Starting phenix.real_space_refine on Thu May 15 08:03:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tii_41289/05_2025/8tii_41289_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tii_41289/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tii_41289/05_2025/8tii_41289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tii_41289/05_2025/8tii_41289.map" model { file = "/net/cci-nas-00/data/ceres_data/8tii_41289/05_2025/8tii_41289_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tii_41289/05_2025/8tii_41289_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.86, per 1000 atoms: 0.53 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: 3.58 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.53 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: 4.52 Time building geometry restraints manager: 4.23 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: 0.980 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: 0.220 Extract box with map and model: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 30.700 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:10.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.500 ------------------------------------------------------------------------------- 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 : 4.86 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (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 TRP 0.004 0.001 TRP H 50 HIS 0.003 0.001 HIS H 38 PHE 0.011 0.001 PHE A 277 TYR 0.009 0.001 TYR H 36 ARG 0.003 0.000 ARG H 101 Details of bonding type rmsd hydrogen bonds : bond 0.11850 ( 229) hydrogen bonds : angle 6.74739 ( 699) SS BOND : bond 0.00250 ( 5) SS BOND : angle 0.71292 ( 10) covalent geometry : bond 0.00326 ( 6678) covalent geometry : angle 0.55645 ( 9062) *********************** 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 : 1.085 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: 0.6023 (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: 1.9706 time to fit residues: 274.6186 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 : 0.956 ------------------------------------------------------------------------------- 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 68 optimal weight: 3.9990 chunk 61 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- 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 = 0.4409 r_free = 0.4409 target = 0.191423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.151174 restraints weight = 18549.112| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.17 r_work: 0.3803 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.1522 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= 0.117 Angle : 0.517 4.999 9072 Z= 0.270 Chirality : 0.045 0.152 1019 Planarity : 0.004 0.053 1143 Dihedral : 7.489 79.205 934 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.62 % Allowed : 14.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.31), residues: 801 helix: 0.02 (1.13), residues: 22 sheet: -0.03 (0.27), residues: 412 loop : -1.31 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 122 HIS 0.005 0.001 HIS A 210 PHE 0.013 0.001 PHE A 277 TYR 0.009 0.001 TYR A 113 ARG 0.005 0.000 ARG N 67 Details of bonding type rmsd hydrogen bonds : bond 0.03332 ( 229) hydrogen bonds : angle 5.56437 ( 699) SS BOND : bond 0.00241 ( 5) SS BOND : angle 0.69377 ( 10) covalent geometry : bond 0.00275 ( 6678) covalent geometry : angle 0.51666 ( 9062) *********************** 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 98 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.978 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: A 145 GLU cc_start: 0.6336 (tt0) cc_final: 0.6131 (tt0) REVERT: A 192 MET cc_start: 0.7921 (mtt) cc_final: 0.7464 (mtp) REVERT: A 290 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.6911 (m-30) REVERT: H 15 VAL cc_start: 0.7609 (OUTLIER) cc_final: 0.7348 (p) REVERT: L 28 GLN cc_start: 0.7495 (tt0) cc_final: 0.6958 (mp10) REVERT: L 150 LYS cc_start: 0.6162 (mttt) cc_final: 0.5875 (mmmt) REVERT: L 162 GLU cc_start: 0.7371 (mp0) cc_final: 0.7144 (mp0) REVERT: N 36 TRP cc_start: 0.6578 (m100) cc_final: 0.6325 (m100) REVERT: N 104 TYR cc_start: 0.6441 (OUTLIER) cc_final: 0.4431 (m-80) REVERT: N 115 THR cc_start: 0.7285 (m) cc_final: 0.6746 (p) outliers start: 19 outliers final: 11 residues processed: 96 average time/residue: 1.8577 time to fit residues: 190.9152 Evaluate side-chains 85 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 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 15 optimal weight: 0.8980 chunk 46 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 45 optimal weight: 0.0270 chunk 3 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.0070 chunk 34 optimal weight: 0.6980 overall best weight: 0.4256 ------------------------------------------------------------------------------- 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 = 0.4371 r_free = 0.4371 target = 0.187144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.142188 restraints weight = 18824.025| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.37 r_work: 0.3810 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 6683 Z= 0.097 Angle : 0.491 4.977 9072 Z= 0.253 Chirality : 0.044 0.149 1019 Planarity : 0.004 0.061 1143 Dihedral : 7.235 79.255 930 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.90 % Allowed : 14.62 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.31), residues: 801 helix: -0.58 (1.00), residues: 24 sheet: 0.10 (0.27), residues: 418 loop : -1.24 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 50 HIS 0.003 0.001 HIS L 199 PHE 0.009 0.001 PHE N 47 TYR 0.012 0.001 TYR H 195 ARG 0.008 0.000 ARG A 103 Details of bonding type rmsd hydrogen bonds : bond 0.02908 ( 229) hydrogen bonds : angle 5.25996 ( 699) SS BOND : bond 0.00305 ( 5) SS BOND : angle 0.61283 ( 10) covalent geometry : bond 0.00233 ( 6678) covalent geometry : angle 0.49095 ( 9062) *********************** 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 100 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.6218 (tt0) cc_final: 0.5858 (tt0) REVERT: A 192 MET cc_start: 0.8024 (mtt) cc_final: 0.7526 (mtp) REVERT: A 290 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.6872 (m-30) REVERT: H 15 VAL cc_start: 0.7501 (OUTLIER) cc_final: 0.7264 (p) REVERT: H 223 ASN cc_start: 0.7160 (m-40) cc_final: 0.6938 (p0) REVERT: L 28 GLN cc_start: 0.7479 (tt0) cc_final: 0.6879 (mp10) REVERT: L 150 LYS cc_start: 0.6150 (mttt) cc_final: 0.5815 (mmmt) REVERT: N 36 TRP cc_start: 0.6663 (m100) cc_final: 0.6376 (m100) REVERT: N 104 TYR cc_start: 0.6367 (OUTLIER) cc_final: 0.4368 (m-80) REVERT: N 115 THR cc_start: 0.7242 (m) cc_final: 0.6696 (p) outliers start: 21 outliers final: 13 residues processed: 97 average time/residue: 1.5509 time to fit residues: 163.0241 Evaluate side-chains 86 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 52 ARG 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 74 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4395 r_free = 0.4395 target = 0.190004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.149003 restraints weight = 18579.538| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.19 r_work: 0.3789 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 6683 Z= 0.134 Angle : 0.515 4.645 9072 Z= 0.267 Chirality : 0.045 0.156 1019 Planarity : 0.004 0.041 1143 Dihedral : 7.314 79.081 930 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.59 % Allowed : 14.90 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.31), residues: 801 helix: -0.25 (1.07), residues: 22 sheet: 0.09 (0.27), residues: 418 loop : -1.25 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 50 HIS 0.003 0.001 HIS L 199 PHE 0.015 0.002 PHE A 277 TYR 0.017 0.001 TYR H 164 ARG 0.007 0.000 ARG N 67 Details of bonding type rmsd hydrogen bonds : bond 0.03043 ( 229) hydrogen bonds : angle 5.25259 ( 699) SS BOND : bond 0.00339 ( 5) SS BOND : angle 0.85473 ( 10) covalent geometry : bond 0.00326 ( 6678) covalent geometry : angle 0.51413 ( 9062) *********************** 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 99 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.8014 (mtt) cc_final: 0.7522 (mtp) REVERT: H 15 VAL cc_start: 0.7483 (OUTLIER) cc_final: 0.7232 (p) REVERT: H 223 ASN cc_start: 0.7156 (m-40) cc_final: 0.6939 (p0) REVERT: L 28 GLN cc_start: 0.7519 (tt0) cc_final: 0.6931 (mp10) REVERT: L 150 LYS cc_start: 0.6130 (mttt) cc_final: 0.5831 (mmmt) REVERT: N 36 TRP cc_start: 0.6453 (m100) cc_final: 0.6151 (m100) REVERT: N 52 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6470 (ttp80) REVERT: N 104 TYR cc_start: 0.6343 (OUTLIER) cc_final: 0.4406 (m-80) REVERT: N 115 THR cc_start: 0.7302 (m) cc_final: 0.6774 (p) outliers start: 26 outliers final: 13 residues processed: 95 average time/residue: 1.5487 time to fit residues: 159.3574 Evaluate side-chains 86 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4375 r_free = 0.4375 target = 0.188074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.146353 restraints weight = 18523.046| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.19 r_work: 0.3767 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 6683 Z= 0.175 Angle : 0.554 4.702 9072 Z= 0.289 Chirality : 0.045 0.164 1019 Planarity : 0.005 0.036 1143 Dihedral : 7.533 79.050 930 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.86 % Allowed : 15.86 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.31), residues: 801 helix: -0.27 (1.09), residues: 22 sheet: -0.05 (0.27), residues: 419 loop : -1.31 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP L 36 HIS 0.004 0.001 HIS L 199 PHE 0.015 0.002 PHE L 140 TYR 0.020 0.002 TYR H 164 ARG 0.004 0.000 ARG A 103 Details of bonding type rmsd hydrogen bonds : bond 0.03246 ( 229) hydrogen bonds : angle 5.41960 ( 699) SS BOND : bond 0.00371 ( 5) SS BOND : angle 1.05359 ( 10) covalent geometry : bond 0.00421 ( 6678) covalent geometry : angle 0.55348 ( 9062) *********************** 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 99 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 VAL cc_start: 0.1400 (OUTLIER) cc_final: 0.1165 (p) REVERT: A 192 MET cc_start: 0.8070 (mtt) cc_final: 0.7594 (mtp) REVERT: H 15 VAL cc_start: 0.7570 (OUTLIER) cc_final: 0.7332 (p) REVERT: L 28 GLN cc_start: 0.7380 (tt0) cc_final: 0.6892 (mp10) REVERT: L 150 LYS cc_start: 0.6149 (mttt) cc_final: 0.5814 (mmmt) REVERT: N 36 TRP cc_start: 0.6528 (m100) cc_final: 0.6238 (m100) REVERT: N 115 THR cc_start: 0.7229 (m) cc_final: 0.6691 (p) outliers start: 28 outliers final: 19 residues processed: 94 average time/residue: 1.5273 time to fit residues: 156.1514 Evaluate side-chains 89 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 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 203 VAL 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 171 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4391 r_free = 0.4391 target = 0.189897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.148886 restraints weight = 18702.833| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.17 r_work: 0.3795 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 6683 Z= 0.122 Angle : 0.513 4.774 9072 Z= 0.265 Chirality : 0.045 0.157 1019 Planarity : 0.004 0.037 1143 Dihedral : 7.014 79.429 926 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.45 % Allowed : 16.55 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.31), residues: 801 helix: -0.22 (1.07), residues: 22 sheet: 0.03 (0.27), residues: 419 loop : -1.26 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 50 HIS 0.003 0.001 HIS H 38 PHE 0.012 0.001 PHE A 277 TYR 0.021 0.001 TYR H 164 ARG 0.003 0.000 ARG A 103 Details of bonding type rmsd hydrogen bonds : bond 0.02930 ( 229) hydrogen bonds : angle 5.24327 ( 699) SS BOND : bond 0.00283 ( 5) SS BOND : angle 0.86722 ( 10) covalent geometry : bond 0.00292 ( 6678) covalent geometry : angle 0.51242 ( 9062) *********************** 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 97 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 1.007 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: 0.1446 (OUTLIER) cc_final: 0.1215 (p) REVERT: A 192 MET cc_start: 0.8061 (mtt) cc_final: 0.7590 (mtp) REVERT: H 15 VAL cc_start: 0.7530 (OUTLIER) cc_final: 0.7288 (p) REVERT: H 126 THR cc_start: 0.7390 (OUTLIER) cc_final: 0.7129 (p) REVERT: L 28 GLN cc_start: 0.7411 (tt0) cc_final: 0.6931 (mp10) REVERT: L 150 LYS cc_start: 0.6065 (mttt) cc_final: 0.5767 (mmmt) REVERT: N 104 TYR cc_start: 0.6331 (OUTLIER) cc_final: 0.4424 (m-80) REVERT: N 115 THR cc_start: 0.7227 (m) cc_final: 0.6718 (p) outliers start: 25 outliers final: 18 residues processed: 92 average time/residue: 1.4610 time to fit residues: 146.5819 Evaluate side-chains 89 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.0870 overall best weight: 0.8962 ------------------------------------------------------------------------------- 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 = 0.4390 r_free = 0.4390 target = 0.189817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.148289 restraints weight = 18559.523| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.18 r_work: 0.3809 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 6683 Z= 0.137 Angle : 0.522 4.566 9072 Z= 0.271 Chirality : 0.045 0.157 1019 Planarity : 0.004 0.038 1143 Dihedral : 6.965 79.181 926 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.72 % Allowed : 16.55 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.31), residues: 801 helix: -0.16 (1.07), residues: 22 sheet: 0.02 (0.27), residues: 419 loop : -1.28 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 36 HIS 0.003 0.001 HIS H 38 PHE 0.012 0.002 PHE L 140 TYR 0.023 0.001 TYR H 164 ARG 0.003 0.000 ARG A 103 Details of bonding type rmsd hydrogen bonds : bond 0.02969 ( 229) hydrogen bonds : angle 5.24824 ( 699) SS BOND : bond 0.00290 ( 5) SS BOND : angle 0.94974 ( 10) covalent geometry : bond 0.00329 ( 6678) covalent geometry : angle 0.52084 ( 9062) *********************** 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 92 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 1.016 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: 0.1462 (OUTLIER) cc_final: 0.1228 (p) REVERT: A 192 MET cc_start: 0.8105 (mtt) cc_final: 0.7657 (mtp) REVERT: H 15 VAL cc_start: 0.7530 (OUTLIER) cc_final: 0.7290 (p) REVERT: H 126 THR cc_start: 0.7432 (OUTLIER) cc_final: 0.7134 (p) REVERT: L 28 GLN cc_start: 0.7415 (tt0) cc_final: 0.6942 (mp10) REVERT: L 150 LYS cc_start: 0.6044 (mttt) cc_final: 0.5756 (mmmt) REVERT: N 36 TRP cc_start: 0.6380 (m100) cc_final: 0.6015 (m100) REVERT: N 104 TYR cc_start: 0.6336 (OUTLIER) cc_final: 0.4425 (m-80) REVERT: N 115 THR cc_start: 0.7241 (m) cc_final: 0.6745 (p) outliers start: 27 outliers final: 19 residues processed: 88 average time/residue: 1.4602 time to fit residues: 140.2956 Evaluate side-chains 89 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 25 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.186741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.141856 restraints weight = 18608.699| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.40 r_work: 0.3770 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 6683 Z= 0.180 Angle : 0.565 4.760 9072 Z= 0.295 Chirality : 0.046 0.165 1019 Planarity : 0.005 0.040 1143 Dihedral : 7.057 79.247 925 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 4.00 % Allowed : 16.00 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.31), residues: 801 helix: -0.19 (1.01), residues: 24 sheet: -0.07 (0.27), residues: 419 loop : -1.39 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 36 HIS 0.003 0.001 HIS H 38 PHE 0.015 0.002 PHE L 140 TYR 0.023 0.002 TYR H 164 ARG 0.002 0.000 ARG A 103 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 229) hydrogen bonds : angle 5.44451 ( 699) SS BOND : bond 0.00362 ( 5) SS BOND : angle 1.14916 ( 10) covalent geometry : bond 0.00435 ( 6678) covalent geometry : angle 0.56404 ( 9062) *********************** 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 100 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 0.868 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: 0.1401 (OUTLIER) cc_final: 0.1162 (p) REVERT: A 192 MET cc_start: 0.8126 (mtt) cc_final: 0.7675 (mtp) REVERT: H 15 VAL cc_start: 0.7577 (OUTLIER) cc_final: 0.7361 (p) REVERT: L 28 GLN cc_start: 0.7368 (tt0) cc_final: 0.6801 (mp10) REVERT: L 150 LYS cc_start: 0.6202 (mttt) cc_final: 0.5806 (mmmt) REVERT: N 4 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7051 (mt) REVERT: N 36 TRP cc_start: 0.6467 (m100) cc_final: 0.6108 (m100) REVERT: N 104 TYR cc_start: 0.6299 (OUTLIER) cc_final: 0.4301 (m-80) REVERT: N 115 THR cc_start: 0.7082 (m) cc_final: 0.6576 (p) outliers start: 29 outliers final: 19 residues processed: 94 average time/residue: 1.3436 time to fit residues: 138.3401 Evaluate side-chains 92 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 2 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4387 r_free = 0.4387 target = 0.189549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.148848 restraints weight = 18521.133| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.13 r_work: 0.3788 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 6683 Z= 0.133 Angle : 0.529 5.698 9072 Z= 0.274 Chirality : 0.045 0.161 1019 Planarity : 0.004 0.041 1143 Dihedral : 6.914 79.368 925 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.45 % Allowed : 17.66 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.31), residues: 801 helix: 0.13 (1.04), residues: 24 sheet: -0.02 (0.27), residues: 419 loop : -1.32 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 36 HIS 0.003 0.001 HIS H 38 PHE 0.012 0.002 PHE A 277 TYR 0.025 0.001 TYR H 164 ARG 0.002 0.000 ARG L 212 Details of bonding type rmsd hydrogen bonds : bond 0.02966 ( 229) hydrogen bonds : angle 5.29810 ( 699) SS BOND : bond 0.00309 ( 5) SS BOND : angle 1.06460 ( 10) covalent geometry : bond 0.00317 ( 6678) covalent geometry : angle 0.52772 ( 9062) *********************** 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 : 0.966 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: 0.1536 (OUTLIER) cc_final: 0.1298 (p) REVERT: A 192 MET cc_start: 0.8113 (mtt) cc_final: 0.7670 (mtp) REVERT: H 15 VAL cc_start: 0.7532 (OUTLIER) cc_final: 0.7290 (p) REVERT: H 126 THR cc_start: 0.7498 (OUTLIER) cc_final: 0.7200 (p) REVERT: L 28 GLN cc_start: 0.7378 (tt0) cc_final: 0.6908 (mp10) REVERT: L 150 LYS cc_start: 0.6048 (mttt) cc_final: 0.5746 (mmmt) REVERT: N 4 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7128 (mt) REVERT: N 104 TYR cc_start: 0.6359 (OUTLIER) cc_final: 0.4403 (m-80) REVERT: N 115 THR cc_start: 0.7070 (m) cc_final: 0.6597 (p) outliers start: 25 outliers final: 20 residues processed: 88 average time/residue: 1.4455 time to fit residues: 138.8394 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 : 0.908 ------------------------------------------------------------------------------- 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: 0.7980 chunk 50 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4365 r_free = 0.4365 target = 0.186069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.140803 restraints weight = 18635.513| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.42 r_work: 0.3744 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6683 Z= 0.118 Angle : 0.518 7.408 9072 Z= 0.267 Chirality : 0.045 0.156 1019 Planarity : 0.004 0.041 1143 Dihedral : 6.798 79.514 925 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.31), residues: 801 helix: 0.41 (1.07), residues: 24 sheet: 0.13 (0.27), residues: 409 loop : -1.35 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 36 HIS 0.002 0.001 HIS H 38 PHE 0.011 0.001 PHE A 277 TYR 0.028 0.001 TYR H 164 ARG 0.002 0.000 ARG L 212 Details of bonding type rmsd hydrogen bonds : bond 0.02856 ( 229) hydrogen bonds : angle 5.20028 ( 699) SS BOND : bond 0.00341 ( 5) SS BOND : angle 1.14225 ( 10) covalent geometry : bond 0.00284 ( 6678) covalent geometry : angle 0.51708 ( 9062) ********************** 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 91 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.957 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: 0.1418 (OUTLIER) cc_final: 0.1184 (p) REVERT: A 170 LYS cc_start: 0.6185 (mtpp) cc_final: 0.5826 (mttt) REVERT: A 192 MET cc_start: 0.8103 (mtt) cc_final: 0.7658 (mtp) REVERT: A 290 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7052 (m-30) REVERT: H 15 VAL cc_start: 0.7535 (OUTLIER) cc_final: 0.7305 (p) REVERT: H 126 THR cc_start: 0.7447 (OUTLIER) cc_final: 0.7113 (p) REVERT: H 164 TYR cc_start: 0.7043 (p90) cc_final: 0.6708 (p90) REVERT: L 28 GLN cc_start: 0.7463 (tt0) cc_final: 0.6861 (mp10) REVERT: L 150 LYS cc_start: 0.6194 (mttt) cc_final: 0.5809 (mmmt) REVERT: N 104 TYR cc_start: 0.6257 (OUTLIER) cc_final: 0.4342 (m-80) REVERT: N 115 THR cc_start: 0.7016 (m) cc_final: 0.6502 (p) outliers start: 24 outliers final: 19 residues processed: 87 average time/residue: 1.4289 time to fit residues: 135.7767 Evaluate side-chains 90 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 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 20 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4401 r_free = 0.4401 target = 0.189886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.145533 restraints weight = 18339.476| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.40 r_work: 0.3767 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 6683 Z= 0.129 Angle : 0.524 7.413 9072 Z= 0.270 Chirality : 0.045 0.157 1019 Planarity : 0.004 0.043 1143 Dihedral : 6.789 79.280 925 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.31), residues: 801 helix: 0.65 (1.09), residues: 24 sheet: 0.15 (0.27), residues: 409 loop : -1.35 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 36 HIS 0.003 0.001 HIS H 38 PHE 0.010 0.001 PHE L 140 TYR 0.027 0.001 TYR H 164 ARG 0.002 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.02891 ( 229) hydrogen bonds : angle 5.19175 ( 699) SS BOND : bond 0.00319 ( 5) SS BOND : angle 1.20147 ( 10) covalent geometry : bond 0.00310 ( 6678) covalent geometry : angle 0.52251 ( 9062) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10056.05 seconds wall clock time: 172 minutes 22.70 seconds (10342.70 seconds total)