Starting phenix.real_space_refine on Thu Mar 5 11:48:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ziq_11228/03_2026/6ziq_11228.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ziq_11228/03_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_11228/03_2026/6ziq_11228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ziq_11228/03_2026/6ziq_11228.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ziq_11228/03_2026/6ziq_11228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ziq_11228/03_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 3.10, per 1000 atoms: 0.14 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: 1.90 Conformation dependent library (CDL) restraints added in 609.2 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: 0.31 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: 4.64 Time building geometry restraints manager: 2.62 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: 9316 17.82 - 35.63: 864 35.63 - 53.45: 241 53.45 - 71.27: 80 71.27 - 89.09: 11 Dihedral angle restraints: 10512 sinusoidal: 5779 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 10509 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: 10.700 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: 0.080 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 19.030 Find NCS groups from input model: 0.100 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 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 covalent geometry : bond 0.00466 (11158) covalent geometry : angle 0.74386 (15079) hydrogen bonds : bond 0.13761 ( 771) hydrogen bonds : angle 6.78348 ( 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 : 0.391 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: 0.1764 time to fit residues: 61.8558 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 : 0.631 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3571 r_free = 0.3571 target = 0.076303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.065524 restraints weight = 162712.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.067707 restraints weight = 74714.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.069031 restraints weight = 44621.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.069811 restraints weight = 31615.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.070328 restraints weight = 25439.023| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11158 Z= 0.153 Angle : 0.652 10.857 15079 Z= 0.340 Chirality : 0.081 1.776 1745 Planarity : 0.005 0.058 1860 Dihedral : 5.632 47.631 1494 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.08 % Allowed : 2.88 % Favored : 97.03 % 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: -0.20 (0.23), residues: 1344 helix: 0.59 (0.17), residues: 933 sheet: -1.01 (0.96), residues: 37 loop : -1.77 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG b 141 TYR 0.017 0.001 TYR e 15 PHE 0.043 0.001 PHE O 63 TRP 0.030 0.001 TRP a 109 HIS 0.005 0.001 HIS b 172 Details of bonding type rmsd covalent geometry : bond 0.00322 (11158) covalent geometry : angle 0.65184 (15079) hydrogen bonds : bond 0.05492 ( 771) hydrogen bonds : angle 5.32769 ( 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: 1 poor density : 224 time to evaluate : 0.406 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: a 140 MET cc_start: 0.7994 (mpp) cc_final: 0.6809 (tmm) REVERT: e 24 TYR cc_start: 0.9135 (t80) cc_final: 0.8932 (t80) REVERT: j 31 MET cc_start: 0.7961 (mmt) cc_final: 0.7476 (mmp) REVERT: N 51 ILE cc_start: 0.7927 (mp) cc_final: 0.7409 (tp) REVERT: S 109 MET cc_start: 0.8439 (tpt) cc_final: 0.8234 (tpt) REVERT: S 126 LEU cc_start: 0.8184 (mm) cc_final: 0.7969 (mm) REVERT: C 13 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8432 (tm-30) REVERT: C 14 GLU cc_start: 0.9016 (mp0) cc_final: 0.8660 (mp0) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.1631 time to fit residues: 57.7614 Evaluate side-chains 186 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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: 0.9980 chunk 64 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 110 optimal weight: 0.0070 chunk 70 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 119 ASN ** N 45 GLN ** 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 = 0.3566 r_free = 0.3566 target = 0.076241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.065993 restraints weight = 159308.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.068035 restraints weight = 73643.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.069251 restraints weight = 44302.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.070009 restraints weight = 31420.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.070337 restraints weight = 25046.061| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11158 Z= 0.145 Angle : 0.625 11.097 15079 Z= 0.321 Chirality : 0.081 1.760 1745 Planarity : 0.004 0.051 1860 Dihedral : 5.421 46.531 1494 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % 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: 0.32 (0.23), residues: 1344 helix: 0.93 (0.17), residues: 943 sheet: -0.71 (0.97), residues: 37 loop : -1.48 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG b 154 TYR 0.022 0.001 TYR S 23 PHE 0.034 0.001 PHE O 63 TRP 0.020 0.001 TRP a 109 HIS 0.004 0.001 HIS a 168 Details of bonding type rmsd covalent geometry : bond 0.00312 (11158) covalent geometry : angle 0.62494 (15079) hydrogen bonds : bond 0.05103 ( 771) hydrogen bonds : angle 5.06370 ( 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 233 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.609 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: 0.8182 (mpp) cc_final: 0.6935 (tmm) REVERT: e 24 TYR cc_start: 0.9142 (t80) cc_final: 0.8851 (t80) REVERT: N 51 ILE cc_start: 0.7902 (mp) cc_final: 0.7390 (tp) REVERT: S 109 MET cc_start: 0.8333 (tpt) cc_final: 0.8078 (tpt) REVERT: S 159 MET cc_start: 0.5556 (tpt) cc_final: 0.5217 (tpt) REVERT: S 184 ARG cc_start: 0.7633 (tpm170) cc_final: 0.7351 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.1849 time to fit residues: 66.0620 Evaluate side-chains 188 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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: 1.9990 chunk 122 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 128 optimal weight: 0.0170 overall best weight: 1.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3569 r_free = 0.3569 target = 0.076368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.065963 restraints weight = 160980.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.068044 restraints weight = 75265.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.069296 restraints weight = 45295.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.070056 restraints weight = 32248.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.070540 restraints weight = 25780.873| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 11158 Z= 0.178 Angle : 0.635 11.166 15079 Z= 0.328 Chirality : 0.081 1.747 1745 Planarity : 0.005 0.046 1860 Dihedral : 5.330 46.182 1494 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % 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: 0.43 (0.23), residues: 1344 helix: 1.03 (0.17), residues: 944 sheet: -0.82 (0.95), residues: 37 loop : -1.49 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG h 19 TYR 0.020 0.002 TYR h 18 PHE 0.025 0.001 PHE O 63 TRP 0.013 0.001 TRP a 109 HIS 0.004 0.001 HIS b 145 Details of bonding type rmsd covalent geometry : bond 0.00389 (11158) covalent geometry : angle 0.63458 (15079) hydrogen bonds : bond 0.04965 ( 771) hydrogen bonds : angle 5.04791 ( 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 226 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.572 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: a 140 MET cc_start: 0.8191 (mpp) cc_final: 0.6986 (tmm) REVERT: e 24 TYR cc_start: 0.9148 (t80) cc_final: 0.8875 (t80) REVERT: N 51 ILE cc_start: 0.7867 (mp) cc_final: 0.7366 (tp) REVERT: S 126 LEU cc_start: 0.8195 (mm) cc_final: 0.7963 (mm) REVERT: C 13 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8497 (tm-30) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.1807 time to fit residues: 61.7389 Evaluate side-chains 189 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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: 2.9990 chunk 114 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 6 optimal weight: 0.2980 chunk 1 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3571 r_free = 0.3571 target = 0.076477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.065923 restraints weight = 158603.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.068085 restraints weight = 72090.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.069366 restraints weight = 42615.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.070139 restraints weight = 30139.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.070622 restraints weight = 23841.165| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11158 Z= 0.157 Angle : 0.622 11.240 15079 Z= 0.319 Chirality : 0.081 1.753 1745 Planarity : 0.004 0.044 1860 Dihedral : 5.217 45.992 1494 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % 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: 0.59 (0.23), residues: 1344 helix: 1.12 (0.17), residues: 945 sheet: -0.84 (0.94), residues: 37 loop : -1.34 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG h 19 TYR 0.014 0.001 TYR e 15 PHE 0.035 0.001 PHE O 63 TRP 0.013 0.001 TRP a 109 HIS 0.004 0.001 HIS b 145 Details of bonding type rmsd covalent geometry : bond 0.00337 (11158) covalent geometry : angle 0.62237 (15079) hydrogen bonds : bond 0.04862 ( 771) hydrogen bonds : angle 4.93695 ( 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 222 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.518 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: a 140 MET cc_start: 0.8059 (mpp) cc_final: 0.6937 (tmm) REVERT: N 51 ILE cc_start: 0.7854 (mp) cc_final: 0.7371 (tp) REVERT: N 70 LEU cc_start: 0.8129 (mt) cc_final: 0.7685 (tp) REVERT: S 159 MET cc_start: 0.5524 (tpt) cc_final: 0.5055 (tpt) REVERT: S 166 ILE cc_start: 0.8531 (mm) cc_final: 0.7782 (mm) REVERT: C 11 ILE cc_start: 0.8643 (tp) cc_final: 0.8345 (tp) REVERT: C 14 GLU cc_start: 0.9001 (mp0) cc_final: 0.8708 (mp0) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1867 time to fit residues: 62.3562 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 : 0.937 ------------------------------------------------------------------------------- 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: 2.9990 chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 14 optimal weight: 0.4980 chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3567 r_free = 0.3567 target = 0.076144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.065860 restraints weight = 162283.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.067855 restraints weight = 75104.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.069117 restraints weight = 45443.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.069841 restraints weight = 32188.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.070381 restraints weight = 25930.943| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11158 Z= 0.183 Angle : 0.631 10.697 15079 Z= 0.327 Chirality : 0.079 1.768 1745 Planarity : 0.005 0.071 1860 Dihedral : 5.217 45.706 1494 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.08 % Allowed : 1.36 % Favored : 98.56 % 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: 0.54 (0.23), residues: 1344 helix: 1.10 (0.17), residues: 945 sheet: -0.90 (0.93), residues: 37 loop : -1.42 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 38 TYR 0.022 0.002 TYR O 49 PHE 0.040 0.002 PHE O 63 TRP 0.011 0.001 TRP a 109 HIS 0.004 0.001 HIS b 145 Details of bonding type rmsd covalent geometry : bond 0.00392 (11158) covalent geometry : angle 0.63134 (15079) hydrogen bonds : bond 0.04843 ( 771) hydrogen bonds : angle 4.97118 ( 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 223 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 0.655 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: a 140 MET cc_start: 0.8054 (mpp) cc_final: 0.6909 (tmm) REVERT: g 29 PHE cc_start: 0.7911 (p90) cc_final: 0.7685 (p90) REVERT: N 51 ILE cc_start: 0.7872 (mp) cc_final: 0.7361 (tp) REVERT: N 70 LEU cc_start: 0.8108 (mt) cc_final: 0.7655 (tp) REVERT: O 65 LEU cc_start: 0.8880 (tt) cc_final: 0.8343 (mt) REVERT: b 165 MET cc_start: 0.8473 (mtt) cc_final: 0.8253 (mtt) REVERT: S 109 MET cc_start: 0.8559 (tpt) cc_final: 0.8218 (tpt) REVERT: S 159 MET cc_start: 0.5686 (tpt) cc_final: 0.5255 (tpt) REVERT: C 13 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8512 (tm-30) outliers start: 1 outliers final: 0 residues processed: 223 average time/residue: 0.1843 time to fit residues: 62.8863 Evaluate side-chains 188 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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: 0.9990 chunk 10 optimal weight: 0.0970 chunk 108 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3573 r_free = 0.3573 target = 0.076531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.066226 restraints weight = 159689.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.068275 restraints weight = 74035.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.069502 restraints weight = 44422.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.070270 restraints weight = 31532.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.070678 restraints weight = 25099.500| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11158 Z= 0.167 Angle : 0.625 11.025 15079 Z= 0.322 Chirality : 0.081 1.767 1745 Planarity : 0.005 0.065 1860 Dihedral : 5.146 45.713 1494 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % 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: 0.70 (0.23), residues: 1344 helix: 1.22 (0.17), residues: 944 sheet: -0.93 (0.93), residues: 37 loop : -1.35 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG h 19 TYR 0.024 0.002 TYR S 23 PHE 0.037 0.002 PHE O 63 TRP 0.011 0.001 TRP a 109 HIS 0.004 0.001 HIS b 145 Details of bonding type rmsd covalent geometry : bond 0.00361 (11158) covalent geometry : angle 0.62496 (15079) hydrogen bonds : bond 0.04793 ( 771) hydrogen bonds : angle 4.87225 ( 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 228 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.645 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: a 140 MET cc_start: 0.8051 (mpp) cc_final: 0.6861 (tmm) REVERT: N 51 ILE cc_start: 0.7836 (mp) cc_final: 0.7343 (tp) REVERT: N 70 LEU cc_start: 0.8169 (mt) cc_final: 0.7751 (tp) REVERT: C 13 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8457 (tm-30) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1789 time to fit residues: 62.3300 Evaluate side-chains 192 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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: 2.9990 chunk 101 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 119 ASN a 163 ASN a 168 HIS b 122 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.076706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.066344 restraints weight = 157865.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.068440 restraints weight = 71474.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.069731 restraints weight = 42068.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.070508 restraints weight = 29435.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.070953 restraints weight = 23193.004| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2719 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= 0.140 Angle : 0.602 12.025 15079 Z= 0.306 Chirality : 0.080 1.759 1745 Planarity : 0.004 0.042 1860 Dihedral : 5.004 45.852 1494 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % 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: 1.02 (0.24), residues: 1344 helix: 1.44 (0.17), residues: 944 sheet: -0.86 (0.93), residues: 37 loop : -1.15 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 38 TYR 0.020 0.001 TYR S 23 PHE 0.035 0.001 PHE O 63 TRP 0.012 0.001 TRP a 109 HIS 0.004 0.001 HIS b 145 Details of bonding type rmsd covalent geometry : bond 0.00304 (11158) covalent geometry : angle 0.60176 (15079) hydrogen bonds : bond 0.04666 ( 771) hydrogen bonds : angle 4.70083 ( 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 232 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.718 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: 0.8121 (mpp) cc_final: 0.6866 (tmm) REVERT: N 51 ILE cc_start: 0.7796 (mp) cc_final: 0.7276 (tp) REVERT: N 70 LEU cc_start: 0.8129 (mt) cc_final: 0.7749 (tp) REVERT: S 159 MET cc_start: 0.5658 (tpt) cc_final: 0.5320 (tpt) REVERT: C 13 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8408 (tm-30) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.1915 time to fit residues: 67.2401 Evaluate side-chains 198 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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: 1.9990 chunk 11 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3569 r_free = 0.3569 target = 0.076407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.065929 restraints weight = 159267.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.068021 restraints weight = 72575.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.069282 restraints weight = 43118.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.070044 restraints weight = 30391.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.070492 restraints weight = 24126.650| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11158 Z= 0.155 Angle : 0.614 11.997 15079 Z= 0.316 Chirality : 0.080 1.756 1745 Planarity : 0.004 0.042 1860 Dihedral : 4.963 45.476 1494 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % 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: 1.06 (0.24), residues: 1344 helix: 1.48 (0.17), residues: 943 sheet: -0.91 (0.93), residues: 37 loop : -1.13 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG h 19 TYR 0.024 0.001 TYR f 66 PHE 0.035 0.001 PHE O 63 TRP 0.016 0.001 TRP a 109 HIS 0.004 0.001 HIS b 145 Details of bonding type rmsd covalent geometry : bond 0.00335 (11158) covalent geometry : angle 0.61376 (15079) hydrogen bonds : bond 0.04634 ( 771) hydrogen bonds : angle 4.72921 ( 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 226 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.636 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: a 140 MET cc_start: 0.8084 (mpp) cc_final: 0.6854 (tmm) REVERT: N 51 ILE cc_start: 0.7812 (mp) cc_final: 0.7294 (tp) REVERT: N 70 LEU cc_start: 0.8120 (mt) cc_final: 0.7740 (tp) REVERT: b 165 MET cc_start: 0.8524 (mtt) cc_final: 0.8226 (mtm) REVERT: S 109 MET cc_start: 0.8482 (tpt) cc_final: 0.8214 (tpt) REVERT: C 11 ILE cc_start: 0.8633 (tp) cc_final: 0.8368 (tp) REVERT: C 13 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8324 (tm-30) REVERT: C 14 GLU cc_start: 0.9068 (mp0) cc_final: 0.8641 (mp0) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.1860 time to fit residues: 63.4161 Evaluate side-chains 192 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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: 0.9980 chunk 16 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 0.0870 chunk 123 optimal weight: 0.3980 chunk 64 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3582 r_free = 0.3582 target = 0.076879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.066451 restraints weight = 157938.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.068604 restraints weight = 71359.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.069893 restraints weight = 42130.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.070638 restraints weight = 29546.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.071193 restraints weight = 23658.772| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3081 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= 0.133 Angle : 0.616 12.017 15079 Z= 0.316 Chirality : 0.080 1.746 1745 Planarity : 0.004 0.041 1860 Dihedral : 4.893 45.283 1494 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.08 % Allowed : 0.25 % 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: 1.21 (0.24), residues: 1344 helix: 1.57 (0.17), residues: 944 sheet: -0.70 (0.95), residues: 37 loop : -1.04 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 38 TYR 0.017 0.001 TYR S 23 PHE 0.039 0.002 PHE M 69 TRP 0.014 0.001 TRP a 109 HIS 0.005 0.001 HIS a 168 Details of bonding type rmsd covalent geometry : bond 0.00289 (11158) covalent geometry : angle 0.61609 (15079) hydrogen bonds : bond 0.04601 ( 771) hydrogen bonds : angle 4.64812 ( 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 235 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 0.574 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: 0.8088 (mpp) cc_final: 0.6802 (tmm) REVERT: N 51 ILE cc_start: 0.7877 (mp) cc_final: 0.7349 (tp) REVERT: N 70 LEU cc_start: 0.8116 (mt) cc_final: 0.7742 (tp) REVERT: O 66 MET cc_start: 0.7793 (tpp) cc_final: 0.7156 (tmm) REVERT: b 66 PHE cc_start: 0.8672 (t80) cc_final: 0.8409 (t80) REVERT: b 109 ASP cc_start: 0.8379 (m-30) cc_final: 0.7731 (t0) REVERT: b 165 MET cc_start: 0.8545 (mtt) cc_final: 0.8258 (mtm) REVERT: S 159 MET cc_start: 0.5822 (tpt) cc_final: 0.5424 (tpt) REVERT: S 184 ARG cc_start: 0.7635 (tpm170) cc_final: 0.7383 (tpp-160) REVERT: C 13 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8284 (tm-30) outliers start: 1 outliers final: 0 residues processed: 235 average time/residue: 0.1954 time to fit residues: 68.2809 Evaluate side-chains 195 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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: 4.9990 chunk 55 optimal weight: 0.8980 chunk 128 optimal weight: 0.1980 chunk 15 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.076976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.066731 restraints weight = 157991.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.068794 restraints weight = 73293.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.070067 restraints weight = 43851.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.070830 restraints weight = 30942.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.071268 restraints weight = 24613.296| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11158 Z= 0.133 Angle : 0.599 11.986 15079 Z= 0.305 Chirality : 0.080 1.739 1745 Planarity : 0.004 0.040 1860 Dihedral : 4.823 45.081 1494 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.08 % Allowed : 0.59 % Favored : 99.32 % 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: 1.30 (0.24), residues: 1344 helix: 1.64 (0.17), residues: 948 sheet: -0.70 (0.96), residues: 37 loop : -1.04 (0.35), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG h 19 TYR 0.022 0.001 TYR f 66 PHE 0.031 0.001 PHE O 63 TRP 0.015 0.001 TRP a 109 HIS 0.005 0.001 HIS a 168 Details of bonding type rmsd covalent geometry : bond 0.00290 (11158) covalent geometry : angle 0.59905 (15079) hydrogen bonds : bond 0.04491 ( 771) hydrogen bonds : angle 4.61340 ( 2271) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3447.61 seconds wall clock time: 59 minutes 37.31 seconds (3577.31 seconds total)