Starting phenix.real_space_refine on Thu Mar 6 04:18:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mmv_48404/03_2025/9mmv_48404.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mmv_48404/03_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_48404/03_2025/9mmv_48404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mmv_48404/03_2025/9mmv_48404.map" model { file = "/net/cci-nas-00/data/ceres_data/9mmv_48404/03_2025/9mmv_48404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mmv_48404/03_2025/9mmv_48404.cif" } resolution = 3.79 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= 0.369 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'HIS:plan': 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, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 6, '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: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 3, 'HIS:plan': 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: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 188 Time building chain proxies: 3.44, per 1000 atoms: 0.69 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: 1.14 Conformation dependent library (CDL) restraints added in 748.4 milliseconds 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: 0.90 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: 1.37 Time building geometry restraints manager: 1.37 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: 0.470 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.420 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.160 ------------------------------------------------------------------------------- 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 5041 Z= 0.281 Angle : 0.815 23.757 6674 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 : 10.87 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.41 % 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 (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: 1.43 (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 TRP 0.008 0.001 TRP M 47 HIS 0.003 0.002 HIS H 35 PHE 0.010 0.002 PHE H 68 TYR 0.015 0.001 TYR M 112 ARG 0.008 0.001 ARG M 16 *********************** 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 : 0.531 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: 0.1853 time to fit residues: 33.3429 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 : 0.562 ------------------------------------------------------------------------------- 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 70 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 34 optimal weight: 50.0000 chunk 21 optimal weight: 0.0770 chunk 42 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 39 optimal weight: 50.0000 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- 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 = 0.3126 r_free = 0.3126 target = 0.082608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.068715 restraints weight = 12803.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.070362 restraints weight = 7385.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.071493 restraints weight = 5079.653| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5041 Z= 0.191 Angle : 0.541 5.674 6674 Z= 0.300 Chirality : 0.042 0.139 522 Planarity : 0.005 0.073 995 Dihedral : 4.450 28.855 876 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.17 % Favored : 96.59 % Rotamer: Outliers : 5.66 % Allowed : 28.30 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 1.36 (0.30), residues: 821 helix: 1.54 (1.48), residues: 16 sheet: 1.62 (0.27), residues: 361 loop : 0.32 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 47 HIS 0.004 0.003 HIS H 35 PHE 0.016 0.002 PHE N 96 TYR 0.012 0.001 TYR L 47 ARG 0.005 0.001 ARG M 16 *********************** 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: 21 poor density : 150 time to evaluate : 0.519 Fit side-chains REVERT: H 76 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8219 (tmtt) REVERT: L 16 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8238 (tm-30) REVERT: L 101 THR cc_start: 0.8878 (m) cc_final: 0.8557 (p) REVERT: M 122 THR cc_start: 0.9232 (m) cc_final: 0.8968 (p) outliers start: 21 outliers final: 7 residues processed: 157 average time/residue: 0.1816 time to fit residues: 35.1904 Evaluate side-chains 154 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 11 LEU Chi-restraints excluded: chain M residue 62 TYR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 21 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 37 optimal weight: 50.0000 chunk 60 optimal weight: 50.0000 chunk 12 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 80 optimal weight: 40.0000 chunk 50 optimal weight: 9.9990 chunk 33 optimal weight: 0.0370 chunk 40 optimal weight: 4.9990 overall best weight: 5.4066 ------------------------------------------------------------------------------- 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 = 0.3066 r_free = 0.3066 target = 0.079913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.065762 restraints weight = 13206.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.067381 restraints weight = 7627.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.068528 restraints weight = 5276.099| |-----------------------------------------------------------------------------| r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5041 Z= 0.329 Angle : 0.606 8.734 6674 Z= 0.332 Chirality : 0.044 0.176 522 Planarity : 0.005 0.058 995 Dihedral : 4.615 18.021 875 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.02 % Favored : 95.86 % Rotamer: Outliers : 4.04 % Allowed : 31.54 % Favored : 64.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 1.22 (0.30), residues: 821 helix: 1.37 (1.49), residues: 16 sheet: 1.58 (0.27), residues: 362 loop : 0.18 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 47 HIS 0.005 0.003 HIS H 35 PHE 0.026 0.003 PHE N 94 TYR 0.018 0.002 TYR L 47 ARG 0.005 0.001 ARG H 98 *********************** 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 163 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.596 Fit side-chains REVERT: H 76 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8246 (tmtt) REVERT: L 16 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8219 (tm-30) REVERT: L 101 THR cc_start: 0.8915 (m) cc_final: 0.8604 (p) REVERT: N 4 MET cc_start: 0.8414 (mmm) cc_final: 0.8140 (mmm) REVERT: N 73 LEU cc_start: 0.8761 (mt) cc_final: 0.8552 (mt) outliers start: 15 outliers final: 11 residues processed: 152 average time/residue: 0.1803 time to fit residues: 34.0616 Evaluate side-chains 156 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 2 ILE Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 30 TYR 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 19 VAL Chi-restraints excluded: chain N residue 33 LEU 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 75 optimal weight: 40.0000 chunk 7 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 50.0000 chunk 5 optimal weight: 6.9990 chunk 61 optimal weight: 40.0000 overall best weight: 6.3988 ------------------------------------------------------------------------------- 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 = 0.3045 r_free = 0.3045 target = 0.078795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.064533 restraints weight = 13394.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.066240 restraints weight = 7570.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.067456 restraints weight = 5121.373| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5041 Z= 0.371 Angle : 0.635 9.514 6674 Z= 0.349 Chirality : 0.045 0.187 522 Planarity : 0.005 0.056 995 Dihedral : 4.862 19.053 875 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.87 % Favored : 95.01 % Rotamer: Outliers : 6.47 % Allowed : 31.00 % 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 (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: 0.97 (0.30), residues: 821 helix: 1.00 (1.44), residues: 16 sheet: 1.41 (0.26), residues: 361 loop : 0.02 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 47 HIS 0.005 0.003 HIS H 35 PHE 0.021 0.003 PHE N 94 TYR 0.019 0.002 TYR L 47 ARG 0.006 0.001 ARG M 16 *********************** 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 174 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.554 Fit side-chains REVERT: H 76 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8257 (tmtt) REVERT: L 16 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8268 (tm-30) REVERT: L 101 THR cc_start: 0.8899 (m) cc_final: 0.8523 (p) REVERT: N 50 ASP cc_start: 0.7807 (m-30) cc_final: 0.7293 (m-30) outliers start: 24 outliers final: 14 residues processed: 159 average time/residue: 0.1858 time to fit residues: 36.7820 Evaluate side-chains 162 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 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 53 SER 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 5 THR 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 1 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 78 optimal weight: 30.0000 chunk 45 optimal weight: 5.9990 chunk 81 optimal weight: 50.0000 chunk 80 optimal weight: 30.0000 chunk 47 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 overall best weight: 5.5588 ------------------------------------------------------------------------------- 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 = 0.3050 r_free = 0.3050 target = 0.079086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.064772 restraints weight = 13322.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.066473 restraints weight = 7555.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.067680 restraints weight = 5132.824| |-----------------------------------------------------------------------------| r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5041 Z= 0.335 Angle : 0.615 7.621 6674 Z= 0.338 Chirality : 0.044 0.182 522 Planarity : 0.005 0.056 995 Dihedral : 4.786 18.961 875 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.51 % Favored : 95.37 % Rotamer: Outliers : 5.39 % Allowed : 32.08 % 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 (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: 0.90 (0.30), residues: 821 helix: 0.97 (1.44), residues: 16 sheet: 1.33 (0.26), residues: 362 loop : -0.01 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 47 HIS 0.004 0.002 HIS H 35 PHE 0.019 0.003 PHE H 68 TYR 0.018 0.002 TYR L 47 ARG 0.005 0.001 ARG H 98 *********************** 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 166 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.553 Fit side-chains REVERT: H 76 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8259 (tmtt) REVERT: H 83 MET cc_start: 0.9081 (mtp) cc_final: 0.8838 (mtm) REVERT: L 16 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8295 (tm-30) REVERT: L 101 THR cc_start: 0.8904 (m) cc_final: 0.8549 (p) outliers start: 20 outliers final: 16 residues processed: 154 average time/residue: 0.1892 time to fit residues: 36.0113 Evaluate side-chains 160 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 75 ASP 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 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 2 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 13 optimal weight: 50.0000 chunk 38 optimal weight: 0.0870 chunk 69 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 35 optimal weight: 40.0000 overall best weight: 5.6166 ------------------------------------------------------------------------------- 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 = 0.078704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.064601 restraints weight = 13445.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.066202 restraints weight = 7510.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.067365 restraints weight = 5140.201| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5041 Z= 0.336 Angle : 0.620 7.424 6674 Z= 0.340 Chirality : 0.044 0.185 522 Planarity : 0.005 0.056 995 Dihedral : 4.811 19.058 875 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.24 % Favored : 94.64 % Rotamer: Outliers : 6.47 % Allowed : 30.46 % Favored : 63.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 0.88 (0.30), residues: 821 helix: 1.04 (1.46), residues: 16 sheet: 1.27 (0.26), residues: 362 loop : 0.02 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 47 HIS 0.004 0.002 HIS H 35 PHE 0.026 0.003 PHE H 68 TYR 0.021 0.002 TYR M 112 ARG 0.008 0.001 ARG H 19 *********************** 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 171 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.548 Fit side-chains REVERT: H 76 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8267 (tmtt) REVERT: L 16 GLN cc_start: 0.8756 (tm-30) cc_final: 0.8318 (tm-30) REVERT: L 101 THR cc_start: 0.8888 (m) cc_final: 0.8543 (p) outliers start: 24 outliers final: 20 residues processed: 157 average time/residue: 0.1820 time to fit residues: 35.4952 Evaluate side-chains 167 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 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 75 ASP 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 7 SER 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 34 optimal weight: 30.0000 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 20.0000 chunk 59 optimal weight: 50.0000 chunk 50 optimal weight: 9.9990 chunk 15 optimal weight: 40.0000 chunk 62 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 = 0.3034 r_free = 0.3034 target = 0.078314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.064338 restraints weight = 13269.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.065912 restraints weight = 7704.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.067058 restraints weight = 5340.458| |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5041 Z= 0.364 Angle : 0.638 8.203 6674 Z= 0.351 Chirality : 0.045 0.192 522 Planarity : 0.005 0.059 995 Dihedral : 4.906 19.509 875 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.24 % Favored : 94.64 % Rotamer: Outliers : 7.55 % Allowed : 30.19 % Favored : 62.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 0.82 (0.30), residues: 821 helix: 0.95 (1.45), residues: 16 sheet: 1.23 (0.26), residues: 362 loop : -0.01 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 47 HIS 0.004 0.002 HIS H 35 PHE 0.028 0.003 PHE H 68 TYR 0.027 0.002 TYR M 112 ARG 0.007 0.001 ARG H 19 *********************** 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 176 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.558 Fit side-chains REVERT: H 76 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8259 (tmtt) REVERT: L 16 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8356 (tm-30) REVERT: L 101 THR cc_start: 0.8885 (m) cc_final: 0.8487 (p) outliers start: 28 outliers final: 19 residues processed: 160 average time/residue: 0.1881 time to fit residues: 37.3711 Evaluate side-chains 165 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 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 75 ASP 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 7 SER 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 78 optimal weight: 30.0000 chunk 68 optimal weight: 10.0000 chunk 56 optimal weight: 30.0000 chunk 38 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 76 optimal weight: 30.0000 chunk 73 optimal weight: 50.0000 chunk 28 optimal weight: 6.9990 chunk 63 optimal weight: 20.0000 chunk 9 optimal weight: 0.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.078716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.064433 restraints weight = 13519.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.066126 restraints weight = 7638.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.067335 restraints weight = 5191.538| |-----------------------------------------------------------------------------| r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5041 Z= 0.328 Angle : 0.634 7.684 6674 Z= 0.346 Chirality : 0.044 0.184 522 Planarity : 0.005 0.059 995 Dihedral : 4.817 19.124 875 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.87 % Favored : 95.01 % Rotamer: Outliers : 7.01 % Allowed : 31.81 % Favored : 61.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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 (0.30), residues: 821 helix: 1.05 (1.46), residues: 16 sheet: 1.18 (0.26), residues: 369 loop : -0.00 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 47 HIS 0.003 0.002 HIS H 35 PHE 0.030 0.003 PHE H 68 TYR 0.024 0.002 TYR M 112 ARG 0.006 0.001 ARG H 19 *********************** 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 173 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.629 Fit side-chains REVERT: H 76 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8257 (tmtt) REVERT: L 16 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8346 (tm-30) outliers start: 26 outliers final: 21 residues processed: 158 average time/residue: 0.2498 time to fit residues: 49.6668 Evaluate side-chains 167 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 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 75 ASP 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 7 SER 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: 30.0000 chunk 51 optimal weight: 10.0000 chunk 55 optimal weight: 30.0000 chunk 58 optimal weight: 20.0000 chunk 20 optimal weight: 50.0000 chunk 23 optimal weight: 20.0000 chunk 40 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 40.0000 chunk 70 optimal weight: 7.9990 overall best weight: 6.7790 ------------------------------------------------------------------------------- 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 = 0.3028 r_free = 0.3028 target = 0.078119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.063921 restraints weight = 13225.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.065582 restraints weight = 7500.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.066732 restraints weight = 5090.026| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 5041 Z= 0.398 Angle : 0.674 9.062 6674 Z= 0.369 Chirality : 0.046 0.197 522 Planarity : 0.005 0.061 995 Dihedral : 5.033 19.821 875 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.48 % Favored : 94.40 % Rotamer: Outliers : 6.74 % Allowed : 31.81 % Favored : 61.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 0.72 (0.30), residues: 821 helix: 0.91 (1.45), residues: 16 sheet: 1.13 (0.26), residues: 379 loop : -0.09 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 47 HIS 0.004 0.002 HIS H 35 PHE 0.035 0.003 PHE H 68 TYR 0.030 0.002 TYR M 112 ARG 0.006 0.001 ARG H 19 *********************** 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: 25 poor density : 143 time to evaluate : 0.809 Fit side-chains REVERT: H 76 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8282 (tmtt) REVERT: L 16 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8329 (tm-30) outliers start: 25 outliers final: 18 residues processed: 154 average time/residue: 0.2491 time to fit residues: 48.4867 Evaluate side-chains 160 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 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 75 ASP 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 7 SER 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 27 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 78 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 40.0000 chunk 45 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3061 r_free = 0.3061 target = 0.079558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.065269 restraints weight = 13217.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.066935 restraints weight = 7545.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.068132 restraints weight = 5169.750| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5041 Z= 0.257 Angle : 0.607 7.330 6674 Z= 0.331 Chirality : 0.043 0.171 522 Planarity : 0.005 0.060 995 Dihedral : 4.616 18.448 875 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.63 % Favored : 95.25 % Rotamer: Outliers : 6.20 % Allowed : 33.15 % Favored : 60.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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 (0.30), residues: 821 helix: 1.23 (1.47), residues: 16 sheet: 1.11 (0.26), residues: 372 loop : 0.01 (0.32), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 47 HIS 0.003 0.002 HIS H 35 PHE 0.028 0.003 PHE H 68 TYR 0.023 0.002 TYR M 112 ARG 0.006 0.001 ARG M 19 ********************** 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 168 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.573 Fit side-chains REVERT: H 76 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8229 (tmtt) REVERT: L 16 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8325 (tm-30) REVERT: L 81 GLU cc_start: 0.8209 (pm20) cc_final: 0.7952 (pm20) REVERT: N 17 ASP cc_start: 0.8162 (m-30) cc_final: 0.7949 (m-30) outliers start: 23 outliers final: 19 residues processed: 153 average time/residue: 0.2467 time to fit residues: 47.3469 Evaluate side-chains 166 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 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 85 MET Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 7 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 39 optimal weight: 40.0000 chunk 37 optimal weight: 50.0000 chunk 80 optimal weight: 40.0000 chunk 36 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 50.0000 chunk 25 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 28 optimal weight: 0.3980 overall best weight: 3.6586 ------------------------------------------------------------------------------- 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 = 0.3065 r_free = 0.3065 target = 0.079768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.065780 restraints weight = 13365.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.067376 restraints weight = 7767.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.068530 restraints weight = 5344.767| |-----------------------------------------------------------------------------| r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5041 Z= 0.252 Angle : 0.602 7.006 6674 Z= 0.327 Chirality : 0.043 0.169 522 Planarity : 0.005 0.060 995 Dihedral : 4.522 18.257 875 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.75 % Favored : 95.13 % Rotamer: Outliers : 5.39 % Allowed : 34.77 % Favored : 59.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % 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: 0.77 (0.30), residues: 821 helix: 1.42 (1.48), residues: 16 sheet: 1.06 (0.26), residues: 375 loop : 0.04 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 47 HIS 0.003 0.002 HIS H 35 PHE 0.026 0.003 PHE H 68 TYR 0.022 0.002 TYR M 112 ARG 0.007 0.001 ARG M 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2270.99 seconds wall clock time: 41 minutes 13.43 seconds (2473.43 seconds total)