Starting phenix.real_space_refine on Wed Aug 5 22:52:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cau_45404/08_2026/9cau_45404_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cau_45404/08_2026/9cau_45404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cau_45404/08_2026/9cau_45404_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cau_45404/08_2026/9cau_45404_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cau_45404/08_2026/9cau_45404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cau_45404/08_2026/9cau_45404.map" } resolution = 4.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 292 5.49 5 S 4 5.16 5 C 6589 2.51 5 N 2240 2.21 5 O 2824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11949 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "B" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} 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: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} 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: "G" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3010 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2976 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LEU B 23 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU B 23 " occ=0.00 residue: pdb=" N ARG B 24 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG B 24 " occ=0.00 Time building chain proxies: 2.19, per 1000 atoms: 0.18 Number of scatterers: 11949 At special positions: 0 Unit cell: (117.103, 99.0869, 144.126, 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 4 16.00 P 292 15.00 O 2824 8.00 N 2240 7.00 C 6589 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: 0.61 Conformation dependent library (CDL) restraints added in 190.7 milliseconds 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1412 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 7 sheets defined 69.2% alpha, 1.9% beta 143 base pairs and 256 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.502A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.877A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.521A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 43 removed outlier: 3.612A pdb=" N ILE B 35 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 77 removed outlier: 4.359A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASP B 69 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 removed outlier: 4.275A pdb=" N VAL B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.200A pdb=" N VAL C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 removed outlier: 3.625A pdb=" N ASN C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'D' and resid 40 through 52 Processing helix chain 'D' and resid 58 through 87 removed outlier: 3.638A pdb=" N ASN D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 105 removed outlier: 4.099A pdb=" N ILE D 97 " --> pdb=" O SER D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 127 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.720A pdb=" N ILE E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 31 through 43 Processing helix chain 'F' and resid 50 through 77 removed outlier: 4.467A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLU F 64 " --> pdb=" O LYS F 60 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN F 65 " --> pdb=" O VAL F 61 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL F 66 " --> pdb=" O PHE F 62 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR F 72 " --> pdb=" O ARG F 68 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR F 73 " --> pdb=" O ASP F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 4.067A pdb=" N VAL F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.212A pdb=" N VAL G 50 " --> pdb=" O SER G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 90 Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'H' and resid 40 through 50 Processing helix chain 'H' and resid 58 through 88 removed outlier: 3.503A pdb=" N ASN H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 105 removed outlier: 3.660A pdb=" N ILE H 97 " --> pdb=" O SER H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 126 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.977A pdb=" N ARG A 83 " --> 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 118 through 119 Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 44 removed outlier: 6.577A pdb=" N ARG C 43 " --> pdb=" O ILE D 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.135A pdb=" N ARG G 43 " --> pdb=" O ILE H 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 78 through 79 373 hydrogen bonds defined for protein. 1119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 256 stacking parallelities Total time for adding SS restraints: 1.42 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2065 1.33 - 1.45: 4512 1.45 - 1.58: 5588 1.58 - 1.70: 582 1.70 - 1.82: 8 Bond restraints: 12755 Sorted by residual: bond pdb=" C1' DC I 37 " pdb=" N1 DC I 37 " ideal model delta sigma weight residual 1.468 1.530 -0.062 1.40e-02 5.10e+03 1.95e+01 bond pdb=" C1' DT I -61 " pdb=" N1 DT I -61 " ideal model delta sigma weight residual 1.468 1.529 -0.061 1.40e-02 5.10e+03 1.93e+01 bond pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " ideal model delta sigma weight residual 1.435 1.487 -0.052 1.30e-02 5.92e+03 1.58e+01 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.435 1.485 -0.050 1.30e-02 5.92e+03 1.47e+01 bond pdb=" C1' DC J 49 " pdb=" N1 DC J 49 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.28e+01 ... (remaining 12750 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 18104 3.06 - 6.12: 320 6.12 - 9.17: 38 9.17 - 12.23: 10 12.23 - 15.29: 5 Bond angle restraints: 18477 Sorted by residual: angle pdb=" N GLY H 107 " pdb=" CA GLY H 107 " pdb=" C GLY H 107 " ideal model delta sigma weight residual 112.73 119.89 -7.16 1.20e+00 6.94e-01 3.56e+01 angle pdb=" CB GLN A 93 " pdb=" CG GLN A 93 " pdb=" CD GLN A 93 " ideal model delta sigma weight residual 112.60 102.95 9.65 1.70e+00 3.46e-01 3.22e+01 angle pdb=" C GLY D 107 " pdb=" N GLU D 108 " pdb=" CA GLU D 108 " ideal model delta sigma weight residual 121.54 132.17 -10.63 1.91e+00 2.74e-01 3.10e+01 angle pdb=" N GLU B 64 " pdb=" CA GLU B 64 " pdb=" CB GLU B 64 " ideal model delta sigma weight residual 110.30 118.72 -8.42 1.54e+00 4.22e-01 2.99e+01 angle pdb=" C THR A 80 " pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta sigma weight residual 121.54 131.80 -10.26 1.91e+00 2.74e-01 2.89e+01 ... (remaining 18472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 5450 35.72 - 71.44: 1432 71.44 - 107.16: 28 107.16 - 142.88: 0 142.88 - 178.60: 3 Dihedral angle restraints: 6913 sinusoidal: 4727 harmonic: 2186 Sorted by residual: 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 -151.00 -29.00 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA ASN B 65 " pdb=" C ASN B 65 " pdb=" N VAL B 66 " pdb=" CA VAL B 66 " ideal model delta harmonic sigma weight residual 180.00 154.38 25.62 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA LYS B 80 " pdb=" C LYS B 80 " pdb=" N THR B 81 " pdb=" CA THR B 81 " ideal model delta harmonic sigma weight residual 180.00 154.68 25.32 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 6910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1461 0.053 - 0.106: 499 0.106 - 0.159: 115 0.159 - 0.212: 25 0.212 - 0.265: 5 Chirality restraints: 2105 Sorted by residual: chirality pdb=" CB VAL A 96 " pdb=" CA VAL A 96 " pdb=" CG1 VAL A 96 " pdb=" CG2 VAL A 96 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CG LEU H 105 " pdb=" CB LEU H 105 " pdb=" CD1 LEU H 105 " pdb=" CD2 LEU H 105 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB THR H 118 " pdb=" CA THR H 118 " pdb=" OG1 THR H 118 " pdb=" CG2 THR H 118 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 2102 not shown) Planarity restraints: 1327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 67 " -0.010 2.00e-02 2.50e+03 2.78e-02 1.35e+01 pdb=" CG PHE A 67 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 67 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE A 67 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 PHE A 67 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 67 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 67 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 89 " 0.024 2.00e-02 2.50e+03 2.34e-02 1.10e+01 pdb=" CG TYR B 89 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR B 89 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 89 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR B 89 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 89 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 89 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 89 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 73 " -0.013 2.00e-02 2.50e+03 2.42e-02 1.03e+01 pdb=" CG PHE H 73 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE H 73 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE H 73 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 PHE H 73 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE H 73 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE H 73 " 0.001 2.00e-02 2.50e+03 ... (remaining 1324 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.86: 3493 2.86 - 3.37: 10831 3.37 - 3.88: 24645 3.88 - 4.39: 27217 4.39 - 4.90: 37204 Nonbonded interactions: 103390 Sorted by model distance: nonbonded pdb=" NH1 ARG C 33 " pdb=" OP1 DA J -44 " model vdw 2.345 3.120 nonbonded pdb=" O HIS B 76 " pdb=" NH1 ARG D 95 " model vdw 2.356 3.120 nonbonded pdb=" OE1 GLU A 73 " pdb=" ND2 ASN B 26 " model vdw 2.360 3.120 nonbonded pdb=" OH TYR E 99 " pdb=" OE2 GLU E 133 " model vdw 2.364 3.040 nonbonded pdb=" OH TYR D 43 " pdb=" OP1 DG I 48 " model vdw 2.371 3.040 ... (remaining 103385 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' selection = chain 'E' } 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 62 or (resid 63 and (name N or name CA or name \ C or name O or name CB )) or resid 64 through 87 or (resid 88 and (name N or nam \ e CA or name C or name O or name CB )) or resid 89 through 120)) selection = (chain 'G' and resid 16 through 120) } ncs_group { reference = chain 'D' selection = chain 'H' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 6.210 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.390 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 12755 Z= 0.566 Angle : 1.134 15.291 18477 Z= 0.841 Chirality : 0.057 0.265 2105 Planarity : 0.008 0.071 1327 Dihedral : 29.098 178.598 5501 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.26), residues: 738 helix: -1.61 (0.19), residues: 508 sheet: None (None), residues: 0 loop : -1.51 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 89 TYR 0.058 0.004 TYR B 89 PHE 0.058 0.004 PHE A 67 HIS 0.013 0.002 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00692 / 0.57 (12755) covalent geometry : angle 1.13423 / 0.84 (18477) hydrogen bonds : bond 0.10902 / 7.56 ( 741) hydrogen bonds : angle 5.14104 / 3.56 ( 1855) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.6691 (mmm160) cc_final: 0.5256 (ttp80) REVERT: A 50 GLU cc_start: 0.8394 (pp20) cc_final: 0.8137 (pp20) REVERT: A 56 LYS cc_start: 0.8486 (tptp) cc_final: 0.8276 (tmtt) REVERT: A 58 THR cc_start: 0.7629 (m) cc_final: 0.7251 (t) REVERT: A 94 GLU cc_start: 0.8386 (tt0) cc_final: 0.7676 (tt0) REVERT: A 105 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8182 (tm-30) REVERT: A 131 ARG cc_start: 0.8530 (mmm-85) cc_final: 0.8257 (mmm-85) REVERT: B 51 ILE cc_start: 0.8407 (mm) cc_final: 0.7765 (mt) REVERT: B 80 LYS cc_start: 0.8726 (pttm) cc_final: 0.7951 (ttmm) REVERT: B 85 MET cc_start: 0.8177 (mmm) cc_final: 0.7312 (tpp) REVERT: C 37 ARG cc_start: 0.8238 (ptp90) cc_final: 0.8034 (ptp90) REVERT: C 42 GLN cc_start: 0.7677 (pp30) cc_final: 0.7301 (pp30) REVERT: C 46 SER cc_start: 0.8773 (p) cc_final: 0.8523 (m) REVERT: C 111 ASN cc_start: 0.8685 (m110) cc_final: 0.8419 (m110) REVERT: D 71 ASP cc_start: 0.9022 (t70) cc_final: 0.8668 (t0) REVERT: D 124 TYR cc_start: 0.8874 (t80) cc_final: 0.8621 (t80) REVERT: E 46 VAL cc_start: 0.6430 (m) cc_final: 0.6203 (m) REVERT: E 59 GLU cc_start: 0.8561 (tp30) cc_final: 0.7884 (pp20) REVERT: E 60 LEU cc_start: 0.8836 (mt) cc_final: 0.8406 (mm) REVERT: E 61 LEU cc_start: 0.8695 (mt) cc_final: 0.8263 (mt) REVERT: E 65 LEU cc_start: 0.9077 (tt) cc_final: 0.8671 (tp) REVERT: E 74 ILE cc_start: 0.9038 (tt) cc_final: 0.8426 (mm) REVERT: E 78 PHE cc_start: 0.7821 (m-10) cc_final: 0.7047 (m-10) REVERT: E 121 LYS cc_start: 0.8932 (ptmm) cc_final: 0.8672 (ptmt) REVERT: F 27 ILE cc_start: 0.7599 (mm) cc_final: 0.7082 (mp) REVERT: F 50 LEU cc_start: 0.9035 (pt) cc_final: 0.8570 (tp) REVERT: F 63 LEU cc_start: 0.9215 (pp) cc_final: 0.8880 (mp) REVERT: F 68 ARG cc_start: 0.8712 (mtm110) cc_final: 0.8489 (mtm-85) REVERT: G 21 LYS cc_start: 0.8733 (tmtt) cc_final: 0.8196 (tptt) REVERT: G 57 GLU cc_start: 0.8197 (tt0) cc_final: 0.7858 (tt0) REVERT: G 69 ASN cc_start: 0.8717 (m-40) cc_final: 0.8441 (m-40) REVERT: G 86 LEU cc_start: 0.9019 (mt) cc_final: 0.8655 (mt) REVERT: G 93 GLU cc_start: 0.8110 (pt0) cc_final: 0.7604 (pt0) REVERT: G 95 ASN cc_start: 0.8660 (m-40) cc_final: 0.8188 (m110) REVERT: G 98 LEU cc_start: 0.9250 (mm) cc_final: 0.8998 (mm) REVERT: G 103 ILE cc_start: 0.9117 (mp) cc_final: 0.8875 (pt) REVERT: G 115 ASN cc_start: 0.7625 (t0) cc_final: 0.7370 (t0) REVERT: H 55 THR cc_start: 0.8821 (m) cc_final: 0.8424 (m) REVERT: H 71 ASP cc_start: 0.8998 (t70) cc_final: 0.8518 (t0) REVERT: H 79 GLU cc_start: 0.9136 (tm-30) cc_final: 0.8917 (tm-30) REVERT: H 112 HIS cc_start: 0.8691 (m170) cc_final: 0.8134 (m90) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.1342 time to fit residues: 57.0792 Evaluate side-chains 215 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.0970 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 76 HIS ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 HIS E 68 GLN E 108 ASN ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.077579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.055703 restraints weight = 66980.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.056728 restraints weight = 37059.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.057421 restraints weight = 26263.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.057857 restraints weight = 21676.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.058064 restraints weight = 19526.645| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12755 Z= 0.166 Angle : 0.729 9.937 18477 Z= 0.420 Chirality : 0.049 0.258 2105 Planarity : 0.006 0.060 1327 Dihedral : 32.160 178.923 4019 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.48 % Allowed : 4.62 % Favored : 94.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.29), residues: 738 helix: -0.24 (0.21), residues: 517 sheet: None (None), residues: 0 loop : -1.27 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 131 TYR 0.038 0.002 TYR H 86 PHE 0.021 0.002 PHE E 104 HIS 0.009 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.17 (12755) covalent geometry : angle 0.72867 / 0.42 (18477) hydrogen bonds : bond 0.04761 / 3.15 ( 741) hydrogen bonds : angle 3.64358 / 2.58 ( 1855) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 260 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.6372 (mmm160) cc_final: 0.4484 (ttp80) REVERT: A 45 THR cc_start: 0.8367 (t) cc_final: 0.8048 (t) REVERT: A 59 GLU cc_start: 0.7210 (mp0) cc_final: 0.6937 (mp0) REVERT: A 73 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7240 (mt-10) REVERT: A 105 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7810 (tm-30) REVERT: B 80 LYS cc_start: 0.8527 (pttm) cc_final: 0.7744 (ttmm) REVERT: B 85 MET cc_start: 0.7574 (mmm) cc_final: 0.7217 (tpt) REVERT: C 42 GLN cc_start: 0.7543 (pp30) cc_final: 0.6905 (pp30) REVERT: C 69 ASN cc_start: 0.8778 (m110) cc_final: 0.8567 (m110) REVERT: D 51 THR cc_start: 0.8623 (t) cc_final: 0.8374 (t) REVERT: D 74 GLU cc_start: 0.8653 (pt0) cc_final: 0.8424 (pt0) REVERT: D 119 ARG cc_start: 0.8827 (tmm160) cc_final: 0.8594 (ttp80) REVERT: E 95 SER cc_start: 0.9600 (t) cc_final: 0.9206 (p) REVERT: E 105 GLU cc_start: 0.8748 (tt0) cc_final: 0.8274 (tp30) REVERT: E 121 LYS cc_start: 0.9069 (ptmm) cc_final: 0.8854 (ptmt) REVERT: F 45 LYS cc_start: 0.8979 (mtpt) cc_final: 0.8771 (mtpp) REVERT: F 50 LEU cc_start: 0.8698 (pt) cc_final: 0.8477 (tp) REVERT: G 21 LYS cc_start: 0.8900 (tmtt) cc_final: 0.8572 (tptt) REVERT: G 74 ASN cc_start: 0.8885 (t0) cc_final: 0.8634 (t0) REVERT: G 93 GLU cc_start: 0.7512 (pt0) cc_final: 0.6836 (pt0) REVERT: H 48 LEU cc_start: 0.9335 (pt) cc_final: 0.9041 (pt) REVERT: H 82 LYS cc_start: 0.9022 (ttmm) cc_final: 0.8775 (tptp) outliers start: 3 outliers final: 0 residues processed: 261 average time/residue: 0.1225 time to fit residues: 41.9972 Evaluate side-chains 196 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 75 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 89 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN G 42 GLN H 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.075501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.053061 restraints weight = 67003.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.054096 restraints weight = 36942.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.054775 restraints weight = 26141.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.055142 restraints weight = 21605.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.055414 restraints weight = 19654.166| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12755 Z= 0.182 Angle : 0.686 8.006 18477 Z= 0.400 Chirality : 0.047 0.273 2105 Planarity : 0.005 0.062 1327 Dihedral : 31.978 177.861 4019 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.64 % Allowed : 5.41 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.30), residues: 738 helix: 0.60 (0.22), residues: 512 sheet: None (None), residues: 0 loop : -1.29 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 69 TYR 0.042 0.003 TYR B 89 PHE 0.014 0.002 PHE H 73 HIS 0.008 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.18 (12755) covalent geometry : angle 0.68649 / 0.40 (18477) hydrogen bonds : bond 0.05085 / 3.37 ( 741) hydrogen bonds : angle 3.30329 / 2.34 ( 1855) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 240 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7685 (mp0) cc_final: 0.7462 (mp0) REVERT: A 94 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7643 (tt0) REVERT: A 105 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7722 (tm-30) REVERT: B 80 LYS cc_start: 0.8696 (pttm) cc_final: 0.7806 (ttmm) REVERT: B 89 TYR cc_start: 0.8161 (m-80) cc_final: 0.7296 (m-80) REVERT: C 69 ASN cc_start: 0.8821 (m110) cc_final: 0.8598 (m110) REVERT: D 38 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7244 (pt0) REVERT: D 86 TYR cc_start: 0.8573 (m-80) cc_final: 0.8060 (m-80) REVERT: D 109 LEU cc_start: 0.9067 (mp) cc_final: 0.8438 (mt) REVERT: D 119 ARG cc_start: 0.8935 (tmm160) cc_final: 0.8673 (ttp80) REVERT: E 105 GLU cc_start: 0.8772 (tt0) cc_final: 0.8319 (tp30) REVERT: F 40 ARG cc_start: 0.8876 (mmt90) cc_final: 0.8665 (tpp80) REVERT: F 45 LYS cc_start: 0.9130 (mtpt) cc_final: 0.8917 (mtpp) REVERT: F 68 ARG cc_start: 0.8517 (mtm-85) cc_final: 0.8031 (mtm-85) REVERT: G 21 LYS cc_start: 0.8986 (tmtt) cc_final: 0.8600 (tptt) REVERT: G 74 ASN cc_start: 0.8981 (t0) cc_final: 0.8551 (t0) REVERT: G 91 ASP cc_start: 0.9096 (t0) cc_final: 0.8811 (t0) REVERT: G 93 GLU cc_start: 0.7582 (pt0) cc_final: 0.6714 (pt0) outliers start: 4 outliers final: 2 residues processed: 242 average time/residue: 0.1238 time to fit residues: 39.7208 Evaluate side-chains 183 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 181 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 5 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 0.0270 chunk 72 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 14 optimal weight: 4.9990 overall best weight: 0.6642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 HIS E 68 GLN E 108 ASN ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.075918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.053814 restraints weight = 66183.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.054822 restraints weight = 36108.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.055484 restraints weight = 25458.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.055893 restraints weight = 21038.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.056079 restraints weight = 18991.974| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12755 Z= 0.152 Angle : 0.651 9.215 18477 Z= 0.380 Chirality : 0.045 0.266 2105 Planarity : 0.005 0.057 1327 Dihedral : 31.906 179.235 4019 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.16 % Allowed : 4.14 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.30), residues: 738 helix: 0.96 (0.22), residues: 512 sheet: None (None), residues: 0 loop : -1.21 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 49 TYR 0.042 0.002 TYR H 86 PHE 0.019 0.002 PHE B 101 HIS 0.012 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (12755) covalent geometry : angle 0.65150 / 0.38 (18477) hydrogen bonds : bond 0.04219 / 2.77 ( 741) hydrogen bonds : angle 3.17729 / 2.25 ( 1855) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7646 (mp0) cc_final: 0.7444 (mp0) REVERT: A 105 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7799 (tm-30) REVERT: B 64 GLU cc_start: 0.8759 (pm20) cc_final: 0.8514 (mp0) REVERT: B 80 LYS cc_start: 0.8743 (pttm) cc_final: 0.7828 (ttmm) REVERT: B 89 TYR cc_start: 0.8206 (m-80) cc_final: 0.7958 (m-80) REVERT: D 38 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7232 (pt0) REVERT: D 119 ARG cc_start: 0.8946 (tmm160) cc_final: 0.8671 (ttp80) REVERT: E 77 ASP cc_start: 0.8800 (p0) cc_final: 0.8471 (p0) REVERT: E 95 SER cc_start: 0.9635 (t) cc_final: 0.9264 (p) REVERT: E 105 GLU cc_start: 0.8786 (tt0) cc_final: 0.8203 (tp30) REVERT: F 40 ARG cc_start: 0.8819 (mmt90) cc_final: 0.8495 (tpp80) REVERT: F 45 LYS cc_start: 0.9111 (mtpt) cc_final: 0.8850 (mttp) REVERT: F 50 LEU cc_start: 0.8988 (tp) cc_final: 0.8702 (tp) REVERT: G 21 LYS cc_start: 0.8999 (tmtt) cc_final: 0.8585 (tptt) REVERT: G 74 ASN cc_start: 0.8899 (t0) cc_final: 0.8550 (t0) REVERT: G 91 ASP cc_start: 0.8987 (t0) cc_final: 0.8716 (t0) REVERT: G 93 GLU cc_start: 0.7470 (pt0) cc_final: 0.6701 (pt0) REVERT: H 50 GLN cc_start: 0.8910 (pt0) cc_final: 0.8699 (pp30) REVERT: H 79 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8733 (tp30) REVERT: H 102 ARG cc_start: 0.8794 (mtm-85) cc_final: 0.8564 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 234 average time/residue: 0.1138 time to fit residues: 35.5970 Evaluate side-chains 176 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 4 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 84 optimal weight: 50.0000 chunk 75 optimal weight: 10.0000 chunk 50 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 HIS ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 HIS E 68 GLN F 94 GLN G 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.075225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.052894 restraints weight = 65684.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.053854 restraints weight = 36031.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.054499 restraints weight = 25595.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.054909 restraints weight = 21368.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.055007 restraints weight = 19374.311| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12755 Z= 0.162 Angle : 0.660 8.232 18477 Z= 0.381 Chirality : 0.045 0.268 2105 Planarity : 0.005 0.060 1327 Dihedral : 31.861 178.957 4019 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.30), residues: 738 helix: 1.04 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -1.22 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 72 TYR 0.023 0.002 TYR D 86 PHE 0.013 0.002 PHE A 104 HIS 0.008 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.16 (12755) covalent geometry : angle 0.65980 / 0.38 (18477) hydrogen bonds : bond 0.04408 / 2.90 ( 741) hydrogen bonds : angle 3.19713 / 2.26 ( 1855) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7703 (mp0) cc_final: 0.7501 (mp0) REVERT: A 105 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7914 (tm-30) REVERT: B 64 GLU cc_start: 0.8835 (pm20) cc_final: 0.8541 (pm20) REVERT: B 80 LYS cc_start: 0.8714 (pttm) cc_final: 0.7880 (ttmm) REVERT: D 38 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7167 (pt0) REVERT: D 82 LYS cc_start: 0.8952 (mtmm) cc_final: 0.8442 (mttp) REVERT: D 86 TYR cc_start: 0.8464 (m-80) cc_final: 0.7811 (m-80) REVERT: E 95 SER cc_start: 0.9672 (t) cc_final: 0.9302 (p) REVERT: E 105 GLU cc_start: 0.8810 (tt0) cc_final: 0.8201 (tp30) REVERT: F 40 ARG cc_start: 0.8865 (mmt90) cc_final: 0.8638 (tpp80) REVERT: F 45 LYS cc_start: 0.9145 (mtpt) cc_final: 0.8901 (mttp) REVERT: G 21 LYS cc_start: 0.9086 (tttt) cc_final: 0.8688 (tptt) REVERT: G 74 ASN cc_start: 0.8971 (t0) cc_final: 0.8579 (t0) REVERT: G 82 ARG cc_start: 0.8671 (tpp80) cc_final: 0.8336 (tpp80) REVERT: G 91 ASP cc_start: 0.8950 (t0) cc_final: 0.8728 (t0) REVERT: G 93 GLU cc_start: 0.7534 (pt0) cc_final: 0.6765 (pt0) REVERT: H 36 ARG cc_start: 0.7059 (tpp-160) cc_final: 0.5914 (tpp80) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.1173 time to fit residues: 33.1937 Evaluate side-chains 176 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 41 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN C 113 HIS ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 HIS E 68 GLN ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 GLN H 87 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.075590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.053298 restraints weight = 65374.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.054248 restraints weight = 35303.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.054915 restraints weight = 24903.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.055295 restraints weight = 20610.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.055516 restraints weight = 18723.401| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12755 Z= 0.143 Angle : 0.641 9.587 18477 Z= 0.370 Chirality : 0.044 0.266 2105 Planarity : 0.005 0.058 1327 Dihedral : 31.768 179.564 4019 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.16 % Allowed : 2.55 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.31), residues: 738 helix: 1.16 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -1.11 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 68 TYR 0.023 0.002 TYR D 86 PHE 0.015 0.002 PHE C 26 HIS 0.011 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 (12755) covalent geometry : angle 0.64095 / 0.37 (18477) hydrogen bonds : bond 0.03947 / 2.57 ( 741) hydrogen bonds : angle 3.15252 / 2.23 ( 1855) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 213 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7737 (mp0) cc_final: 0.7530 (mp0) REVERT: A 105 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7918 (tm-30) REVERT: B 80 LYS cc_start: 0.8727 (pttm) cc_final: 0.7835 (ttmm) REVERT: D 38 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7147 (pt0) REVERT: D 86 TYR cc_start: 0.8561 (m-80) cc_final: 0.7777 (m-80) REVERT: E 105 GLU cc_start: 0.8789 (tt0) cc_final: 0.8176 (tp30) REVERT: F 40 ARG cc_start: 0.8837 (mmt90) cc_final: 0.8609 (tpp80) REVERT: F 45 LYS cc_start: 0.9153 (mtpt) cc_final: 0.8917 (mttp) REVERT: F 68 ARG cc_start: 0.8498 (mtm-85) cc_final: 0.8280 (mtm110) REVERT: G 21 LYS cc_start: 0.9059 (tttt) cc_final: 0.8636 (tptt) REVERT: G 74 ASN cc_start: 0.8903 (t0) cc_final: 0.8643 (t0) REVERT: G 82 ARG cc_start: 0.8621 (tpp80) cc_final: 0.8324 (tpp80) REVERT: G 93 GLU cc_start: 0.7670 (pt0) cc_final: 0.6743 (pt0) REVERT: G 96 LYS cc_start: 0.9198 (tppt) cc_final: 0.8880 (mmmt) REVERT: H 36 ARG cc_start: 0.6983 (tpp-160) cc_final: 0.6576 (tpp80) outliers start: 1 outliers final: 0 residues processed: 213 average time/residue: 0.1092 time to fit residues: 30.9545 Evaluate side-chains 179 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 52 optimal weight: 0.0000 chunk 70 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN C 113 HIS ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 94 GLN G 32 HIS G 114 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.075648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.053364 restraints weight = 65311.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.054277 restraints weight = 35940.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.054921 restraints weight = 25682.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.055299 restraints weight = 21501.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.055496 restraints weight = 19606.370| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12755 Z= 0.142 Angle : 0.640 8.324 18477 Z= 0.370 Chirality : 0.043 0.267 2105 Planarity : 0.005 0.058 1327 Dihedral : 31.720 179.664 4019 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.16 % Allowed : 2.71 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.31), residues: 738 helix: 1.19 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.07 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 33 TYR 0.025 0.002 TYR B 89 PHE 0.013 0.002 PHE E 54 HIS 0.008 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (12755) covalent geometry : angle 0.64040 / 0.37 (18477) hydrogen bonds : bond 0.03950 / 2.59 ( 741) hydrogen bonds : angle 3.13661 / 2.21 ( 1855) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7756 (mp0) cc_final: 0.7541 (mp0) REVERT: A 105 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7902 (tm-30) REVERT: B 80 LYS cc_start: 0.8710 (pttm) cc_final: 0.7859 (ttmm) REVERT: B 89 TYR cc_start: 0.8096 (m-80) cc_final: 0.7079 (m-80) REVERT: D 38 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7112 (pt0) REVERT: D 86 TYR cc_start: 0.8609 (m-80) cc_final: 0.7682 (m-80) REVERT: E 105 GLU cc_start: 0.8806 (tt0) cc_final: 0.8191 (tp30) REVERT: F 40 ARG cc_start: 0.8809 (mmt90) cc_final: 0.8587 (tpp80) REVERT: F 45 LYS cc_start: 0.9134 (mtpt) cc_final: 0.8900 (mttp) REVERT: G 21 LYS cc_start: 0.9077 (tttt) cc_final: 0.8710 (tptt) REVERT: G 74 ASN cc_start: 0.8913 (t0) cc_final: 0.8627 (t0) REVERT: G 82 ARG cc_start: 0.8560 (tpp80) cc_final: 0.8194 (tpp80) REVERT: G 93 GLU cc_start: 0.7777 (pt0) cc_final: 0.6955 (pt0) REVERT: G 96 LYS cc_start: 0.9245 (tppt) cc_final: 0.8939 (mmmt) REVERT: H 36 ARG cc_start: 0.7219 (tpp-160) cc_final: 0.6023 (tpp80) REVERT: H 50 GLN cc_start: 0.8857 (pt0) cc_final: 0.8553 (pp30) outliers start: 1 outliers final: 0 residues processed: 214 average time/residue: 0.1304 time to fit residues: 36.6515 Evaluate side-chains 176 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 31 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 86 optimal weight: 30.0000 chunk 94 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 85 optimal weight: 40.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN C 113 HIS D 50 GLN E 68 GLN ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 GLN G 32 HIS H 87 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.075232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.052915 restraints weight = 65431.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.053807 restraints weight = 36157.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.054448 restraints weight = 25787.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.054819 restraints weight = 21564.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.055020 restraints weight = 19715.167| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12755 Z= 0.156 Angle : 0.666 9.152 18477 Z= 0.378 Chirality : 0.044 0.270 2105 Planarity : 0.005 0.058 1327 Dihedral : 31.711 179.584 4019 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.32 % Allowed : 1.91 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.31), residues: 738 helix: 1.24 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.09 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 68 TYR 0.022 0.002 TYR B 89 PHE 0.013 0.002 PHE C 26 HIS 0.012 0.002 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.16 (12755) covalent geometry : angle 0.66605 / 0.38 (18477) hydrogen bonds : bond 0.04090 / 2.69 ( 741) hydrogen bonds : angle 3.10628 / 2.20 ( 1855) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 212 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7899 (tm-30) REVERT: B 80 LYS cc_start: 0.8718 (pttm) cc_final: 0.7844 (ttmm) REVERT: D 38 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7126 (pt0) REVERT: D 82 LYS cc_start: 0.8919 (mtmm) cc_final: 0.8569 (mttp) REVERT: D 86 TYR cc_start: 0.8659 (m-80) cc_final: 0.7901 (m-80) REVERT: E 105 GLU cc_start: 0.8813 (tt0) cc_final: 0.8226 (tp30) REVERT: F 40 ARG cc_start: 0.8820 (mmt90) cc_final: 0.8571 (tpp80) REVERT: F 45 LYS cc_start: 0.9138 (mtpt) cc_final: 0.8884 (mttp) REVERT: G 21 LYS cc_start: 0.9088 (tttt) cc_final: 0.8647 (tptt) REVERT: G 74 ASN cc_start: 0.8945 (t0) cc_final: 0.8672 (t0) REVERT: G 96 LYS cc_start: 0.9235 (tppt) cc_final: 0.8912 (mmmt) REVERT: H 36 ARG cc_start: 0.6959 (tpp-160) cc_final: 0.5981 (tpp80) REVERT: H 39 THR cc_start: 0.7941 (t) cc_final: 0.7550 (m) REVERT: H 50 GLN cc_start: 0.8875 (pt0) cc_final: 0.8553 (pp30) outliers start: 2 outliers final: 0 residues processed: 213 average time/residue: 0.1250 time to fit residues: 35.3874 Evaluate side-chains 174 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 78 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 54 optimal weight: 0.3980 chunk 96 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 86 optimal weight: 30.0000 chunk 11 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 93 GLN F 65 ASN F 76 HIS F 94 GLN G 114 GLN H 98 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.074699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.052208 restraints weight = 65348.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.053134 restraints weight = 35871.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.053771 restraints weight = 25761.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.054127 restraints weight = 21599.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.054330 restraints weight = 19750.461| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12755 Z= 0.168 Angle : 0.674 8.204 18477 Z= 0.383 Chirality : 0.044 0.275 2105 Planarity : 0.005 0.062 1327 Dihedral : 31.773 179.364 4019 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.16 % Allowed : 1.27 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.31), residues: 738 helix: 1.19 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.17 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 49 TYR 0.026 0.002 TYR B 89 PHE 0.012 0.002 PHE C 26 HIS 0.009 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.17 (12755) covalent geometry : angle 0.67425 / 0.38 (18477) hydrogen bonds : bond 0.04340 / 2.87 ( 741) hydrogen bonds : angle 3.19581 / 2.28 ( 1855) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.8504 (t80) cc_final: 0.8227 (t80) REVERT: A 105 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7918 (tm-30) REVERT: B 54 GLU cc_start: 0.8705 (pp20) cc_final: 0.8433 (pp20) REVERT: B 80 LYS cc_start: 0.8727 (pttm) cc_final: 0.7963 (ttmm) REVERT: D 38 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7107 (pt0) REVERT: D 86 TYR cc_start: 0.8589 (m-80) cc_final: 0.7921 (m-80) REVERT: E 105 GLU cc_start: 0.8838 (tt0) cc_final: 0.8240 (tp30) REVERT: G 74 ASN cc_start: 0.8947 (t0) cc_final: 0.8722 (t0) REVERT: G 93 GLU cc_start: 0.7631 (pt0) cc_final: 0.7156 (pt0) REVERT: H 39 THR cc_start: 0.8028 (t) cc_final: 0.7664 (m) REVERT: H 46 LYS cc_start: 0.9303 (ptpt) cc_final: 0.9072 (ptpp) REVERT: H 50 GLN cc_start: 0.8873 (pt0) cc_final: 0.8535 (pp30) REVERT: H 119 ARG cc_start: 0.8627 (ptm-80) cc_final: 0.8340 (ptm-80) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.1193 time to fit residues: 33.1826 Evaluate side-chains 170 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 85 optimal weight: 50.0000 chunk 97 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 94 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.074106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.051745 restraints weight = 65239.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.052662 restraints weight = 35631.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.053251 restraints weight = 25497.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.053600 restraints weight = 21468.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.053792 restraints weight = 19666.125| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12755 Z= 0.177 Angle : 0.691 10.340 18477 Z= 0.391 Chirality : 0.045 0.280 2105 Planarity : 0.005 0.060 1327 Dihedral : 31.822 179.153 4019 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.30), residues: 738 helix: 1.21 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.19 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 68 TYR 0.030 0.003 TYR B 89 PHE 0.024 0.003 PHE E 54 HIS 0.011 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.18 (12755) covalent geometry : angle 0.69134 / 0.39 (18477) hydrogen bonds : bond 0.04452 / 2.93 ( 741) hydrogen bonds : angle 3.21432 / 2.29 ( 1855) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9060 (mppt) cc_final: 0.8853 (mmtm) REVERT: A 105 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7888 (tm-30) REVERT: B 80 LYS cc_start: 0.8699 (pttm) cc_final: 0.7950 (ttmm) REVERT: D 38 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7139 (pt0) REVERT: D 82 LYS cc_start: 0.8907 (mtmm) cc_final: 0.8614 (mttp) REVERT: D 86 TYR cc_start: 0.8675 (m-80) cc_final: 0.8027 (m-80) REVERT: E 68 GLN cc_start: 0.8540 (tm130) cc_final: 0.8279 (tm-30) REVERT: E 105 GLU cc_start: 0.8845 (tt0) cc_final: 0.8275 (tp30) REVERT: F 45 LYS cc_start: 0.9177 (mtpt) cc_final: 0.8844 (mttp) REVERT: G 42 GLN cc_start: 0.8493 (mp-120) cc_final: 0.8202 (mm-40) REVERT: G 93 GLU cc_start: 0.7654 (pt0) cc_final: 0.7127 (pt0) REVERT: G 96 LYS cc_start: 0.9285 (tppt) cc_final: 0.8972 (mmmt) REVERT: H 39 THR cc_start: 0.8083 (t) cc_final: 0.7749 (m) REVERT: H 46 LYS cc_start: 0.9307 (ptpt) cc_final: 0.9084 (ptpp) REVERT: H 50 GLN cc_start: 0.8893 (pt0) cc_final: 0.8520 (pp30) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.1119 time to fit residues: 31.5784 Evaluate side-chains 168 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 63 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 HIS ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 93 GLN F 94 GLN G 114 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.074809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.052345 restraints weight = 65301.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.053290 restraints weight = 35612.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.053895 restraints weight = 25592.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.054260 restraints weight = 21514.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.054426 restraints weight = 19679.468| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12755 Z= 0.150 Angle : 0.678 10.157 18477 Z= 0.383 Chirality : 0.044 0.276 2105 Planarity : 0.005 0.059 1327 Dihedral : 31.767 179.561 4019 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.16 % Allowed : 0.80 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.31), residues: 738 helix: 1.25 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.06 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 40 TYR 0.030 0.002 TYR B 89 PHE 0.022 0.002 PHE E 54 HIS 0.008 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 (12755) covalent geometry : angle 0.67769 / 0.38 (18477) hydrogen bonds : bond 0.04040 / 2.66 ( 741) hydrogen bonds : angle 3.19420 / 2.27 ( 1855) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1854.15 seconds wall clock time: 32 minutes 36.87 seconds (1956.87 seconds total)