Starting phenix.real_space_refine on Sun Sep 13 08:28:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ziq_11228/09_2026/6ziq_11228.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ziq_11228/09_2026/6ziq_11228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ziq_11228/09_2026/6ziq_11228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ziq_11228/09_2026/6ziq_11228.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6ziq_11228/09_2026/6ziq_11228.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ziq_11228/09_2026/6ziq_11228.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ziq_11228/09_2026/6ziq_11228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ziq_11228/09_2026/6ziq_11228.map" } resolution = 4.33 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 S 55 5.16 5 C 7133 2.51 5 N 1803 2.21 5 O 1948 1.98 5 H 11373 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22312 Number of models: 1 Model: "" Number of chains: 15 Chain: "8" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 696 Classifications: {'peptide': 41} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "a" Number of atoms: 3611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3611 Classifications: {'peptide': 226} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 213} Chain: "d" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 2549 Classifications: {'peptide': 155} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 143} Chain: "e" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 687 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "f" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1411 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "g" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1291 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "j" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 828 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "k" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 596 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "M" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 994 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1096 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 707 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3456 Classifications: {'peptide': 209} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 7, 'TRANS': 201} Chain: "h" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1009 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 5, 'TRANS': 56} Chain: "S" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 2048 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain breaks: 1 Chain: "C" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1333 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Time building chain proxies: 4.00, per 1000 atoms: 0.18 Number of scatterers: 22312 At special positions: 0 Unit cell: (103.752, 125.76, 246.28, 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 55 16.00 O 1948 8.00 N 1803 7.00 C 7133 6.00 H 11373 1.00 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: 2.01 Conformation dependent library (CDL) restraints added in 528.5 milliseconds 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2590 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 3 sheets defined 73.9% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain '8' and resid 1 through 7 removed outlier: 5.743A pdb=" N THR 8 6 " --> pdb=" O GLN 8 3 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N SER 8 7 " --> pdb=" O LEU 8 4 " (cutoff:3.500A) Processing helix chain '8' and resid 8 through 21 removed outlier: 3.698A pdb=" N THR 8 19 " --> pdb=" O SER 8 15 " (cutoff:3.500A) Processing helix chain '8' and resid 22 through 30 Processing helix chain 'a' and resid 5 through 10 removed outlier: 3.911A pdb=" N SER a 8 " --> pdb=" O LEU a 5 " (cutoff:3.500A) Processing helix chain 'a' and resid 19 through 26 removed outlier: 3.778A pdb=" N ILE a 23 " --> pdb=" O LEU a 19 " (cutoff:3.500A) Processing helix chain 'a' and resid 27 through 31 Processing helix chain 'a' and resid 40 through 59 removed outlier: 4.163A pdb=" N GLN a 46 " --> pdb=" O PHE a 42 " (cutoff:3.500A) Processing helix chain 'a' and resid 62 through 67 Processing helix chain 'a' and resid 68 through 87 Processing helix chain 'a' and resid 97 through 119 removed outlier: 3.679A pdb=" N ASN a 101 " --> pdb=" O GLN a 97 " (cutoff:3.500A) Proline residue: a 107 - end of helix Processing helix chain 'a' and resid 121 through 127 removed outlier: 3.551A pdb=" N LEU a 125 " --> pdb=" O THR a 121 " (cutoff:3.500A) Processing helix chain 'a' and resid 134 through 136 No H-bonds generated for 'chain 'a' and resid 134 through 136' Processing helix chain 'a' and resid 137 through 182 removed outlier: 4.872A pdb=" N ILE a 144 " --> pdb=" O MET a 140 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU a 145 " --> pdb=" O LEU a 141 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN a 152 " --> pdb=" O SER a 148 " (cutoff:3.500A) Proline residue: a 153 - end of helix Processing helix chain 'a' and resid 185 through 225 removed outlier: 4.095A pdb=" N ALA a 189 " --> pdb=" O SER a 185 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET a 208 " --> pdb=" O PHE a 204 " (cutoff:3.500A) Processing helix chain 'd' and resid 11 through 16 Processing helix chain 'd' and resid 20 through 22 No H-bonds generated for 'chain 'd' and resid 20 through 22' Processing helix chain 'd' and resid 23 through 44 removed outlier: 3.585A pdb=" N ALA d 27 " --> pdb=" O GLN d 23 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU d 44 " --> pdb=" O ARG d 40 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 60 Processing helix chain 'd' and resid 64 through 76 Processing helix chain 'd' and resid 87 through 89 No H-bonds generated for 'chain 'd' and resid 87 through 89' Processing helix chain 'd' and resid 90 through 101 removed outlier: 3.563A pdb=" N LYS d 94 " --> pdb=" O ASP d 90 " (cutoff:3.500A) Processing helix chain 'd' and resid 103 through 120 Processing helix chain 'd' and resid 126 through 130 removed outlier: 3.833A pdb=" N MET d 130 " --> pdb=" O PHE d 127 " (cutoff:3.500A) Processing helix chain 'd' and resid 131 through 139 Processing helix chain 'e' and resid 7 through 42 Proline residue: e 34 - end of helix Processing helix chain 'f' and resid 18 through 26 removed outlier: 3.927A pdb=" N LEU f 24 " --> pdb=" O PRO f 20 " (cutoff:3.500A) Processing helix chain 'f' and resid 29 through 49 removed outlier: 4.331A pdb=" N ARG f 39 " --> pdb=" O GLY f 35 " (cutoff:3.500A) Processing helix chain 'f' and resid 56 through 74 removed outlier: 3.752A pdb=" N MET f 61 " --> pdb=" O ALA f 57 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL f 62 " --> pdb=" O GLY f 58 " (cutoff:3.500A) Processing helix chain 'f' and resid 75 through 79 Processing helix chain 'g' and resid 21 through 37 removed outlier: 4.120A pdb=" N ARG g 25 " --> pdb=" O TYR g 21 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL g 35 " --> pdb=" O TYR g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 43 through 61 removed outlier: 4.065A pdb=" N THR g 47 " --> pdb=" O ALA g 43 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 67 removed outlier: 4.308A pdb=" N LYS g 65 " --> pdb=" O GLY g 62 " (cutoff:3.500A) Processing helix chain 'g' and resid 68 through 94 removed outlier: 3.659A pdb=" N TRP g 85 " --> pdb=" O GLU g 81 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE g 86 " --> pdb=" O VAL g 82 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TYR g 87 " --> pdb=" O TRP g 83 " (cutoff:3.500A) Processing helix chain 'j' and resid 3 through 10 Processing helix chain 'j' and resid 13 through 19 Processing helix chain 'j' and resid 21 through 47 Processing helix chain 'k' and resid 13 through 18 Processing helix chain 'k' and resid 22 through 45 Processing helix chain 'M' and resid 9 through 15 Processing helix chain 'M' and resid 17 through 39 removed outlier: 4.208A pdb=" N SER M 21 " --> pdb=" O GLY M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 74 removed outlier: 4.318A pdb=" N LEU M 46 " --> pdb=" O LEU M 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 15 Processing helix chain 'N' and resid 17 through 39 Processing helix chain 'N' and resid 42 through 74 removed outlier: 3.986A pdb=" N LEU N 46 " --> pdb=" O LEU N 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 38 Processing helix chain 'O' and resid 42 through 72 removed outlier: 4.003A pdb=" N LEU O 46 " --> pdb=" O LEU O 42 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS O 64 " --> pdb=" O MET O 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 19 through 30 Proline residue: b 27 - end of helix Processing helix chain 'b' and resid 32 through 48 Processing helix chain 'b' and resid 54 through 121 removed outlier: 4.326A pdb=" N TYR b 69 " --> pdb=" O GLY b 65 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ALA b 76 " --> pdb=" O LYS b 72 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N SER b 77 " --> pdb=" O LYS b 73 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL b 96 " --> pdb=" O GLN b 92 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN b 119 " --> pdb=" O GLN b 115 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS b 120 " --> pdb=" O ALA b 116 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 186 removed outlier: 3.925A pdb=" N HIS b 158 " --> pdb=" O ARG b 154 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER b 186 " --> pdb=" O VAL b 182 " (cutoff:3.500A) Processing helix chain 'b' and resid 189 through 209 Processing helix chain 'h' and resid 8 through 25 Processing helix chain 'h' and resid 31 through 51 removed outlier: 3.507A pdb=" N TYR h 35 " --> pdb=" O ALA h 31 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN h 36 " --> pdb=" O GLY h 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 28 removed outlier: 3.669A pdb=" N LYS S 28 " --> pdb=" O SER S 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 31 through 44 removed outlier: 4.034A pdb=" N GLN S 44 " --> pdb=" O LEU S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 101 through 113 Processing helix chain 'S' and resid 127 through 142 Processing helix chain 'S' and resid 175 through 188 removed outlier: 3.706A pdb=" N GLU S 188 " --> pdb=" O ARG S 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 18 Processing sheet with id=AA1, first strand: chain 'b' and resid 12 through 13 removed outlier: 3.704A pdb=" N ILE b 17 " --> pdb=" O ARG b 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'S' and resid 147 through 149 Processing sheet with id=AA3, first strand: chain 'C' and resid 28 through 35 removed outlier: 5.647A pdb=" N VAL C 31 " --> pdb=" O HIS C 42 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N HIS C 42 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASN C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LEU C 66 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 64 " --> pdb=" O GLY C 72 " (cutoff:3.500A) 771 hydrogen bonds defined for protein. 2271 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.96 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11311 1.03 - 1.23: 88 1.23 - 1.42: 4455 1.42 - 1.62: 6575 1.62 - 1.81: 102 Bond restraints: 22531 Sorted by residual: bond pdb=" CA M3L M 43 " pdb=" HA M3L M 43 " ideal model delta sigma weight residual 0.970 1.133 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" CA M3L N 43 " pdb=" HA M3L N 43 " ideal model delta sigma weight residual 0.970 1.133 -0.163 2.00e-02 2.50e+03 6.63e+01 bond pdb=" CA M3L O 43 " pdb=" HA M3L O 43 " ideal model delta sigma weight residual 0.970 1.132 -0.162 2.00e-02 2.50e+03 6.60e+01 bond pdb=" CE M3L O 43 " pdb=" HE2 M3L O 43 " ideal model delta sigma weight residual 0.970 1.129 -0.159 2.00e-02 2.50e+03 6.33e+01 bond pdb=" CE M3L N 43 " pdb=" HE2 M3L N 43 " ideal model delta sigma weight residual 0.970 1.129 -0.159 2.00e-02 2.50e+03 6.31e+01 ... (remaining 22526 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.04: 40903 5.04 - 10.08: 23 10.08 - 15.12: 2 15.12 - 20.15: 0 20.15 - 25.19: 9 Bond angle restraints: 40937 Sorted by residual: angle pdb=" CB LEU O 65 " pdb=" CG LEU O 65 " pdb=" HG LEU O 65 " ideal model delta sigma weight residual 109.00 83.81 25.19 3.00e+00 1.11e-01 7.05e+01 angle pdb=" CB LEU O 52 " pdb=" CG LEU O 52 " pdb=" HG LEU O 52 " ideal model delta sigma weight residual 109.00 84.69 24.31 3.00e+00 1.11e-01 6.56e+01 angle pdb=" CD2 LEU O 65 " pdb=" CG LEU O 65 " pdb=" HG LEU O 65 " ideal model delta sigma weight residual 108.00 83.76 24.24 3.00e+00 1.11e-01 6.53e+01 angle pdb=" CD1 LEU O 65 " pdb=" CG LEU O 65 " pdb=" HG LEU O 65 " ideal model delta sigma weight residual 108.00 83.84 24.16 3.00e+00 1.11e-01 6.48e+01 angle pdb=" CB LEU O 70 " pdb=" CG LEU O 70 " pdb=" HG LEU O 70 " ideal model delta sigma weight residual 109.00 85.14 23.86 3.00e+00 1.11e-01 6.33e+01 ... (remaining 40932 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 9311 17.82 - 35.63: 862 35.63 - 53.45: 238 53.45 - 71.27: 80 71.27 - 89.09: 9 Dihedral angle restraints: 10500 sinusoidal: 5767 harmonic: 4733 Sorted by residual: dihedral pdb=" CA ILE d 18 " pdb=" C ILE d 18 " pdb=" N ILE d 19 " pdb=" CA ILE d 19 " ideal model delta harmonic sigma weight residual -180.00 -157.00 -23.00 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA HIS 8 31 " pdb=" C HIS 8 31 " pdb=" N ASN 8 32 " pdb=" CA ASN 8 32 " ideal model delta harmonic sigma weight residual 180.00 -157.31 -22.69 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ALA d 63 " pdb=" C ALA d 63 " pdb=" N GLY d 64 " pdb=" CA GLY d 64 " ideal model delta harmonic sigma weight residual -180.00 -158.86 -21.14 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 10497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.357: 1742 0.357 - 0.714: 0 0.714 - 1.071: 0 1.071 - 1.427: 0 1.427 - 1.784: 3 Chirality restraints: 1745 Sorted by residual: chirality pdb=" CG LEU O 70 " pdb=" CB LEU O 70 " pdb=" CD1 LEU O 70 " pdb=" CD2 LEU O 70 " both_signs ideal model delta sigma weight residual False -2.59 -0.81 -1.78 2.00e-01 2.50e+01 7.96e+01 chirality pdb=" CG LEU O 52 " pdb=" CB LEU O 52 " pdb=" CD1 LEU O 52 " pdb=" CD2 LEU O 52 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.18e+01 chirality pdb=" CG LEU O 65 " pdb=" CB LEU O 65 " pdb=" CD1 LEU O 65 " pdb=" CD2 LEU O 65 " both_signs ideal model delta sigma weight residual False -2.59 -1.03 -1.56 2.00e-01 2.50e+01 6.05e+01 ... (remaining 1742 not shown) Planarity restraints: 3170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP a 109 " -0.026 2.00e-02 2.50e+03 1.69e-02 1.14e+01 pdb=" CG TRP a 109 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP a 109 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP a 109 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP a 109 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP a 109 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP a 109 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 109 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 109 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP a 109 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP a 109 " -0.011 2.00e-02 2.50e+03 pdb=" HE1 TRP a 109 " -0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP a 109 " 0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP a 109 " -0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP a 109 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP a 109 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE O 63 " -0.032 2.00e-02 2.50e+03 1.47e-02 6.47e+00 pdb=" CG PHE O 63 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE O 63 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE O 63 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE O 63 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE O 63 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE O 63 " -0.014 2.00e-02 2.50e+03 pdb=" HD1 PHE O 63 " 0.005 2.00e-02 2.50e+03 pdb=" HD2 PHE O 63 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE O 63 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE O 63 " 0.000 2.00e-02 2.50e+03 pdb=" HZ PHE O 63 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL d 78 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO d 79 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO d 79 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO d 79 " -0.027 5.00e-02 4.00e+02 ... (remaining 3167 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 535 2.08 - 2.71: 38500 2.71 - 3.34: 67043 3.34 - 3.97: 78246 3.97 - 4.60: 122666 Nonbonded interactions: 306990 Sorted by model distance: nonbonded pdb=" OE1 GLU S 33 " pdb=" H GLU S 33 " model vdw 1.445 2.450 nonbonded pdb=" OD1 ASN a 2 " pdb=" H GLU a 3 " model vdw 1.509 2.450 nonbonded pdb=" O M3L M 43 " pdb=" H LEU M 46 " model vdw 1.512 2.450 nonbonded pdb=" O VAL N 16 " pdb=" H ALA N 19 " model vdw 1.524 2.450 nonbonded pdb=" OE1 GLU d 133 " pdb=" H GLU d 133 " model vdw 1.541 2.450 ... (remaining 306985 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 'M' selection = (chain 'N' and (resid 8 through 74 or (resid 75 and (name N or name CA or name C \ or name O or name CB or name CG or name SD or name CE or name HA or name HB2 or \ name HB3 or name HG2 or name HG3 or name HE1 or name HE2 or name HE3)))) } 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 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: 8.660 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: 0.160 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.140 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 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 0.075 11158 Z= 0.223 Angle : 0.744 10.482 15079 Z= 0.408 Chirality : 0.081 1.784 1745 Planarity : 0.005 0.048 1860 Dihedral : 14.687 89.086 4138 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -1.50 (0.22), residues: 1344 helix: -0.39 (0.16), residues: 922 sheet: -2.13 (0.85), residues: 41 loop : -2.13 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG a 159 TYR 0.022 0.002 TYR S 23 PHE 0.036 0.002 PHE O 63 TRP 0.056 0.002 TRP a 109 HIS 0.003 0.001 HIS a 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.22 (11158) covalent geometry : angle 0.74386 / 0.41 (15079) hydrogen bonds : bond 0.13761 / 9.18 ( 771) hydrogen bonds : angle 6.78348 / 4.81 ( 2271) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 100 MET cc_start: 0.7905 (ttm) cc_final: 0.7684 (ttm) REVERT: j 31 MET cc_start: 0.7879 (mmt) cc_final: 0.7114 (mmp) REVERT: N 51 ILE cc_start: 0.8038 (mp) cc_final: 0.7394 (tp) REVERT: b 142 GLU cc_start: 0.8128 (pp20) cc_final: 0.7897 (pp20) REVERT: b 173 MET cc_start: 0.8544 (ttp) cc_final: 0.7862 (tpp) REVERT: S 126 LEU cc_start: 0.8194 (mm) cc_final: 0.7989 (mm) REVERT: S 159 MET cc_start: 0.5535 (tpt) cc_final: 0.5239 (tpt) REVERT: C 11 ILE cc_start: 0.8658 (tp) cc_final: 0.8410 (tp) REVERT: C 42 HIS cc_start: 0.7030 (t70) cc_final: 0.6791 (t-90) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.1834 time to fit residues: 65.0562 Evaluate side-chains 180 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.0980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 36 ASN a 101 ASN a 119 ASN a 163 ASN a 168 HIS g 57 ASN ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.075876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.065219 restraints weight = 162278.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.067410 restraints weight = 74237.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.068731 restraints weight = 43965.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.069537 restraints weight = 30935.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.069988 restraints weight = 24586.771| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11158 Z= 0.159 Angle : 0.656 10.964 15079 Z= 0.342 Chirality : 0.081 1.769 1745 Planarity : 0.005 0.053 1860 Dihedral : 5.652 47.757 1494 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.17 % Allowed : 2.12 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -0.28 (0.23), residues: 1344 helix: 0.54 (0.17), residues: 932 sheet: -1.05 (0.96), residues: 37 loop : -1.82 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG b 154 TYR 0.016 0.001 TYR e 15 PHE 0.042 0.001 PHE O 63 TRP 0.028 0.001 TRP a 109 HIS 0.004 0.001 HIS b 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (11158) covalent geometry : angle 0.65624 / 0.34 (15079) hydrogen bonds : bond 0.05704 / 3.69 ( 771) hydrogen bonds : angle 5.39356 / 3.83 ( 2271) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 223 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 140 MET cc_start: 0.8023 (mpp) cc_final: 0.6613 (tmm) REVERT: j 31 MET cc_start: 0.7847 (mmt) cc_final: 0.7367 (mmp) REVERT: N 51 ILE cc_start: 0.7920 (mp) cc_final: 0.7399 (tp) REVERT: b 173 MET cc_start: 0.8784 (ttp) cc_final: 0.8307 (tpp) REVERT: S 126 LEU cc_start: 0.8195 (mm) cc_final: 0.7973 (mm) REVERT: C 13 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8445 (tm-30) REVERT: C 14 GLU cc_start: 0.8993 (mp0) cc_final: 0.8611 (mp0) outliers start: 2 outliers final: 0 residues processed: 225 average time/residue: 0.1738 time to fit residues: 62.1757 Evaluate side-chains 185 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 122 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.0470 chunk 55 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 119 ASN a 168 HIS ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.076000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.065411 restraints weight = 161241.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.067528 restraints weight = 73782.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.068815 restraints weight = 43976.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.069564 restraints weight = 31228.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.070094 restraints weight = 25295.434| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11158 Z= 0.145 Angle : 0.623 11.008 15079 Z= 0.320 Chirality : 0.081 1.759 1745 Planarity : 0.005 0.053 1860 Dihedral : 5.433 46.727 1494 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.17 % Allowed : 2.29 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 0.28 (0.23), residues: 1344 helix: 0.90 (0.17), residues: 943 sheet: -0.70 (0.98), residues: 37 loop : -1.53 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 154 TYR 0.015 0.001 TYR N 49 PHE 0.035 0.001 PHE O 63 TRP 0.020 0.001 TRP a 109 HIS 0.006 0.001 HIS a 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (11158) covalent geometry : angle 0.62294 / 0.32 (15079) hydrogen bonds : bond 0.05102 / 3.30 ( 771) hydrogen bonds : angle 5.06680 / 3.58 ( 2271) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 229 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 140 MET cc_start: 0.8091 (mpp) cc_final: 0.6923 (tmm) REVERT: e 24 TYR cc_start: 0.9134 (t80) cc_final: 0.8891 (t80) REVERT: j 31 MET cc_start: 0.7800 (mmt) cc_final: 0.7355 (mmp) REVERT: N 51 ILE cc_start: 0.7909 (mp) cc_final: 0.7390 (tp) REVERT: S 109 MET cc_start: 0.8372 (tpt) cc_final: 0.8101 (tpt) REVERT: S 159 MET cc_start: 0.5536 (tpt) cc_final: 0.5220 (tpt) outliers start: 2 outliers final: 0 residues processed: 231 average time/residue: 0.1822 time to fit residues: 65.5574 Evaluate side-chains 187 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 100 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 51 GLN a 119 ASN a 168 HIS g 75 ASN O 45 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.076348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.065980 restraints weight = 160571.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.068040 restraints weight = 74887.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.069267 restraints weight = 45020.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.069959 restraints weight = 32039.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.070461 restraints weight = 25969.625| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 11158 Z= 0.177 Angle : 0.632 11.139 15079 Z= 0.327 Chirality : 0.081 1.749 1745 Planarity : 0.005 0.058 1860 Dihedral : 5.342 46.236 1494 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.08 % Allowed : 2.20 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 0.39 (0.23), residues: 1344 helix: 1.00 (0.17), residues: 944 sheet: -0.82 (0.95), residues: 37 loop : -1.51 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 187 TYR 0.023 0.002 TYR h 18 PHE 0.035 0.001 PHE O 63 TRP 0.015 0.001 TRP a 109 HIS 0.007 0.001 HIS S 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (11158) covalent geometry : angle 0.63227 / 0.33 (15079) hydrogen bonds : bond 0.04983 / 3.20 ( 771) hydrogen bonds : angle 5.05590 / 3.58 ( 2271) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 140 MET cc_start: 0.8187 (mpp) cc_final: 0.6969 (tmm) REVERT: e 24 TYR cc_start: 0.9152 (t80) cc_final: 0.8875 (t80) REVERT: N 51 ILE cc_start: 0.7873 (mp) cc_final: 0.7369 (tp) REVERT: S 109 MET cc_start: 0.8561 (tpt) cc_final: 0.8251 (tpt) REVERT: S 126 LEU cc_start: 0.8244 (mm) cc_final: 0.8023 (mm) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.1759 time to fit residues: 61.5757 Evaluate side-chains 190 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 13 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 119 ASN a 163 ASN a 168 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.076426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.066052 restraints weight = 159955.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.068081 restraints weight = 74012.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.069340 restraints weight = 44770.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.070089 restraints weight = 31834.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.070523 restraints weight = 25482.130| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11158 Z= 0.161 Angle : 0.619 11.209 15079 Z= 0.320 Chirality : 0.081 1.755 1745 Planarity : 0.004 0.047 1860 Dihedral : 5.235 46.061 1494 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.08 % Allowed : 2.29 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 0.57 (0.23), residues: 1344 helix: 1.11 (0.17), residues: 945 sheet: -0.85 (0.94), residues: 37 loop : -1.38 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG h 19 TYR 0.024 0.001 TYR S 23 PHE 0.035 0.001 PHE O 63 TRP 0.013 0.001 TRP a 109 HIS 0.005 0.001 HIS a 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (11158) covalent geometry : angle 0.61905 / 0.32 (15079) hydrogen bonds : bond 0.04895 / 3.14 ( 771) hydrogen bonds : angle 4.92946 / 3.50 ( 2271) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 140 MET cc_start: 0.8070 (mpp) cc_final: 0.6930 (tmm) REVERT: N 51 ILE cc_start: 0.7874 (mp) cc_final: 0.7386 (tp) REVERT: N 70 LEU cc_start: 0.8108 (mt) cc_final: 0.7649 (tp) REVERT: S 159 MET cc_start: 0.5549 (tpt) cc_final: 0.5074 (tpt) REVERT: S 166 ILE cc_start: 0.8536 (mm) cc_final: 0.7803 (mm) REVERT: C 13 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8463 (tm-30) outliers start: 1 outliers final: 0 residues processed: 229 average time/residue: 0.1936 time to fit residues: 67.5373 Evaluate side-chains 191 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 129 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 119 ASN a 168 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.076590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.066143 restraints weight = 161271.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.068306 restraints weight = 72580.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.069595 restraints weight = 42615.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.070341 restraints weight = 29806.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.070861 restraints weight = 23879.010| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11158 Z= 0.148 Angle : 0.612 10.838 15079 Z= 0.315 Chirality : 0.078 1.758 1745 Planarity : 0.005 0.068 1860 Dihedral : 5.150 45.970 1494 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.08 % Allowed : 1.10 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.23), residues: 1344 helix: 1.20 (0.17), residues: 945 sheet: -0.81 (0.94), residues: 37 loop : -1.35 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG N 38 TYR 0.021 0.001 TYR O 49 PHE 0.059 0.002 PHE O 63 TRP 0.012 0.001 TRP a 109 HIS 0.005 0.001 HIS a 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (11158) covalent geometry : angle 0.61164 / 0.32 (15079) hydrogen bonds : bond 0.04775 / 3.08 ( 771) hydrogen bonds : angle 4.88487 / 3.47 ( 2271) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 231 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 140 MET cc_start: 0.8018 (mpp) cc_final: 0.6895 (tmm) REVERT: N 51 ILE cc_start: 0.7844 (mp) cc_final: 0.7345 (tp) REVERT: N 70 LEU cc_start: 0.8065 (mt) cc_final: 0.7725 (tp) REVERT: O 65 LEU cc_start: 0.8806 (tt) cc_final: 0.8206 (mt) REVERT: S 109 MET cc_start: 0.8522 (tpt) cc_final: 0.8198 (tpt) REVERT: S 159 MET cc_start: 0.5639 (tpt) cc_final: 0.5382 (tpt) REVERT: C 13 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8456 (tm-30) outliers start: 1 outliers final: 0 residues processed: 232 average time/residue: 0.1914 time to fit residues: 68.4903 Evaluate side-chains 197 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 26 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 108 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 79 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 123 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 119 ASN a 163 ASN ** a 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 122 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.077063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.066687 restraints weight = 157267.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.068778 restraints weight = 71154.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.070051 restraints weight = 42323.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.070810 restraints weight = 29726.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.071260 restraints weight = 23489.266| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11158 Z= 0.131 Angle : 0.587 11.097 15079 Z= 0.299 Chirality : 0.080 1.756 1745 Planarity : 0.004 0.053 1860 Dihedral : 5.023 45.939 1494 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 0.97 (0.24), residues: 1344 helix: 1.39 (0.17), residues: 945 sheet: -0.73 (0.95), residues: 37 loop : -1.16 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 38 TYR 0.018 0.001 TYR O 49 PHE 0.026 0.001 PHE O 63 TRP 0.011 0.001 TRP a 109 HIS 0.008 0.001 HIS a 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (11158) covalent geometry : angle 0.58740 / 0.30 (15079) hydrogen bonds : bond 0.04634 / 2.99 ( 771) hydrogen bonds : angle 4.69153 / 3.35 ( 2271) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 140 MET cc_start: 0.8025 (mpp) cc_final: 0.6864 (tmm) REVERT: N 51 ILE cc_start: 0.7798 (mp) cc_final: 0.7313 (tp) REVERT: N 70 LEU cc_start: 0.8264 (mt) cc_final: 0.7850 (tp) REVERT: O 66 MET cc_start: 0.7475 (tpp) cc_final: 0.7071 (tmm) REVERT: b 109 ASP cc_start: 0.8239 (m-30) cc_final: 0.7759 (t0) REVERT: S 184 ARG cc_start: 0.7671 (tpm170) cc_final: 0.7312 (tpp-160) REVERT: C 13 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8421 (tm-30) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.2010 time to fit residues: 71.5800 Evaluate side-chains 199 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 99 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 119 ASN a 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.076235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.065900 restraints weight = 161195.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.067935 restraints weight = 75317.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.069135 restraints weight = 45290.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.069897 restraints weight = 32512.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.070384 restraints weight = 25995.065| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11158 Z= 0.195 Angle : 0.631 12.051 15079 Z= 0.330 Chirality : 0.081 1.752 1745 Planarity : 0.004 0.048 1860 Dihedral : 5.065 45.207 1494 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 0.83 (0.23), residues: 1344 helix: 1.30 (0.17), residues: 943 sheet: -0.86 (0.94), residues: 37 loop : -1.22 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG h 19 TYR 0.024 0.002 TYR f 66 PHE 0.034 0.002 PHE O 63 TRP 0.012 0.001 TRP a 109 HIS 0.005 0.001 HIS b 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.20 (11158) covalent geometry : angle 0.63075 / 0.33 (15079) hydrogen bonds : bond 0.04711 / 3.02 ( 771) hydrogen bonds : angle 4.85938 / 3.47 ( 2271) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 5 ASP cc_start: 0.8596 (t0) cc_final: 0.8321 (t0) REVERT: a 140 MET cc_start: 0.8035 (mpp) cc_final: 0.6882 (tmm) REVERT: e 24 TYR cc_start: 0.9105 (t80) cc_final: 0.8705 (t80) REVERT: N 51 ILE cc_start: 0.7886 (mp) cc_final: 0.7372 (tp) REVERT: N 70 LEU cc_start: 0.8303 (mt) cc_final: 0.7887 (tp) REVERT: O 66 MET cc_start: 0.7645 (tpp) cc_final: 0.7164 (tmm) REVERT: S 159 MET cc_start: 0.5570 (tpt) cc_final: 0.5153 (tpt) REVERT: C 13 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8467 (tm-30) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.1889 time to fit residues: 65.3262 Evaluate side-chains 194 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 78 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 119 ASN ** a 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.076563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.066200 restraints weight = 157255.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.068286 restraints weight = 70327.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.069543 restraints weight = 41381.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.070322 restraints weight = 28995.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.070762 restraints weight = 22908.200| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11158 Z= 0.136 Angle : 0.615 12.287 15079 Z= 0.314 Chirality : 0.080 1.763 1745 Planarity : 0.004 0.049 1860 Dihedral : 4.979 45.407 1494 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 1.10 (0.24), residues: 1344 helix: 1.47 (0.17), residues: 948 sheet: -0.71 (0.96), residues: 37 loop : -1.07 (0.35), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 38 TYR 0.026 0.001 TYR f 66 PHE 0.034 0.001 PHE M 47 TRP 0.014 0.001 TRP a 109 HIS 0.005 0.001 HIS a 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (11158) covalent geometry : angle 0.61493 / 0.31 (15079) hydrogen bonds : bond 0.04642 / 3.00 ( 771) hydrogen bonds : angle 4.66058 / 3.32 ( 2271) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 5 ASP cc_start: 0.8505 (t0) cc_final: 0.8248 (t0) REVERT: a 140 MET cc_start: 0.7999 (mpp) cc_final: 0.6869 (tmm) REVERT: e 24 TYR cc_start: 0.9036 (t80) cc_final: 0.8721 (t80) REVERT: N 51 ILE cc_start: 0.7792 (mp) cc_final: 0.7267 (tp) REVERT: N 70 LEU cc_start: 0.8246 (mt) cc_final: 0.7802 (tp) REVERT: O 66 MET cc_start: 0.7633 (tpp) cc_final: 0.7187 (tmm) REVERT: b 109 ASP cc_start: 0.8242 (m-30) cc_final: 0.7763 (t0) REVERT: C 11 ILE cc_start: 0.8518 (tp) cc_final: 0.8295 (tp) REVERT: C 14 GLU cc_start: 0.8929 (mp0) cc_final: 0.8726 (mp0) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1982 time to fit residues: 68.2139 Evaluate side-chains 201 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 119 ASN a 168 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.076321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.065828 restraints weight = 158691.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.067866 restraints weight = 71838.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.069144 restraints weight = 43001.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.069882 restraints weight = 30381.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.070414 restraints weight = 24489.556| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11158 Z= 0.144 Angle : 0.610 12.323 15079 Z= 0.311 Chirality : 0.080 1.752 1745 Planarity : 0.004 0.049 1860 Dihedral : 4.929 45.095 1494 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.08 % Allowed : 0.42 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 1.19 (0.24), residues: 1344 helix: 1.55 (0.17), residues: 948 sheet: -0.75 (0.95), residues: 37 loop : -1.06 (0.35), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG h 19 TYR 0.023 0.001 TYR f 66 PHE 0.040 0.001 PHE M 69 TRP 0.015 0.001 TRP a 109 HIS 0.004 0.001 HIS b 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (11158) covalent geometry : angle 0.60952 / 0.31 (15079) hydrogen bonds : bond 0.04582 / 2.96 ( 771) hydrogen bonds : angle 4.66247 / 3.32 ( 2271) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 5 ASP cc_start: 0.8604 (t0) cc_final: 0.8255 (t0) REVERT: 8 12 MET cc_start: 0.8620 (tpp) cc_final: 0.8419 (tpp) REVERT: a 140 MET cc_start: 0.8006 (mpp) cc_final: 0.6848 (tmm) REVERT: e 24 TYR cc_start: 0.9030 (t80) cc_final: 0.8714 (t80) REVERT: f 81 GLU cc_start: 0.7752 (tt0) cc_final: 0.6507 (tm-30) REVERT: N 70 LEU cc_start: 0.8273 (mt) cc_final: 0.7811 (tp) REVERT: O 66 MET cc_start: 0.7635 (tpp) cc_final: 0.7219 (tmm) REVERT: b 109 ASP cc_start: 0.8247 (m-30) cc_final: 0.7768 (t0) REVERT: S 159 MET cc_start: 0.5706 (tpt) cc_final: 0.5305 (tpt) REVERT: S 184 ARG cc_start: 0.7648 (tpm170) cc_final: 0.7251 (tpp-160) REVERT: C 11 ILE cc_start: 0.8469 (tp) cc_final: 0.8224 (tp) REVERT: C 13 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8221 (tm-30) REVERT: C 14 GLU cc_start: 0.9009 (mp0) cc_final: 0.8619 (mp0) outliers start: 1 outliers final: 0 residues processed: 229 average time/residue: 0.1955 time to fit residues: 67.2009 Evaluate side-chains 193 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 32 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 55 optimal weight: 0.1980 chunk 128 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 109 optimal weight: 0.0980 chunk 57 optimal weight: 2.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 119 ASN a 168 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.076805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.066523 restraints weight = 157409.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.068564 restraints weight = 72713.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.069769 restraints weight = 43513.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.070530 restraints weight = 31221.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.071000 restraints weight = 24768.566| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11158 Z= 0.132 Angle : 0.606 12.176 15079 Z= 0.307 Chirality : 0.080 1.745 1745 Planarity : 0.004 0.045 1860 Dihedral : 4.847 45.171 1494 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.08 % Allowed : 0.17 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 1.29 (0.24), residues: 1344 helix: 1.62 (0.17), residues: 949 sheet: -0.69 (0.96), residues: 37 loop : -1.02 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 38 TYR 0.016 0.001 TYR O 49 PHE 0.026 0.001 PHE O 63 TRP 0.015 0.001 TRP a 109 HIS 0.007 0.001 HIS S 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (11158) covalent geometry : angle 0.60561 / 0.31 (15079) hydrogen bonds : bond 0.04506 / 2.90 ( 771) hydrogen bonds : angle 4.58788 / 3.27 ( 2271) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3615.06 seconds wall clock time: 62 minutes 35.63 seconds (3755.63 seconds total)