Starting phenix.real_space_refine on Sat Aug 23 15:11:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tii_41289/08_2025/8tii_41289_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tii_41289/08_2025/8tii_41289.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tii_41289/08_2025/8tii_41289_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tii_41289/08_2025/8tii_41289_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tii_41289/08_2025/8tii_41289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tii_41289/08_2025/8tii_41289.map" } resolution = 3.0 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= 0.001 sd= 0.103 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 25 5.16 5 C 4149 2.51 5 N 1101 2.21 5 O 1256 1.98 5 H 6420 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12953 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 4794 Classifications: {'peptide': 297} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 273} Chain breaks: 7 Chain: "H" Number of atoms: 3182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3182 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Chain breaks: 3 Chain: "L" Number of atoms: 3116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 3116 Classifications: {'peptide': 204} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 192} Chain breaks: 1 Chain: "N" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1752 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 109 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.94, per 1000 atoms: 0.15 Number of scatterers: 12953 At special positions: 0 Unit cell: (65.88, 105.84, 128.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 25 16.00 P 2 15.00 O 1256 8.00 N 1101 7.00 C 4149 6.00 H 6420 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 215 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 342.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1574 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 19 sheets defined 4.9% alpha, 48.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.887A pdb=" N ARG A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 220 through 223 Processing helix chain 'L' and resid 122 through 129 removed outlier: 3.571A pdb=" N SER L 128 " --> pdb=" O SER L 124 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY L 129 " --> pdb=" O GLN L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 188 removed outlier: 3.640A pdb=" N GLU L 188 " --> pdb=" O LYS L 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 184 through 188' Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.920A pdb=" N GLN N 65 " --> pdb=" O ASP N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 118 removed outlier: 3.521A pdb=" N VAL A 40 " --> pdb=" O TYR A 21 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 42 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR A 19 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL A 8 " --> pdb=" O SEP R 355 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SEP R 355 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS A 10 " --> pdb=" O GLU R 353 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.545A pdb=" N ILE A 168 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A 141 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL A 53 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLN A 85 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL A 55 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN A 83 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 57 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL A 81 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N CYS A 59 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA4, first strand: chain 'A' and resid 183 through 187 Processing sheet with id=AA5, first strand: chain 'A' and resid 249 through 258 removed outlier: 6.365A pdb=" N LYS A 250 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ALA A 239 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLN A 237 " --> pdb=" O PRO A 252 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA7, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.514A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR H 121 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.514A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N SER H 55 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N SER H 35 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 139 through 143 removed outlier: 5.089A pdb=" N ALA H 156 " --> pdb=" O VAL H 203 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL H 203 " --> pdb=" O ALA H 156 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLY H 158 " --> pdb=" O VAL H 201 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL H 201 " --> pdb=" O GLY H 158 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LEU H 160 " --> pdb=" O SER H 199 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N SER H 199 " --> pdb=" O LEU H 160 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS H 162 " --> pdb=" O LEU H 197 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU H 197 " --> pdb=" O LYS H 162 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 139 through 143 removed outlier: 5.089A pdb=" N ALA H 156 " --> pdb=" O VAL H 203 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL H 203 " --> pdb=" O ALA H 156 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLY H 158 " --> pdb=" O VAL H 201 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL H 201 " --> pdb=" O GLY H 158 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LEU H 160 " --> pdb=" O SER H 199 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N SER H 199 " --> pdb=" O LEU H 160 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS H 162 " --> pdb=" O LEU H 197 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU H 197 " --> pdb=" O LYS H 162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 170 through 173 removed outlier: 3.538A pdb=" N TYR H 213 " --> pdb=" O VAL H 230 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AB4, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.791A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.331A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.519A pdb=" N ASN L 139 " --> pdb=" O TYR L 174 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR L 179 " --> pdb=" O GLN L 161 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.519A pdb=" N ASN L 139 " --> pdb=" O TYR L 174 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER L 175 " --> pdb=" O THR L 165 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 145 through 150 Processing sheet with id=AB9, first strand: chain 'N' and resid 5 through 7 Processing sheet with id=AC1, first strand: chain 'N' and resid 58 through 60 removed outlier: 4.011A pdb=" N GLU N 44 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA N 40 " --> pdb=" O GLU N 44 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 266 hydrogen bonds defined for protein. 699 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: 2.55 Time building geometry restraints manager: 1.31 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: 6410 1.03 - 1.23: 38 1.23 - 1.42: 2797 1.42 - 1.62: 3819 1.62 - 1.82: 34 Bond restraints: 13098 Sorted by residual: bond pdb=" CG2 TPO R 352 " pdb="HG23 TPO R 352 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" CG2 TPO R 352 " pdb="HG21 TPO R 352 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" CB TPO R 352 " pdb=" HB TPO R 352 " ideal model delta sigma weight residual 0.970 1.089 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" CG2 TPO R 352 " pdb="HG22 TPO R 352 " ideal model delta sigma weight residual 0.970 1.089 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" OG1 TPO R 352 " pdb=" P TPO R 352 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.81e+01 ... (remaining 13093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 23485 1.97 - 3.94: 120 3.94 - 5.91: 8 5.91 - 7.88: 2 7.88 - 9.85: 2 Bond angle restraints: 23617 Sorted by residual: angle pdb=" CB TPO R 352 " pdb=" OG1 TPO R 352 " pdb=" P TPO R 352 " ideal model delta sigma weight residual 119.31 109.46 9.85 3.00e+00 1.11e-01 1.08e+01 angle pdb=" C SER L 51 " pdb=" N ALA L 52 " pdb=" CA ALA L 52 " ideal model delta sigma weight residual 121.54 127.55 -6.01 1.91e+00 2.74e-01 9.91e+00 angle pdb=" OG1 TPO R 352 " pdb=" P TPO R 352 " pdb=" O1P TPO R 352 " ideal model delta sigma weight residual 100.43 108.99 -8.56 3.00e+00 1.11e-01 8.14e+00 angle pdb=" N PHE L 140 " pdb=" CA PHE L 140 " pdb=" C PHE L 140 " ideal model delta sigma weight residual 108.34 112.95 -4.61 1.64e+00 3.72e-01 7.90e+00 angle pdb=" N MET A 352 " pdb=" CA MET A 352 " pdb=" C MET A 352 " ideal model delta sigma weight residual 108.19 111.51 -3.32 1.29e+00 6.01e-01 6.63e+00 ... (remaining 23612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 5775 16.33 - 32.66: 343 32.66 - 49.00: 111 49.00 - 65.33: 33 65.33 - 81.66: 3 Dihedral angle restraints: 6265 sinusoidal: 3367 harmonic: 2898 Sorted by residual: dihedral pdb=" CA TYR H 116 " pdb=" C TYR H 116 " pdb=" N GLY H 117 " pdb=" CA GLY H 117 " ideal model delta harmonic sigma weight residual -180.00 -160.21 -19.79 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA TRP H 111 " pdb=" CB TRP H 111 " pdb=" CG TRP H 111 " pdb=" CD1 TRP H 111 " ideal model delta sinusoidal sigma weight residual 90.00 169.86 -79.86 2 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA LYS L 170 " pdb=" CB LYS L 170 " pdb=" CG LYS L 170 " pdb=" CD LYS L 170 " ideal model delta sinusoidal sigma weight residual 60.00 119.72 -59.72 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 6262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 646 0.034 - 0.068: 256 0.068 - 0.102: 57 0.102 - 0.136: 57 0.136 - 0.169: 3 Chirality restraints: 1019 Sorted by residual: chirality pdb=" CA VAL H 40 " pdb=" N VAL H 40 " pdb=" C VAL H 40 " pdb=" CB VAL H 40 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA ILE L 22 " pdb=" N ILE L 22 " pdb=" C ILE L 22 " pdb=" CB ILE L 22 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA VAL H 203 " pdb=" N VAL H 203 " pdb=" C VAL H 203 " pdb=" CB VAL H 203 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 1016 not shown) Planarity restraints: 1918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 167 " -0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO H 168 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO H 168 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 168 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 203 " -0.020 5.00e-02 4.00e+02 2.95e-02 1.39e+00 pdb=" N PRO H 204 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO H 204 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 204 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 181 " -0.019 5.00e-02 4.00e+02 2.94e-02 1.38e+00 pdb=" N PRO A 182 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 182 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 182 " -0.017 5.00e-02 4.00e+02 ... (remaining 1915 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 655 2.19 - 2.80: 26747 2.80 - 3.40: 32962 3.40 - 4.00: 46376 4.00 - 4.60: 70629 Nonbonded interactions: 177369 Sorted by model distance: nonbonded pdb=" O LYS L 191 " pdb=" H ARG L 212 " model vdw 1.594 2.450 nonbonded pdb="HH12 ARG A 25 " pdb=" O2P TPO R 352 " model vdw 1.606 2.450 nonbonded pdb=" HE2 HIS A 210 " pdb=" O LEU A 300 " model vdw 1.606 2.450 nonbonded pdb=" OD1 ASP L 168 " pdb=" H SER L 169 " model vdw 1.613 2.450 nonbonded pdb=" O ALA A 263 " pdb=" HG SER A 266 " model vdw 1.616 2.450 ... (remaining 177364 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 0.040 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.170 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 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 : 0.003 0.106 6683 Z= 0.160 Angle : 0.557 9.852 9072 Z= 0.298 Chirality : 0.044 0.169 1019 Planarity : 0.003 0.034 1143 Dihedral : 11.322 81.659 2421 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.90 % Allowed : 7.86 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.31), residues: 801 helix: 0.30 (1.22), residues: 22 sheet: -0.31 (0.26), residues: 424 loop : -1.27 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 101 TYR 0.009 0.001 TYR H 36 PHE 0.011 0.001 PHE A 277 TRP 0.004 0.001 TRP H 50 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 6678) covalent geometry : angle 0.55645 ( 9062) SS BOND : bond 0.00250 ( 5) SS BOND : angle 0.71292 ( 10) hydrogen bonds : bond 0.11850 ( 229) hydrogen bonds : angle 6.74739 ( 699) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.291 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: A 99 ARG cc_start: 0.7394 (mtt180) cc_final: 0.7139 (mmp80) REVERT: A 103 ARG cc_start: 0.6409 (mtt180) cc_final: 0.5965 (mtm110) REVERT: A 145 GLU cc_start: 0.6270 (tt0) cc_final: 0.6003 (tt0) REVERT: A 192 MET cc_start: 0.7897 (mtt) cc_final: 0.7461 (mtp) REVERT: H 15 VAL cc_start: 0.7673 (OUTLIER) cc_final: 0.7426 (p) REVERT: L 28 GLN cc_start: 0.7330 (tt0) cc_final: 0.6929 (mp10) REVERT: L 150 LYS cc_start: 0.6086 (mttt) cc_final: 0.5858 (mmmt) REVERT: L 162 GLU cc_start: 0.7136 (mp0) cc_final: 0.6933 (mp0) REVERT: N 104 TYR cc_start: 0.6471 (OUTLIER) cc_final: 0.4601 (m-80) outliers start: 21 outliers final: 11 residues processed: 131 average time/residue: 0.8298 time to fit residues: 115.4030 Evaluate side-chains 86 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 172 SER Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain N residue 52 ARG Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 104 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.1980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.192018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.151758 restraints weight = 18455.990| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.18 r_work: 0.3800 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6683 Z= 0.106 Angle : 0.509 5.170 9072 Z= 0.265 Chirality : 0.045 0.150 1019 Planarity : 0.004 0.048 1143 Dihedral : 7.451 79.241 934 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.34 % Allowed : 14.34 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.31), residues: 801 helix: 0.03 (1.13), residues: 22 sheet: -0.00 (0.27), residues: 412 loop : -1.28 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 67 TYR 0.009 0.001 TYR A 113 PHE 0.012 0.001 PHE A 277 TRP 0.006 0.001 TRP H 122 HIS 0.005 0.001 HIS A 210 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 6678) covalent geometry : angle 0.50846 ( 9062) SS BOND : bond 0.00364 ( 5) SS BOND : angle 0.73285 ( 10) hydrogen bonds : bond 0.03303 ( 229) hydrogen bonds : angle 5.53689 ( 699) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.275 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: A 145 GLU cc_start: 0.6312 (tt0) cc_final: 0.6092 (tt0) REVERT: A 192 MET cc_start: 0.7919 (mtt) cc_final: 0.7463 (mtp) REVERT: H 15 VAL cc_start: 0.7570 (OUTLIER) cc_final: 0.7305 (p) REVERT: L 28 GLN cc_start: 0.7505 (tt0) cc_final: 0.6920 (mp10) REVERT: L 150 LYS cc_start: 0.6161 (mttt) cc_final: 0.5874 (mmmt) REVERT: L 162 GLU cc_start: 0.7362 (mp0) cc_final: 0.7143 (mp0) REVERT: N 36 TRP cc_start: 0.6718 (m100) cc_final: 0.6472 (m100) REVERT: N 104 TYR cc_start: 0.6420 (OUTLIER) cc_final: 0.4410 (m-80) REVERT: N 115 THR cc_start: 0.7271 (m) cc_final: 0.6732 (p) outliers start: 17 outliers final: 11 residues processed: 95 average time/residue: 0.7485 time to fit residues: 75.9155 Evaluate side-chains 84 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 52 ARG Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 104 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.0070 chunk 17 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.192232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.150786 restraints weight = 18649.007| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.18 r_work: 0.3777 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6683 Z= 0.114 Angle : 0.504 4.911 9072 Z= 0.261 Chirality : 0.044 0.153 1019 Planarity : 0.005 0.064 1143 Dihedral : 7.271 79.291 930 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.17 % Allowed : 14.48 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.31), residues: 801 helix: -0.58 (1.02), residues: 24 sheet: 0.07 (0.27), residues: 418 loop : -1.30 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 212 TYR 0.012 0.001 TYR L 141 PHE 0.011 0.001 PHE N 47 TRP 0.005 0.001 TRP H 50 HIS 0.003 0.001 HIS L 199 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 6678) covalent geometry : angle 0.50413 ( 9062) SS BOND : bond 0.00247 ( 5) SS BOND : angle 0.72581 ( 10) hydrogen bonds : bond 0.03013 ( 229) hydrogen bonds : angle 5.31476 ( 699) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.6373 (tt0) cc_final: 0.6159 (tt0) REVERT: A 192 MET cc_start: 0.8016 (mtt) cc_final: 0.7524 (mtp) REVERT: A 290 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.6925 (m-30) REVERT: H 15 VAL cc_start: 0.7538 (OUTLIER) cc_final: 0.7288 (p) REVERT: L 28 GLN cc_start: 0.7448 (tt0) cc_final: 0.6929 (mp10) REVERT: L 150 LYS cc_start: 0.6048 (mttt) cc_final: 0.5788 (mmmt) REVERT: N 36 TRP cc_start: 0.6687 (m100) cc_final: 0.6410 (m100) REVERT: N 115 THR cc_start: 0.7287 (m) cc_final: 0.6779 (p) outliers start: 23 outliers final: 13 residues processed: 98 average time/residue: 0.6803 time to fit residues: 72.1003 Evaluate side-chains 85 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 104 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 45 optimal weight: 0.1980 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 30 optimal weight: 0.0170 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.192252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.151236 restraints weight = 18499.282| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.15 r_work: 0.3842 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 6683 Z= 0.102 Angle : 0.486 4.768 9072 Z= 0.251 Chirality : 0.044 0.149 1019 Planarity : 0.004 0.043 1143 Dihedral : 6.866 79.271 926 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.17 % Allowed : 15.17 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.31), residues: 801 helix: -0.15 (1.10), residues: 22 sheet: 0.15 (0.27), residues: 418 loop : -1.18 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 67 TYR 0.017 0.001 TYR H 164 PHE 0.013 0.001 PHE A 277 TRP 0.007 0.001 TRP H 50 HIS 0.003 0.001 HIS L 199 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 6678) covalent geometry : angle 0.48580 ( 9062) SS BOND : bond 0.00324 ( 5) SS BOND : angle 0.74014 ( 10) hydrogen bonds : bond 0.02833 ( 229) hydrogen bonds : angle 5.14856 ( 699) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 94 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.6353 (tt0) cc_final: 0.6009 (tt0) REVERT: A 170 LYS cc_start: 0.6166 (mtpp) cc_final: 0.5858 (mttt) REVERT: A 192 MET cc_start: 0.8014 (mtt) cc_final: 0.7524 (mtp) REVERT: A 290 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7000 (m-30) REVERT: H 9 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7216 (tt0) REVERT: H 15 VAL cc_start: 0.7500 (OUTLIER) cc_final: 0.7250 (p) REVERT: H 223 ASN cc_start: 0.7184 (p0) cc_final: 0.6944 (m-40) REVERT: L 28 GLN cc_start: 0.7515 (tt0) cc_final: 0.6986 (mp10) REVERT: N 36 TRP cc_start: 0.6556 (m100) cc_final: 0.6274 (m100) REVERT: N 104 TYR cc_start: 0.6274 (OUTLIER) cc_final: 0.4382 (m-80) REVERT: N 115 THR cc_start: 0.7299 (m) cc_final: 0.6789 (p) outliers start: 23 outliers final: 13 residues processed: 91 average time/residue: 0.6347 time to fit residues: 62.3536 Evaluate side-chains 88 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 52 ARG Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 104 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.188033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.145978 restraints weight = 18724.193| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.21 r_work: 0.3816 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 6683 Z= 0.192 Angle : 0.572 5.151 9072 Z= 0.299 Chirality : 0.046 0.166 1019 Planarity : 0.005 0.036 1143 Dihedral : 7.179 78.910 925 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 3.86 % Allowed : 15.72 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.31), residues: 801 helix: -0.44 (1.07), residues: 22 sheet: -0.05 (0.27), residues: 419 loop : -1.30 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 103 TYR 0.020 0.002 TYR H 164 PHE 0.017 0.002 PHE L 140 TRP 0.009 0.002 TRP L 36 HIS 0.004 0.001 HIS L 199 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 6678) covalent geometry : angle 0.57094 ( 9062) SS BOND : bond 0.00406 ( 5) SS BOND : angle 1.16273 ( 10) hydrogen bonds : bond 0.03350 ( 229) hydrogen bonds : angle 5.45110 ( 699) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 VAL cc_start: 0.1523 (OUTLIER) cc_final: 0.1285 (p) REVERT: A 192 MET cc_start: 0.8074 (mtt) cc_final: 0.7603 (mtp) REVERT: H 9 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: H 15 VAL cc_start: 0.7528 (OUTLIER) cc_final: 0.7280 (p) REVERT: H 223 ASN cc_start: 0.7244 (p0) cc_final: 0.6996 (m-40) REVERT: L 28 GLN cc_start: 0.7405 (tt0) cc_final: 0.6918 (mp10) REVERT: N 36 TRP cc_start: 0.6524 (m100) cc_final: 0.6239 (m100) REVERT: N 104 TYR cc_start: 0.6391 (OUTLIER) cc_final: 0.4503 (m-80) REVERT: N 115 THR cc_start: 0.7343 (m) cc_final: 0.6816 (p) outliers start: 28 outliers final: 16 residues processed: 97 average time/residue: 0.6693 time to fit residues: 70.4705 Evaluate side-chains 90 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 39 TRP Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 52 ARG Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 104 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 54 optimal weight: 0.2980 chunk 24 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.187545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.145566 restraints weight = 18522.339| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.19 r_work: 0.3781 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 6683 Z= 0.194 Angle : 0.578 5.589 9072 Z= 0.302 Chirality : 0.046 0.170 1019 Planarity : 0.005 0.037 1143 Dihedral : 7.160 79.426 925 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.00 % Allowed : 16.41 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.10 (0.31), residues: 801 helix: -0.56 (1.04), residues: 22 sheet: -0.16 (0.27), residues: 421 loop : -1.38 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 103 TYR 0.020 0.002 TYR H 164 PHE 0.015 0.002 PHE A 277 TRP 0.009 0.002 TRP L 36 HIS 0.004 0.001 HIS H 183 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 6678) covalent geometry : angle 0.57646 ( 9062) SS BOND : bond 0.00414 ( 5) SS BOND : angle 1.19454 ( 10) hydrogen bonds : bond 0.03352 ( 229) hydrogen bonds : angle 5.53878 ( 699) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 VAL cc_start: 0.1387 (OUTLIER) cc_final: 0.1146 (p) REVERT: A 192 MET cc_start: 0.8119 (mtt) cc_final: 0.7664 (mtp) REVERT: H 9 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7508 (tt0) REVERT: H 15 VAL cc_start: 0.7578 (OUTLIER) cc_final: 0.7342 (p) REVERT: H 223 ASN cc_start: 0.7303 (p0) cc_final: 0.7010 (m-40) REVERT: L 28 GLN cc_start: 0.7341 (tt0) cc_final: 0.6865 (mp10) REVERT: N 36 TRP cc_start: 0.6466 (m100) cc_final: 0.6170 (m100) REVERT: N 104 TYR cc_start: 0.6436 (OUTLIER) cc_final: 0.4431 (m-80) REVERT: N 115 THR cc_start: 0.7200 (m) cc_final: 0.6668 (p) outliers start: 29 outliers final: 20 residues processed: 96 average time/residue: 0.5691 time to fit residues: 59.5230 Evaluate side-chains 94 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 39 TRP Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 52 ARG Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 104 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.188202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.144007 restraints weight = 18548.080| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.35 r_work: 0.3745 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6683 Z= 0.123 Angle : 0.522 6.290 9072 Z= 0.270 Chirality : 0.045 0.160 1019 Planarity : 0.004 0.039 1143 Dihedral : 6.921 79.525 924 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.00 % Allowed : 16.69 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.31), residues: 801 helix: -0.22 (1.08), residues: 22 sheet: -0.01 (0.27), residues: 419 loop : -1.31 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 212 TYR 0.022 0.001 TYR H 164 PHE 0.012 0.001 PHE A 277 TRP 0.007 0.001 TRP H 50 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 6678) covalent geometry : angle 0.52111 ( 9062) SS BOND : bond 0.00295 ( 5) SS BOND : angle 0.90709 ( 10) hydrogen bonds : bond 0.02948 ( 229) hydrogen bonds : angle 5.30035 ( 699) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 0.362 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: A 164 VAL cc_start: 0.1423 (OUTLIER) cc_final: 0.1188 (p) REVERT: A 192 MET cc_start: 0.8113 (mtt) cc_final: 0.7656 (mtp) REVERT: H 9 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7481 (tt0) REVERT: H 15 VAL cc_start: 0.7541 (OUTLIER) cc_final: 0.7308 (p) REVERT: H 223 ASN cc_start: 0.7415 (p0) cc_final: 0.7134 (m-40) REVERT: L 28 GLN cc_start: 0.7394 (tt0) cc_final: 0.6833 (mp10) REVERT: N 4 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7106 (mt) REVERT: N 104 TYR cc_start: 0.6340 (OUTLIER) cc_final: 0.4309 (m-80) REVERT: N 115 THR cc_start: 0.7032 (m) cc_final: 0.6562 (p) outliers start: 29 outliers final: 21 residues processed: 94 average time/residue: 0.6524 time to fit residues: 66.4324 Evaluate side-chains 94 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 39 TRP Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 162 GLU Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 52 ARG Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 104 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 54 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 72 optimal weight: 0.0270 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.191467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.150768 restraints weight = 18478.128| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 2.18 r_work: 0.3840 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3694 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 6683 Z= 0.103 Angle : 0.501 7.044 9072 Z= 0.257 Chirality : 0.044 0.150 1019 Planarity : 0.004 0.041 1143 Dihedral : 6.703 79.249 924 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.45 % Allowed : 17.10 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.31), residues: 801 helix: 0.20 (1.06), residues: 24 sheet: 0.12 (0.27), residues: 419 loop : -1.26 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 212 TYR 0.023 0.001 TYR H 164 PHE 0.009 0.001 PHE A 277 TRP 0.006 0.001 TRP H 50 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 6678) covalent geometry : angle 0.50018 ( 9062) SS BOND : bond 0.00268 ( 5) SS BOND : angle 0.76316 ( 10) hydrogen bonds : bond 0.02725 ( 229) hydrogen bonds : angle 5.09120 ( 699) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 96 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 VAL cc_start: 0.1455 (OUTLIER) cc_final: 0.1232 (p) REVERT: A 170 LYS cc_start: 0.6149 (mtpp) cc_final: 0.5768 (mttt) REVERT: A 192 MET cc_start: 0.8107 (mtt) cc_final: 0.7661 (mtp) REVERT: H 15 VAL cc_start: 0.7514 (OUTLIER) cc_final: 0.7271 (p) REVERT: H 164 TYR cc_start: 0.6954 (p90) cc_final: 0.6682 (p90) REVERT: H 223 ASN cc_start: 0.7331 (p0) cc_final: 0.6994 (m-40) REVERT: L 28 GLN cc_start: 0.7436 (tt0) cc_final: 0.6947 (mp10) REVERT: N 104 TYR cc_start: 0.6337 (OUTLIER) cc_final: 0.4464 (m-80) REVERT: N 115 THR cc_start: 0.7042 (m) cc_final: 0.6587 (p) outliers start: 25 outliers final: 20 residues processed: 92 average time/residue: 0.6338 time to fit residues: 63.1633 Evaluate side-chains 91 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 39 TRP Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 162 GLU Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 52 ARG Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 104 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 15 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.190869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.149404 restraints weight = 18555.149| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.22 r_work: 0.3813 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 6683 Z= 0.126 Angle : 0.524 7.330 9072 Z= 0.269 Chirality : 0.045 0.154 1019 Planarity : 0.004 0.040 1143 Dihedral : 6.717 79.021 924 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.45 % Allowed : 17.79 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.31), residues: 801 helix: 0.26 (1.05), residues: 24 sheet: 0.10 (0.27), residues: 419 loop : -1.28 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 212 TYR 0.023 0.001 TYR H 164 PHE 0.011 0.001 PHE L 140 TRP 0.006 0.001 TRP H 50 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6678) covalent geometry : angle 0.52294 ( 9062) SS BOND : bond 0.00312 ( 5) SS BOND : angle 1.01688 ( 10) hydrogen bonds : bond 0.02834 ( 229) hydrogen bonds : angle 5.12173 ( 699) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.364 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: A 164 VAL cc_start: 0.1465 (OUTLIER) cc_final: 0.1237 (p) REVERT: A 170 LYS cc_start: 0.6165 (mtpp) cc_final: 0.5803 (mttt) REVERT: A 192 MET cc_start: 0.8092 (mtt) cc_final: 0.7654 (mtp) REVERT: A 290 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7038 (m-30) REVERT: H 15 VAL cc_start: 0.7515 (OUTLIER) cc_final: 0.7278 (p) REVERT: H 126 THR cc_start: 0.7516 (OUTLIER) cc_final: 0.7208 (p) REVERT: H 223 ASN cc_start: 0.7347 (p0) cc_final: 0.7004 (m-40) REVERT: L 28 GLN cc_start: 0.7424 (tt0) cc_final: 0.6924 (mp10) REVERT: N 4 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7142 (mt) REVERT: N 104 TYR cc_start: 0.6333 (OUTLIER) cc_final: 0.4449 (m-80) REVERT: N 115 THR cc_start: 0.7040 (m) cc_final: 0.6566 (p) outliers start: 25 outliers final: 19 residues processed: 88 average time/residue: 0.7498 time to fit residues: 71.4720 Evaluate side-chains 92 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 39 TRP Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 162 GLU Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 52 ARG Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 104 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 27 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.191403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.150526 restraints weight = 18524.300| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 2.18 r_work: 0.3840 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3694 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6683 Z= 0.113 Angle : 0.518 7.970 9072 Z= 0.264 Chirality : 0.044 0.150 1019 Planarity : 0.004 0.041 1143 Dihedral : 6.645 79.244 924 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.31 % Allowed : 17.93 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.31), residues: 801 helix: 0.44 (1.08), residues: 24 sheet: 0.15 (0.27), residues: 419 loop : -1.24 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 212 TYR 0.022 0.001 TYR H 164 PHE 0.010 0.001 PHE A 277 TRP 0.006 0.001 TRP H 50 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 6678) covalent geometry : angle 0.51651 ( 9062) SS BOND : bond 0.00354 ( 5) SS BOND : angle 1.10921 ( 10) hydrogen bonds : bond 0.02757 ( 229) hydrogen bonds : angle 5.06140 ( 699) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.244 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: A 164 VAL cc_start: 0.1481 (OUTLIER) cc_final: 0.1255 (p) REVERT: A 170 LYS cc_start: 0.6115 (mtpp) cc_final: 0.5820 (mttt) REVERT: A 192 MET cc_start: 0.8092 (mtt) cc_final: 0.7661 (mtp) REVERT: A 290 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.6682 (m-30) REVERT: H 15 VAL cc_start: 0.7508 (OUTLIER) cc_final: 0.7270 (p) REVERT: H 223 ASN cc_start: 0.7358 (p0) cc_final: 0.7010 (m-40) REVERT: L 28 GLN cc_start: 0.7398 (tt0) cc_final: 0.6919 (mp10) REVERT: N 104 TYR cc_start: 0.6343 (OUTLIER) cc_final: 0.4476 (m-80) REVERT: N 115 THR cc_start: 0.7044 (m) cc_final: 0.6575 (p) outliers start: 24 outliers final: 19 residues processed: 89 average time/residue: 0.6349 time to fit residues: 61.5049 Evaluate side-chains 90 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 39 TRP Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 111 TRP Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 162 GLU Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain L residue 173 THR Chi-restraints excluded: chain N residue 35 SER Chi-restraints excluded: chain N residue 52 ARG Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 104 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 62 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 21 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.192245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.150123 restraints weight = 18460.196| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 2.25 r_work: 0.3783 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6683 Z= 0.115 Angle : 0.520 8.135 9072 Z= 0.266 Chirality : 0.044 0.152 1019 Planarity : 0.004 0.041 1143 Dihedral : 6.611 79.109 924 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.59 % Allowed : 17.38 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.31), residues: 801 helix: 0.37 (1.03), residues: 24 sheet: 0.25 (0.27), residues: 409 loop : -1.28 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 62 TYR 0.029 0.001 TYR H 164 PHE 0.010 0.001 PHE A 277 TRP 0.006 0.001 TRP H 50 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 6678) covalent geometry : angle 0.51880 ( 9062) SS BOND : bond 0.00355 ( 5) SS BOND : angle 1.14931 ( 10) hydrogen bonds : bond 0.02765 ( 229) hydrogen bonds : angle 5.02693 ( 699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4286.53 seconds wall clock time: 73 minutes 7.66 seconds (4387.66 seconds total)