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8877 (ptm-80) REVERT: C 75 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.9118 (mppt) REVERT: C 86 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9293 (mm) REVERT: D 32 LYS cc_start: 0.8116 (mmtt) cc_final: 0.7693 (mppt) REVERT: D 55 LYS cc_start: 0.9155 (tppp) cc_final: 0.8933 (mmmm) REVERT: D 103 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8329 (mm-30) REVERT: D 106 LYS cc_start: 0.9049 (mtpp) cc_final: 0.8618 (mtpt) REVERT: F 96 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8444 (ptp90) REVERT: G 74 ASN cc_start: 0.9113 (OUTLIER) cc_final: 0.8591 (t0) REVERT: G 91 ASP cc_start: 0.8729 (t0) cc_final: 0.8310 (t0) outliers start: 39 outliers final: 24 residues processed: 303 average time/residue: 1.6251 time to fit residues: 531.7287 Evaluate side-chains 307 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 276 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 93 ARG 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 75 LYS 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 44 LYS Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain F residue 27 ILE 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 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 74 ASN 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 81 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 E 56 GLN G 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.084101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.058553 restraints weight = 28718.905| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.92 r_work: 0.2793 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 12598 Z= 0.306 Angle : 0.723 10.629 18268 Z= 0.411 Chirality : 0.042 0.240 2084 Planarity : 0.005 0.037 1311 Dihedral : 31.219 179.402 3991 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 7.39 % Allowed : 43.84 % Favored : 48.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.31), residues: 728 helix: 1.24 (0.23), residues: 520 sheet: None (None), residues: 0 loop : -1.30 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 114 PHE 0.010 0.001 PHE C 26 TYR 0.036 0.003 TYR F 89 ARG 0.007 0.001 ARG H 77 Details of bonding type rmsd hydrogen bonds : bond 0.03801 ( 735) hydrogen bonds : angle 2.97940 ( 1825) covalent geometry : bond 0.00698 (12598) covalent geometry : angle 0.72262 (18268) *********************** 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 323 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 278 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: B 60 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.9052 (ttmt) REVERT: B 78 LYS cc_start: 0.9483 (OUTLIER) cc_final: 0.8998 (mmtm) REVERT: C 43 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8323 (ptm160) REVERT: C 86 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9320 (mm) REVERT: D 55 LYS cc_start: 0.9224 (tppp) cc_final: 0.8972 (mmmm) REVERT: D 103 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8356 (mm-30) REVERT: D 106 LYS cc_start: 0.9051 (mtpp) cc_final: 0.8573 (mtpt) REVERT: F 78 LYS cc_start: 0.9368 (mmmt) cc_final: 0.9119 (mtpp) REVERT: F 96 ARG cc_start: 0.9273 (OUTLIER) cc_final: 0.8564 (ptp90) REVERT: G 21 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7958 (mtp85) REVERT: G 74 ASN cc_start: 0.9094 (OUTLIER) cc_final: 0.8514 (t0) REVERT: G 91 ASP cc_start: 0.8824 (t0) cc_final: 0.8409 (t0) outliers start: 45 outliers final: 30 residues processed: 297 average time/residue: 1.3004 time to fit residues: 415.2796 Evaluate side-chains 301 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 264 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 130 ARG 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 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 75 LYS Chi-restraints excluded: chain C residue 86 LEU 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 44 LYS Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 83 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 H residue 46 VAL Chi-restraints excluded: chain H residue 64 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 17 THR Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 21 ARG Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 80 ILE 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 21 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN H 107 HIS G 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.086111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.060792 restraints weight = 28711.616| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.91 r_work: 0.2842 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12598 Z= 0.196 Angle : 0.689 10.000 18268 Z= 0.392 Chirality : 0.038 0.198 2084 Planarity : 0.004 0.039 1311 Dihedral : 31.038 179.211 3991 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 6.40 % Allowed : 45.65 % Favored : 47.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.31), residues: 728 helix: 1.37 (0.23), residues: 515 sheet: None (None), residues: 0 loop : -1.20 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS H 107 PHE 0.007 0.001 PHE D 68 TYR 0.032 0.003 TYR G 58 ARG 0.007 0.001 ARG H 77 Details of bonding type rmsd hydrogen bonds : bond 0.03326 ( 735) hydrogen bonds : angle 2.88551 ( 1825) covalent geometry : bond 0.00447 (12598) covalent geometry : angle 0.68897 (18268) *********************** 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 324 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 285 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 60 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.8889 (ttmt) REVERT: B 78 LYS cc_start: 0.9451 (OUTLIER) cc_final: 0.8913 (mmtm) REVERT: C 43 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8313 (ptm160) REVERT: C 75 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.9126 (mppt) REVERT: C 86 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9321 (mm) REVERT: D 55 LYS cc_start: 0.9188 (tppp) cc_final: 0.8951 (mmmm) REVERT: D 106 LYS cc_start: 0.9032 (mtpp) cc_final: 0.8805 (mtpp) REVERT: F 96 ARG cc_start: 0.9246 (OUTLIER) cc_final: 0.8526 (ptp90) REVERT: G 74 ASN cc_start: 0.9156 (OUTLIER) cc_final: 0.8595 (t0) outliers start: 39 outliers final: 22 residues processed: 306 average time/residue: 1.2406 time to fit residues: 410.1958 Evaluate side-chains 304 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 275 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 130 ARG 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 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 75 LYS 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 D residue 44 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 96 ARG Chi-restraints excluded: chain F residue 97 THR 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 G residue 17 THR Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 80 ILE 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 81 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.084988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.059575 restraints weight = 28484.674| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.90 r_work: 0.2818 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 12598 Z= 0.253 Angle : 0.722 12.325 18268 Z= 0.409 Chirality : 0.040 0.216 2084 Planarity : 0.004 0.038 1311 Dihedral : 31.129 179.090 3991 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.75 % Allowed : 47.13 % Favored : 47.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.31), residues: 728 helix: 1.32 (0.23), residues: 520 sheet: None (None), residues: 0 loop : -1.29 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS H 107 PHE 0.007 0.001 PHE C 26 TYR 0.038 0.003 TYR F 89 ARG 0.008 0.001 ARG D 31 Details of bonding type rmsd hydrogen bonds : bond 0.03552 ( 735) hydrogen bonds : angle 2.92338 ( 1825) covalent geometry : bond 0.00580 (12598) covalent geometry : angle 0.72232 (18268) ********************** 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 309 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 274 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 60 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8998 (ttmt) REVERT: B 78 LYS cc_start: 0.9479 (OUTLIER) cc_final: 0.8988 (mmtm) REVERT: C 43 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.8354 (ptm160) REVERT: C 86 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9318 (mm) REVERT: D 55 LYS cc_start: 0.9173 (tppp) cc_final: 0.8943 (mmmm) REVERT: D 103 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8684 (mm-30) REVERT: D 106 LYS cc_start: 0.9068 (mtpp) cc_final: 0.8864 (mtmm) REVERT: F 96 ARG cc_start: 0.9240 (OUTLIER) cc_final: 0.8528 (ptp90) REVERT: G 21 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7782 (mtp85) REVERT: G 74 ASN cc_start: 0.9158 (OUTLIER) cc_final: 0.8581 (t0) outliers start: 35 outliers final: 25 residues processed: 289 average time/residue: 1.2362 time to fit residues: 385.0888 Evaluate side-chains 300 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 268 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 A residue 130 ARG 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 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 75 LYS 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 D residue 44 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 96 ARG Chi-restraints excluded: chain F residue 97 THR 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 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 74 ASN Chi-restraints excluded: chain G residue 80 ILE 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 14 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN E 69 GLN H 107 HIS G 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.085557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.060251 restraints weight = 28772.108| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.91 r_work: 0.2828 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12598 Z= 0.220 Angle : 0.720 12.328 18268 Z= 0.405 Chirality : 0.039 0.203 2084 Planarity : 0.004 0.039 1311 Dihedral : 31.104 179.068 3991 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 5.75 % Allowed : 47.45 % Favored : 46.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.31), residues: 728 helix: 1.34 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -1.26 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS H 107 PHE 0.006 0.001 PHE D 68 TYR 0.039 0.003 TYR F 89 ARG 0.008 0.001 ARG D 31 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 735) hydrogen bonds : angle 2.90376 ( 1825) covalent geometry : bond 0.00504 (12598) covalent geometry : angle 0.71989 (18268) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10122.36 seconds wall clock time: 182 minutes 46.48 seconds (10966.48 seconds total)