Starting phenix.real_space_refine on Fri Aug 22 15:20:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mmv_48404/08_2025/9mmv_48404.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mmv_48404/08_2025/9mmv_48404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mmv_48404/08_2025/9mmv_48404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mmv_48404/08_2025/9mmv_48404.map" model { file = "/net/cci-nas-00/data/ceres_data/9mmv_48404/08_2025/9mmv_48404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mmv_48404/08_2025/9mmv_48404.cif" } resolution = 3.79 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= 0.369 sd= 1.521 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: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 2924 2.51 5 N 961 2.21 5 O 1071 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s 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: 4968 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 1253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1253 Classifications: {'peptide': 210} Incomplete info: {'backbone_only': 89} Link IDs: {'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 333 Unresolved non-hydrogen angles: 495 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 119 Planarities with less than four sites: {'PHE:plan': 3, 'ASP:plan': 2, 'TYR:plan': 3, 'GLU:plan': 2, 'TRP:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 107 Chain: "L" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1137 Classifications: {'peptide': 194} Incomplete info: {'backbone_only': 85} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 178} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 331 Unresolved non-hydrogen angles: 491 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 110 Planarities with less than four sites: {'GLN:plan1': 5, 'PHE:plan': 2, 'GLU:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 1, 'TYR:plan': 4, 'TRP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 132 Chain: "M" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1351 Classifications: {'peptide': 222} Incomplete info: {'backbone_only': 88, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 209} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 335 Unresolved non-hydrogen angles: 497 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'GLU:plan': 3, 'PHE:plan': 3, 'ASP:plan': 2, 'TYR:plan': 3, 'TRP:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 111 Chain: "N" Number of atoms: 1227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1227 Classifications: {'peptide': 211} Incomplete info: {'backbone_only': 102, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 199} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 416 Unresolved non-hydrogen angles: 605 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 129 Planarities with less than four sites: {'ASP:plan': 6, 'ARG:plan': 3, 'PHE:plan': 4, 'GLU:plan': 6, 'GLN:plan1': 6, 'ASN:plan1': 5, 'TYR:plan': 4, 'TRP:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 188 Time building chain proxies: 1.41, per 1000 atoms: 0.28 Number of scatterers: 4968 At special positions: 0 Unit cell: (54, 70.5, 142, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 1071 8.00 N 961 7.00 C 2924 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 86 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 98 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 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: 0.29 Conformation dependent library (CDL) restraints added in 185.9 milliseconds Enol-peptide restraints added in 1.4 microseconds 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 808 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 21 sheets defined 6.8% alpha, 50.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.673A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 190 No H-bonds generated for 'chain 'H' and resid 188 through 190' Processing helix chain 'L' and resid 77 through 81 removed outlier: 3.535A pdb=" N GLU L 81 " --> pdb=" O ALA L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'M' and resid 53 through 57 Processing helix chain 'M' and resid 89 through 93 removed outlier: 3.502A pdb=" N THR M 93 " --> pdb=" O THR M 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 200 removed outlier: 4.247A pdb=" N GLY M 200 " --> pdb=" O SER M 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 196 through 200' Processing helix chain 'N' and resid 121 through 126 removed outlier: 4.353A pdb=" N LYS N 126 " --> pdb=" O ASP N 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 183 through 189 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.099A pdb=" N LEU H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLY H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 121 through 125 removed outlier: 6.038A pdb=" N TYR H 177 " --> pdb=" O ASP H 145 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 121 through 125 removed outlier: 6.038A pdb=" N TYR H 177 " --> pdb=" O ASP H 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 151 through 155 removed outlier: 3.745A pdb=" N TYR H 195 " --> pdb=" O VAL H 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.662A pdb=" N VAL L 10 " --> pdb=" O THR L 104 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TRP L 33 " --> pdb=" O VAL L 45 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.662A pdb=" N VAL L 10 " --> pdb=" O THR L 104 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 18 through 21 Processing sheet with id=AA9, first strand: chain 'L' and resid 114 through 116 removed outlier: 5.038A pdb=" N THR L 131 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU L 180 " --> pdb=" O THR L 131 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N VAL L 133 " --> pdb=" O LEU L 178 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU L 178 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU L 135 " --> pdb=" O SER L 176 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N SER L 176 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N SER L 137 " --> pdb=" O ALA L 174 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ALA L 174 " --> pdb=" O SER L 137 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 114 through 116 removed outlier: 5.038A pdb=" N THR L 131 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU L 180 " --> pdb=" O THR L 131 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N VAL L 133 " --> pdb=" O LEU L 178 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU L 178 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU L 135 " --> pdb=" O SER L 176 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N SER L 176 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N SER L 137 " --> pdb=" O ALA L 174 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ALA L 174 " --> pdb=" O SER L 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 145 through 149 Processing sheet with id=AB3, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.571A pdb=" N SER M 21 " --> pdb=" O SER M 7 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.711A pdb=" N ALA M 33 " --> pdb=" O GLY M 101 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N MET M 34 " --> pdb=" O PHE M 50 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 11 through 12 removed outlier: 6.626A pdb=" N CYS M 98 " --> pdb=" O TRP M 117 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TRP M 117 " --> pdb=" O CYS M 98 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ARG M 100 " --> pdb=" O ASP M 115 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY M 113 " --> pdb=" O ALA M 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 134 through 138 removed outlier: 3.668A pdb=" N CYS M 150 " --> pdb=" O SER M 190 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N TYR M 186 " --> pdb=" O ASP M 154 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 134 through 138 removed outlier: 3.668A pdb=" N CYS M 150 " --> pdb=" O SER M 190 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N TYR M 186 " --> pdb=" O ASP M 154 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 160 through 164 Processing sheet with id=AB9, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.540A pdb=" N THR N 22 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.869A pdb=" N LEU N 33 " --> pdb=" O PHE N 49 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 114 through 118 removed outlier: 4.046A pdb=" N SER N 174 " --> pdb=" O THR N 164 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 153 through 155 removed outlier: 4.308A pdb=" N TRP N 148 " --> pdb=" O GLN N 155 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR N 192 " --> pdb=" O PHE N 209 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS N 194 " --> pdb=" O LYS N 207 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS N 207 " --> pdb=" O CYS N 194 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL N 196 " --> pdb=" O VAL N 205 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL N 205 " --> pdb=" O VAL N 196 " (cutoff:3.500A) 286 hydrogen bonds defined for protein. 708 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: 0.59 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1319 1.33 - 1.45: 1118 1.45 - 1.57: 2588 1.57 - 1.69: 0 1.69 - 1.82: 16 Bond restraints: 5041 Sorted by residual: bond pdb=" CA ASP N 50 " pdb=" C ASP N 50 " ideal model delta sigma weight residual 1.527 1.479 0.048 1.30e-02 5.92e+03 1.37e+01 bond pdb=" CA SER N 10 " pdb=" C SER N 10 " ideal model delta sigma weight residual 1.523 1.488 0.034 1.23e-02 6.61e+03 7.74e+00 bond pdb=" C SER N 10 " pdb=" N LEU N 11 " ideal model delta sigma weight residual 1.331 1.298 0.032 1.34e-02 5.57e+03 5.76e+00 bond pdb=" N PHE N 96 " pdb=" CA PHE N 96 " ideal model delta sigma weight residual 1.463 1.432 0.031 1.30e-02 5.92e+03 5.62e+00 bond pdb=" C ARG N 142 " pdb=" O ARG N 142 " ideal model delta sigma weight residual 1.237 1.210 0.027 1.17e-02 7.31e+03 5.24e+00 ... (remaining 5036 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.75: 6643 4.75 - 9.50: 27 9.50 - 14.25: 2 14.25 - 19.01: 1 19.01 - 23.76: 1 Bond angle restraints: 6674 Sorted by residual: angle pdb=" C GLU M 158 " pdb=" N PRO M 159 " pdb=" CA PRO M 159 " ideal model delta sigma weight residual 119.84 143.60 -23.76 1.25e+00 6.40e-01 3.61e+02 angle pdb=" N GLU M 158 " pdb=" CA GLU M 158 " pdb=" C GLU M 158 " ideal model delta sigma weight residual 108.07 120.12 -12.05 8.90e-01 1.26e+00 1.83e+02 angle pdb=" N SER N 52 " pdb=" CA SER N 52 " pdb=" C SER N 52 " ideal model delta sigma weight residual 111.28 119.43 -8.15 1.09e+00 8.42e-01 5.59e+01 angle pdb=" C TYR N 140 " pdb=" N PRO N 141 " pdb=" CA PRO N 141 " ideal model delta sigma weight residual 127.00 144.88 -17.88 2.40e+00 1.74e-01 5.55e+01 angle pdb=" C GLN N 79 " pdb=" N PRO N 80 " pdb=" CA PRO N 80 " ideal model delta sigma weight residual 119.05 125.68 -6.63 1.11e+00 8.12e-01 3.56e+01 ... (remaining 6669 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.92: 2195 21.92 - 43.85: 209 43.85 - 65.77: 25 65.77 - 87.69: 2 87.69 - 109.62: 3 Dihedral angle restraints: 2434 sinusoidal: 772 harmonic: 1662 Sorted by residual: dihedral pdb=" CA GLU H 149 " pdb=" C GLU H 149 " pdb=" N PRO H 150 " pdb=" CA PRO H 150 " ideal model delta harmonic sigma weight residual 180.00 70.38 109.62 0 5.00e+00 4.00e-02 4.81e+02 dihedral pdb=" CA PHE H 147 " pdb=" C PHE H 147 " pdb=" N PRO H 148 " pdb=" CA PRO H 148 " ideal model delta harmonic sigma weight residual -180.00 -80.95 -99.05 0 5.00e+00 4.00e-02 3.92e+02 dihedral pdb=" CA SER N 7 " pdb=" C SER N 7 " pdb=" N PRO N 8 " pdb=" CA PRO N 8 " ideal model delta harmonic sigma weight residual 0.00 -40.41 40.41 0 5.00e+00 4.00e-02 6.53e+01 ... (remaining 2431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 474 0.087 - 0.174: 43 0.174 - 0.261: 2 0.261 - 0.348: 2 0.348 - 0.435: 1 Chirality restraints: 522 Sorted by residual: chirality pdb=" CA SER N 53 " pdb=" N SER N 53 " pdb=" C SER N 53 " pdb=" CB SER N 53 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.44 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CA SER N 52 " pdb=" N SER N 52 " pdb=" C SER N 52 " pdb=" CB SER N 52 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA LYS H 43 " pdb=" N LYS H 43 " pdb=" C LYS H 43 " pdb=" CB LYS H 43 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 519 not shown) Planarity restraints: 995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG M 13 " -0.074 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO M 14 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO M 14 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO M 14 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA N 43 " -0.047 5.00e-02 4.00e+02 7.16e-02 8.21e+00 pdb=" N PRO N 44 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO N 44 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO N 44 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE N 49 " 0.013 2.00e-02 2.50e+03 2.73e-02 7.43e+00 pdb=" C PHE N 49 " -0.047 2.00e-02 2.50e+03 pdb=" O PHE N 49 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP N 50 " 0.016 2.00e-02 2.50e+03 ... (remaining 992 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 2 2.05 - 2.76: 807 2.76 - 3.48: 6176 3.48 - 4.19: 9974 4.19 - 4.90: 17756 Nonbonded interactions: 34715 Sorted by model distance: nonbonded pdb=" OE2 GLU M 61 " pdb=" CD2 PHE N 94 " model vdw 1.340 3.340 nonbonded pdb=" OE2 GLU M 61 " pdb=" CE2 PHE N 94 " model vdw 1.624 3.340 nonbonded pdb=" NH2 ARG N 61 " pdb=" OE1 GLU N 81 " model vdw 2.103 3.120 nonbonded pdb=" OG SER N 26 " pdb=" OE1 GLN N 27 " model vdw 2.134 3.040 nonbonded pdb=" OH TYR M 104 " pdb=" OD2 ASP N 50 " model vdw 2.146 3.040 ... (remaining 34710 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'H' and (resid 2 through 12 or resid 14 through 15 or resid 17 through 22 \ or resid 25 through 27 or resid 29 or resid 32 or resid 36 through 47 or resid \ 49 or resid 51 or resid 53 or resid 57 or resid 60 through 61 or resid 63 throug \ h 73 or resid 75 through 77 or resid 80 through 86 or resid 89 through 96 or res \ id 98 through 100 or resid 102 through 108 or resid 110 through 128 or resid 135 \ through 214)) selection = (chain 'M' and (resid 2 through 12 or resid 14 through 15 or resid 17 through 22 \ or resid 25 through 27 or resid 29 or resid 32 or resid 36 through 47 or resid \ 49 or resid 51 or resid 53 or resid 59 or resid 62 through 63 or resid 65 throug \ h 75 or resid 77 through 79 or resid 82 through 88 or resid 91 through 98 or res \ id 100 or resid 111 through 112 or resid 115 through 121 or resid 123 through 22 \ 3)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.640 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 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 : 0.004 0.049 5045 Z= 0.252 Angle : 0.815 23.757 6682 Z= 0.532 Chirality : 0.053 0.435 522 Planarity : 0.006 0.110 995 Dihedral : 15.097 109.619 1614 Min Nonbonded Distance : 1.340 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.53 % Favored : 96.22 % Rotamer: Outliers : 1.08 % Allowed : 33.69 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 6.12 % 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: 1.43 (0.31), residues: 821 helix: 1.90 (1.56), residues: 15 sheet: 1.70 (0.27), residues: 358 loop : 0.34 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 16 TYR 0.015 0.001 TYR M 112 PHE 0.010 0.002 PHE H 68 TRP 0.008 0.001 TRP M 47 HIS 0.003 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 5041) covalent geometry : angle 0.81493 ( 6674) SS BOND : bond 0.00359 ( 4) SS BOND : angle 1.16107 ( 8) hydrogen bonds : bond 0.25338 ( 244) hydrogen bonds : angle 9.40701 ( 708) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 144 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: H 6 GLU cc_start: 0.8449 (mp0) cc_final: 0.8237 (mp0) REVERT: H 76 LYS cc_start: 0.8928 (tmtt) cc_final: 0.8718 (tmtt) outliers start: 4 outliers final: 1 residues processed: 145 average time/residue: 0.0733 time to fit residues: 13.2062 Evaluate side-chains 144 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 7 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 30.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 77 GLN N 79 GLN N 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.081214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.066969 restraints weight = 13142.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.068634 restraints weight = 7588.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.069796 restraints weight = 5232.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.070526 restraints weight = 4022.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.071110 restraints weight = 3336.337| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5045 Z= 0.178 Angle : 0.585 6.835 6682 Z= 0.325 Chirality : 0.043 0.159 522 Planarity : 0.005 0.073 995 Dihedral : 4.727 28.848 876 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.78 % Favored : 95.98 % Rotamer: Outliers : 5.93 % Allowed : 28.84 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 1.30 (0.30), residues: 821 helix: 1.46 (1.48), residues: 16 sheet: 1.56 (0.27), residues: 365 loop : 0.30 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 16 TYR 0.015 0.002 TYR L 47 PHE 0.016 0.003 PHE N 96 TRP 0.012 0.002 TRP M 47 HIS 0.005 0.003 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 5041) covalent geometry : angle 0.58318 ( 6674) SS BOND : bond 0.00690 ( 4) SS BOND : angle 1.52483 ( 8) hydrogen bonds : bond 0.03512 ( 244) hydrogen bonds : angle 5.69997 ( 708) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.138 Fit side-chains REVERT: H 76 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8230 (tmtt) REVERT: L 101 THR cc_start: 0.8895 (m) cc_final: 0.8558 (p) outliers start: 22 outliers final: 7 residues processed: 157 average time/residue: 0.0709 time to fit residues: 13.7897 Evaluate side-chains 151 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 30 TYR Chi-restraints excluded: chain M residue 62 TYR Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 100 GLN Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 51 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 14 optimal weight: 40.0000 chunk 16 optimal weight: 50.0000 chunk 38 optimal weight: 50.0000 chunk 42 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 19 optimal weight: 50.0000 chunk 62 optimal weight: 10.0000 chunk 56 optimal weight: 40.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.078998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.064671 restraints weight = 13223.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.066327 restraints weight = 7501.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.067546 restraints weight = 5117.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.068382 restraints weight = 3902.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.068844 restraints weight = 3196.826| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5045 Z= 0.250 Angle : 0.643 9.136 6682 Z= 0.355 Chirality : 0.045 0.184 522 Planarity : 0.005 0.059 995 Dihedral : 4.993 29.328 876 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.51 % Favored : 95.37 % Rotamer: Outliers : 7.01 % Allowed : 30.19 % Favored : 62.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 1.05 (0.30), residues: 821 helix: 1.11 (1.48), residues: 16 sheet: 1.49 (0.26), residues: 360 loop : 0.05 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 16 TYR 0.020 0.002 TYR L 47 PHE 0.029 0.003 PHE N 94 TRP 0.015 0.002 TRP M 47 HIS 0.005 0.003 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 5041) covalent geometry : angle 0.64036 ( 6674) SS BOND : bond 0.00832 ( 4) SS BOND : angle 1.91323 ( 8) hydrogen bonds : bond 0.03650 ( 244) hydrogen bonds : angle 5.55795 ( 708) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.215 Fit side-chains REVERT: H 76 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8233 (tmtt) REVERT: L 101 THR cc_start: 0.8931 (m) cc_final: 0.8579 (p) REVERT: N 73 LEU cc_start: 0.8784 (mt) cc_final: 0.8580 (mt) outliers start: 26 outliers final: 15 residues processed: 156 average time/residue: 0.0745 time to fit residues: 14.5026 Evaluate side-chains 163 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 30 TYR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 75 ASP Chi-restraints excluded: chain M residue 85 MET Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 100 GLN Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 2 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 32 optimal weight: 50.0000 chunk 61 optimal weight: 30.0000 chunk 69 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 77 GLN N 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.079490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.064957 restraints weight = 13116.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.066670 restraints weight = 7443.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.067801 restraints weight = 5096.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.068692 restraints weight = 3931.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.069208 restraints weight = 3228.001| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5045 Z= 0.208 Angle : 0.600 7.942 6682 Z= 0.331 Chirality : 0.044 0.175 522 Planarity : 0.005 0.055 995 Dihedral : 4.777 25.303 876 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.38 % Favored : 95.49 % Rotamer: Outliers : 6.74 % Allowed : 30.46 % Favored : 62.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 0.97 (0.29), residues: 821 helix: 1.03 (1.43), residues: 16 sheet: 1.37 (0.26), residues: 361 loop : 0.05 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 16 TYR 0.017 0.002 TYR L 47 PHE 0.018 0.003 PHE N 94 TRP 0.015 0.002 TRP M 47 HIS 0.004 0.003 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 5041) covalent geometry : angle 0.59635 ( 6674) SS BOND : bond 0.00850 ( 4) SS BOND : angle 1.90234 ( 8) hydrogen bonds : bond 0.03248 ( 244) hydrogen bonds : angle 5.21023 ( 708) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.143 Fit side-chains REVERT: H 76 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8253 (tmtt) REVERT: L 101 THR cc_start: 0.8908 (m) cc_final: 0.8522 (p) REVERT: N 50 ASP cc_start: 0.7859 (m-30) cc_final: 0.7439 (m-30) REVERT: N 73 LEU cc_start: 0.8802 (mt) cc_final: 0.8591 (mt) outliers start: 25 outliers final: 18 residues processed: 157 average time/residue: 0.0680 time to fit residues: 13.3804 Evaluate side-chains 166 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 30 TYR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 75 ASP Chi-restraints excluded: chain M residue 85 MET Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 100 GLN Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 33 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 55 optimal weight: 40.0000 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 78 optimal weight: 30.0000 chunk 79 optimal weight: 40.0000 overall best weight: 8.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.077613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.063209 restraints weight = 13504.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.064952 restraints weight = 7549.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.066029 restraints weight = 5116.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.066964 restraints weight = 3928.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.067519 restraints weight = 3211.807| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 5045 Z= 0.313 Angle : 0.696 9.324 6682 Z= 0.384 Chirality : 0.047 0.200 522 Planarity : 0.005 0.059 995 Dihedral : 5.316 32.020 876 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.60 % Favored : 94.28 % Rotamer: Outliers : 7.55 % Allowed : 28.57 % Favored : 63.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 0.74 (0.29), residues: 821 helix: 0.62 (1.41), residues: 16 sheet: 1.24 (0.26), residues: 368 loop : -0.15 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 19 TYR 0.022 0.002 TYR L 47 PHE 0.028 0.004 PHE H 68 TRP 0.017 0.003 TRP H 104 HIS 0.005 0.003 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00684 ( 5041) covalent geometry : angle 0.69185 ( 6674) SS BOND : bond 0.01091 ( 4) SS BOND : angle 2.19567 ( 8) hydrogen bonds : bond 0.03770 ( 244) hydrogen bonds : angle 5.51281 ( 708) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.167 Fit side-chains REVERT: H 76 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8260 (tmtt) outliers start: 28 outliers final: 20 residues processed: 153 average time/residue: 0.0721 time to fit residues: 13.7729 Evaluate side-chains 162 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 75 ASP Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain M residue 79 ASN Chi-restraints excluded: chain M residue 85 MET Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 100 GLN Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 77 optimal weight: 0.2980 chunk 48 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 7 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN L 36 GLN N 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.081370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.066631 restraints weight = 13373.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.068397 restraints weight = 7452.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.069685 restraints weight = 5055.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.070525 restraints weight = 3818.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.071021 restraints weight = 3127.757| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5045 Z= 0.126 Angle : 0.544 5.691 6682 Z= 0.299 Chirality : 0.042 0.143 522 Planarity : 0.004 0.054 995 Dihedral : 4.392 17.044 876 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.02 % Favored : 95.86 % Rotamer: Outliers : 5.39 % Allowed : 32.61 % Favored : 61.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 0.93 (0.30), residues: 821 helix: 1.30 (1.46), residues: 16 sheet: 1.30 (0.26), residues: 363 loop : 0.06 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 16 TYR 0.011 0.001 TYR L 47 PHE 0.017 0.002 PHE H 68 TRP 0.014 0.002 TRP M 47 HIS 0.003 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 5041) covalent geometry : angle 0.54097 ( 6674) SS BOND : bond 0.00663 ( 4) SS BOND : angle 1.70715 ( 8) hydrogen bonds : bond 0.02710 ( 244) hydrogen bonds : angle 4.71469 ( 708) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.183 Fit side-chains REVERT: H 76 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8196 (tmtt) REVERT: L 16 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8187 (tm-30) REVERT: L 101 THR cc_start: 0.8870 (m) cc_final: 0.8519 (p) REVERT: N 4 MET cc_start: 0.8355 (mmm) cc_final: 0.8101 (mmm) outliers start: 20 outliers final: 16 residues processed: 165 average time/residue: 0.0693 time to fit residues: 14.3060 Evaluate side-chains 165 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 85 MET Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 100 GLN Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 20 optimal weight: 50.0000 chunk 24 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 14 optimal weight: 50.0000 chunk 48 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.078673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.064437 restraints weight = 13433.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.066105 restraints weight = 7584.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.067304 restraints weight = 5129.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.068143 restraints weight = 3904.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.068607 restraints weight = 3189.019| |-----------------------------------------------------------------------------| r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5045 Z= 0.235 Angle : 0.628 8.041 6682 Z= 0.346 Chirality : 0.044 0.187 522 Planarity : 0.005 0.058 995 Dihedral : 4.756 18.305 875 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.99 % Favored : 94.88 % Rotamer: Outliers : 6.74 % Allowed : 30.73 % Favored : 62.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 0.82 (0.30), residues: 821 helix: 1.08 (1.44), residues: 16 sheet: 1.22 (0.26), residues: 369 loop : -0.03 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 16 TYR 0.019 0.002 TYR L 47 PHE 0.028 0.003 PHE H 68 TRP 0.014 0.002 TRP M 47 HIS 0.004 0.003 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 5041) covalent geometry : angle 0.62373 ( 6674) SS BOND : bond 0.00859 ( 4) SS BOND : angle 2.14600 ( 8) hydrogen bonds : bond 0.03291 ( 244) hydrogen bonds : angle 5.02422 ( 708) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.211 Fit side-chains REVERT: H 76 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8280 (tmtt) REVERT: L 16 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8154 (tm-30) REVERT: N 4 MET cc_start: 0.8425 (mmm) cc_final: 0.8175 (mmm) outliers start: 25 outliers final: 21 residues processed: 151 average time/residue: 0.0750 time to fit residues: 14.1004 Evaluate side-chains 164 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain M residue 85 MET Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 27 GLN Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 100 GLN Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 27 optimal weight: 5.9990 chunk 15 optimal weight: 40.0000 chunk 61 optimal weight: 50.0000 chunk 60 optimal weight: 40.0000 chunk 18 optimal weight: 50.0000 chunk 29 optimal weight: 9.9990 chunk 40 optimal weight: 0.4980 chunk 82 optimal weight: 0.3980 chunk 74 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 overall best weight: 3.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.080200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.066049 restraints weight = 13421.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.067674 restraints weight = 7748.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.068842 restraints weight = 5341.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.069607 restraints weight = 4095.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.070174 restraints weight = 3401.120| |-----------------------------------------------------------------------------| r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5045 Z= 0.160 Angle : 0.571 6.038 6682 Z= 0.314 Chirality : 0.043 0.168 522 Planarity : 0.004 0.056 995 Dihedral : 4.458 17.586 875 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.51 % Favored : 95.37 % Rotamer: Outliers : 7.28 % Allowed : 29.92 % Favored : 62.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 0.88 (0.30), residues: 821 helix: 1.32 (1.45), residues: 16 sheet: 1.23 (0.26), residues: 365 loop : 0.05 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 19 TYR 0.014 0.002 TYR L 47 PHE 0.024 0.002 PHE H 68 TRP 0.014 0.002 TRP M 47 HIS 0.003 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 5041) covalent geometry : angle 0.56767 ( 6674) SS BOND : bond 0.00723 ( 4) SS BOND : angle 1.83657 ( 8) hydrogen bonds : bond 0.02885 ( 244) hydrogen bonds : angle 4.74813 ( 708) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.214 Fit side-chains REVERT: H 76 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8220 (tmtt) REVERT: L 16 GLN cc_start: 0.8795 (tm-30) cc_final: 0.8231 (tm-30) outliers start: 27 outliers final: 23 residues processed: 153 average time/residue: 0.0793 time to fit residues: 15.0781 Evaluate side-chains 168 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 30 TYR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain M residue 85 MET Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 27 GLN Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 100 GLN Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 78 optimal weight: 40.0000 chunk 28 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 33 optimal weight: 50.0000 chunk 55 optimal weight: 30.0000 chunk 44 optimal weight: 9.9990 chunk 81 optimal weight: 40.0000 chunk 65 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 40.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.077705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.063309 restraints weight = 13507.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.064973 restraints weight = 7628.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.066183 restraints weight = 5160.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.066917 restraints weight = 3915.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.067538 restraints weight = 3239.542| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 5045 Z= 0.290 Angle : 0.691 8.873 6682 Z= 0.380 Chirality : 0.047 0.201 522 Planarity : 0.005 0.061 995 Dihedral : 5.089 19.104 875 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.36 % Favored : 94.52 % Rotamer: Outliers : 6.47 % Allowed : 30.73 % Favored : 62.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 0.69 (0.30), residues: 821 helix: 0.89 (1.44), residues: 16 sheet: 1.16 (0.26), residues: 367 loop : -0.13 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 16 TYR 0.021 0.002 TYR L 47 PHE 0.034 0.004 PHE H 68 TRP 0.016 0.003 TRP H 104 HIS 0.004 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00635 ( 5041) covalent geometry : angle 0.68732 ( 6674) SS BOND : bond 0.00913 ( 4) SS BOND : angle 2.12537 ( 8) hydrogen bonds : bond 0.03596 ( 244) hydrogen bonds : angle 5.20442 ( 708) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.165 Fit side-chains REVERT: H 76 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8285 (tmtt) REVERT: L 16 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8187 (tm-30) REVERT: L 81 GLU cc_start: 0.8177 (pm20) cc_final: 0.7940 (pm20) outliers start: 24 outliers final: 19 residues processed: 154 average time/residue: 0.0761 time to fit residues: 14.6246 Evaluate side-chains 163 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain M residue 85 MET Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 27 GLN Chi-restraints excluded: chain N residue 100 GLN Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 68 optimal weight: 9.9990 chunk 75 optimal weight: 50.0000 chunk 76 optimal weight: 30.0000 chunk 52 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 13 optimal weight: 50.0000 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.078765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.064840 restraints weight = 13512.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.066438 restraints weight = 7783.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.067588 restraints weight = 5312.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.068325 restraints weight = 4066.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.068894 restraints weight = 3375.571| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5045 Z= 0.208 Angle : 0.639 6.977 6682 Z= 0.350 Chirality : 0.045 0.184 522 Planarity : 0.005 0.062 995 Dihedral : 4.822 17.933 875 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.51 % Favored : 95.37 % Rotamer: Outliers : 5.93 % Allowed : 31.27 % Favored : 62.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 0.69 (0.30), residues: 821 helix: 1.08 (1.46), residues: 16 sheet: 1.12 (0.26), residues: 367 loop : -0.10 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 19 TYR 0.016 0.002 TYR L 47 PHE 0.030 0.003 PHE H 68 TRP 0.014 0.002 TRP M 47 HIS 0.003 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 5041) covalent geometry : angle 0.63600 ( 6674) SS BOND : bond 0.00841 ( 4) SS BOND : angle 2.02917 ( 8) hydrogen bonds : bond 0.03200 ( 244) hydrogen bonds : angle 4.95294 ( 708) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1642 Ramachandran restraints generated. 821 Oldfield, 0 Emsley, 821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.169 Fit side-chains REVERT: H 76 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8227 (tmtt) REVERT: L 16 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8211 (tm-30) REVERT: L 81 GLU cc_start: 0.8153 (pm20) cc_final: 0.7903 (pm20) outliers start: 22 outliers final: 20 residues processed: 151 average time/residue: 0.0754 time to fit residues: 14.1901 Evaluate side-chains 164 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 99 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 30 TYR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain M residue 85 MET Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 100 GLN Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 44 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 36 optimal weight: 50.0000 chunk 79 optimal weight: 0.7980 chunk 74 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 18 optimal weight: 50.0000 chunk 58 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.079773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.065372 restraints weight = 13520.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.067050 restraints weight = 7573.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.068259 restraints weight = 5114.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.069046 restraints weight = 3884.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.069641 restraints weight = 3199.977| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5045 Z= 0.169 Angle : 0.608 7.262 6682 Z= 0.331 Chirality : 0.043 0.168 522 Planarity : 0.005 0.061 995 Dihedral : 4.610 18.442 875 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.12 % Favored : 94.76 % Rotamer: Outliers : 6.20 % Allowed : 31.00 % Favored : 62.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 0.76 (0.30), residues: 821 helix: 1.27 (1.46), residues: 16 sheet: 1.13 (0.26), residues: 370 loop : -0.03 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 19 TYR 0.014 0.002 TYR L 47 PHE 0.026 0.003 PHE H 68 TRP 0.014 0.002 TRP M 47 HIS 0.003 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 5041) covalent geometry : angle 0.60472 ( 6674) SS BOND : bond 0.00756 ( 4) SS BOND : angle 1.87390 ( 8) hydrogen bonds : bond 0.02988 ( 244) hydrogen bonds : angle 4.75427 ( 708) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 862.08 seconds wall clock time: 15 minutes 26.96 seconds (926.96 seconds total)