Starting phenix.real_space_refine on Sun Apr 27 06:37:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mmv_48404/04_2025/9mmv_48404.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mmv_48404/04_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_48404/04_2025/9mmv_48404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mmv_48404/04_2025/9mmv_48404.map" model { file = "/net/cci-nas-00/data/ceres_data/9mmv_48404/04_2025/9mmv_48404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mmv_48404/04_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-5669/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: 3.70, per 1000 atoms: 0.74 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: 1.18 Conformation dependent library (CDL) restraints added in 812.2 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: 1.03 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: 1.50 Time building geometry restraints manager: 1.42 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: 0.410 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.830 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.690 ------------------------------------------------------------------------------- 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 : 10.87 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.25338 ( 244) hydrogen bonds : angle 9.40701 ( 708) SS BOND : bond 0.00359 ( 4) SS BOND : angle 1.16107 ( 8) covalent geometry : bond 0.00410 ( 5041) covalent geometry : angle 0.81493 ( 6674) *********************** 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 : 0.596 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: 0.2026 time to fit residues: 36.3647 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 : 0.590 ------------------------------------------------------------------------------- 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: 1.9990 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: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3117 r_free = 0.3117 target = 0.082180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.068296 restraints weight = 12865.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.069908 restraints weight = 7447.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.071030 restraints weight = 5100.899| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1267 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= 0.139 Angle : 0.553 5.784 6682 Z= 0.307 Chirality : 0.042 0.144 522 Planarity : 0.005 0.073 995 Dihedral : 4.519 32.065 876 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.65 % Favored : 96.10 % Rotamer: Outliers : 5.66 % Allowed : 28.57 % Favored : 65.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 2.04 % 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: 1.35 (0.30), residues: 821 helix: 1.53 (1.48), residues: 16 sheet: 1.62 (0.27), residues: 361 loop : 0.31 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 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 0.000 ARG M 16 Details of bonding type rmsd hydrogen bonds : bond 0.03552 ( 244) hydrogen bonds : angle 5.74781 ( 708) SS BOND : bond 0.00574 ( 4) SS BOND : angle 1.36642 ( 8) covalent geometry : bond 0.00298 ( 5041) covalent geometry : angle 0.55172 ( 6674) *********************** 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 170 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.854 Fit side-chains REVERT: H 6 GLU cc_start: 0.8194 (mp0) cc_final: 0.7968 (mp0) REVERT: H 76 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8222 (tmtt) REVERT: L 16 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8231 (tm-30) REVERT: L 101 THR cc_start: 0.8886 (m) cc_final: 0.8552 (p) outliers start: 21 outliers final: 9 residues processed: 156 average time/residue: 0.2567 time to fit residues: 49.4553 Evaluate side-chains 156 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 7 SER 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 21 optimal weight: 0.0050 chunk 28 optimal weight: 10.0000 chunk 37 optimal weight: 40.0000 chunk 60 optimal weight: 50.0000 chunk 12 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 80 optimal weight: 40.0000 chunk 50 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 overall best weight: 3.7200 ------------------------------------------------------------------------------- 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 = 0.3094 r_free = 0.3094 target = 0.081162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.067270 restraints weight = 13107.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.068875 restraints weight = 7633.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.069991 restraints weight = 5241.554| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5045 Z= 0.161 Angle : 0.560 6.394 6682 Z= 0.307 Chirality : 0.042 0.157 522 Planarity : 0.004 0.059 995 Dihedral : 4.425 20.309 876 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.41 % Favored : 96.47 % Rotamer: Outliers : 4.31 % Allowed : 31.27 % 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: 1.28 (0.30), residues: 821 helix: 1.60 (1.48), residues: 16 sheet: 1.57 (0.26), residues: 366 loop : 0.24 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 47 HIS 0.004 0.003 HIS H 35 PHE 0.022 0.002 PHE N 94 TYR 0.014 0.002 TYR L 47 ARG 0.005 0.001 ARG M 16 Details of bonding type rmsd hydrogen bonds : bond 0.03126 ( 244) hydrogen bonds : angle 5.20688 ( 708) SS BOND : bond 0.00677 ( 4) SS BOND : angle 1.68421 ( 8) covalent geometry : bond 0.00349 ( 5041) covalent geometry : angle 0.55723 ( 6674) *********************** 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 162 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.606 Fit side-chains REVERT: H 76 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8235 (tmtt) REVERT: L 16 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8234 (tm-30) REVERT: L 101 THR cc_start: 0.8904 (m) cc_final: 0.8589 (p) REVERT: M 60 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8236 (mttm) REVERT: N 4 MET cc_start: 0.8426 (mmm) cc_final: 0.8198 (tpp) outliers start: 16 outliers final: 11 residues processed: 150 average time/residue: 0.1861 time to fit residues: 34.7293 Evaluate side-chains 157 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 30 TYR Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 62 TYR 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 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: 8.9990 chunk 70 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 73 optimal weight: 50.0000 chunk 5 optimal weight: 6.9990 chunk 61 optimal weight: 40.0000 overall best weight: 5.9588 ------------------------------------------------------------------------------- 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 = 0.3053 r_free = 0.3053 target = 0.079340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.064872 restraints weight = 13249.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.066541 restraints weight = 7483.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.067768 restraints weight = 5099.163| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5045 Z= 0.234 Angle : 0.626 8.806 6682 Z= 0.343 Chirality : 0.044 0.180 522 Planarity : 0.005 0.055 995 Dihedral : 4.776 18.765 875 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.14 % Favored : 95.74 % Rotamer: Outliers : 7.01 % Allowed : 30.73 % 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: 1.03 (0.30), residues: 821 helix: 1.24 (1.45), residues: 16 sheet: 1.44 (0.26), residues: 362 loop : 0.06 (0.31), residues: 443 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 0.024 0.003 PHE N 94 TYR 0.023 0.002 TYR M 112 ARG 0.006 0.001 ARG M 16 Details of bonding type rmsd hydrogen bonds : bond 0.03392 ( 244) hydrogen bonds : angle 5.31930 ( 708) SS BOND : bond 0.00924 ( 4) SS BOND : angle 1.95765 ( 8) covalent geometry : bond 0.00507 ( 5041) covalent geometry : angle 0.62304 ( 6674) *********************** 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 180 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.539 Fit side-chains REVERT: H 76 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8251 (tmtt) REVERT: L 16 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8267 (tm-30) REVERT: L 101 THR cc_start: 0.8912 (m) cc_final: 0.8506 (p) outliers start: 26 outliers final: 16 residues processed: 164 average time/residue: 0.1858 time to fit residues: 37.7556 Evaluate side-chains 167 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 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 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 5 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 1 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 78 optimal weight: 30.0000 chunk 45 optimal weight: 6.9990 chunk 81 optimal weight: 40.0000 chunk 80 optimal weight: 30.0000 chunk 47 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.3069 r_free = 0.3069 target = 0.080017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.065865 restraints weight = 13158.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.067502 restraints weight = 7584.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.068653 restraints weight = 5238.973| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5045 Z= 0.190 Angle : 0.584 7.207 6682 Z= 0.322 Chirality : 0.043 0.163 522 Planarity : 0.005 0.055 995 Dihedral : 4.624 17.807 875 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.26 % Favored : 95.62 % Rotamer: Outliers : 5.39 % Allowed : 32.35 % 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: 0.98 (0.30), residues: 821 helix: 1.36 (1.45), residues: 16 sheet: 1.33 (0.26), residues: 365 loop : 0.09 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 47 HIS 0.004 0.002 HIS H 35 PHE 0.021 0.003 PHE N 49 TYR 0.023 0.002 TYR M 112 ARG 0.005 0.001 ARG M 16 Details of bonding type rmsd hydrogen bonds : bond 0.03075 ( 244) hydrogen bonds : angle 5.08800 ( 708) SS BOND : bond 0.00793 ( 4) SS BOND : angle 1.67977 ( 8) covalent geometry : bond 0.00414 ( 5041) covalent geometry : angle 0.58179 ( 6674) *********************** 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: 20 poor density : 151 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: H 76 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8240 (tmtt) REVERT: L 16 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8281 (tm-30) REVERT: L 101 THR cc_start: 0.8896 (m) cc_final: 0.8547 (p) outliers start: 20 outliers final: 16 residues processed: 157 average time/residue: 0.1854 time to fit residues: 36.0517 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 : 0.540 ------------------------------------------------------------------------------- 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 87 ARG Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 2 ILE 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 60 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 33 LEU 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: 2.9990 chunk 50 optimal weight: 6.9990 chunk 13 optimal weight: 50.0000 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 = 0.3081 r_free = 0.3081 target = 0.080377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.065599 restraints weight = 13151.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.067332 restraints weight = 7470.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.068522 restraints weight = 5098.631| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5045 Z= 0.177 Angle : 0.573 6.038 6682 Z= 0.315 Chirality : 0.042 0.156 522 Planarity : 0.004 0.054 995 Dihedral : 4.521 17.578 875 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.02 % Favored : 95.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.30), residues: 821 helix: 1.42 (1.45), residues: 16 sheet: 1.28 (0.26), residues: 365 loop : 0.10 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 47 HIS 0.004 0.002 HIS H 35 PHE 0.024 0.002 PHE H 68 TYR 0.022 0.002 TYR M 112 ARG 0.005 0.001 ARG M 16 Details of bonding type rmsd hydrogen bonds : bond 0.02971 ( 244) hydrogen bonds : angle 4.94829 ( 708) SS BOND : bond 0.00758 ( 4) SS BOND : angle 1.74632 ( 8) covalent geometry : bond 0.00385 ( 5041) covalent geometry : angle 0.57020 ( 6674) *********************** 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 175 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.549 Fit side-chains REVERT: H 76 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8265 (tmtt) REVERT: L 16 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8313 (tm-30) REVERT: L 101 THR cc_start: 0.8848 (m) cc_final: 0.8503 (p) outliers start: 25 outliers final: 20 residues processed: 159 average time/residue: 0.2088 time to fit residues: 41.3482 Evaluate side-chains 169 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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 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 62 TYR 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 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: 40.0000 chunk 28 optimal weight: 8.9990 chunk 23 optimal weight: 20.0000 chunk 59 optimal weight: 40.0000 chunk 50 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 overall best weight: 9.5990 ------------------------------------------------------------------------------- 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 = 0.3009 r_free = 0.3009 target = 0.077199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.062809 restraints weight = 13248.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.064466 restraints weight = 7536.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.065684 restraints weight = 5144.740| |-----------------------------------------------------------------------------| r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 5045 Z= 0.357 Angle : 0.740 9.597 6682 Z= 0.409 Chirality : 0.048 0.217 522 Planarity : 0.005 0.061 995 Dihedral : 5.394 20.535 875 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.48 % Favored : 94.28 % Rotamer: Outliers : 8.63 % Allowed : 28.84 % 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: 0.66 (0.29), residues: 821 helix: 0.62 (1.43), residues: 16 sheet: 1.19 (0.26), residues: 374 loop : -0.23 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP H 104 HIS 0.005 0.003 HIS H 35 PHE 0.031 0.004 PHE H 68 TYR 0.034 0.003 TYR M 112 ARG 0.007 0.001 ARG M 16 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 244) hydrogen bonds : angle 5.56580 ( 708) SS BOND : bond 0.01079 ( 4) SS BOND : angle 2.25534 ( 8) covalent geometry : bond 0.00777 ( 5041) covalent geometry : angle 0.73652 ( 6674) *********************** 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 177 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.870 Fit side-chains REVERT: H 76 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8296 (tmtt) REVERT: L 16 GLN cc_start: 0.8793 (tm-30) cc_final: 0.8343 (tm-30) outliers start: 32 outliers final: 22 residues processed: 157 average time/residue: 0.3116 time to fit residues: 62.5050 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 : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 51 ILE 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 30 ASP 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 79 ASN Chi-restraints excluded: chain M residue 85 MET Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 4 MET 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: 0.9980 chunk 56 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 76 optimal weight: 30.0000 chunk 73 optimal weight: 50.0000 chunk 28 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- 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 = 0.3075 r_free = 0.3075 target = 0.080146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.066027 restraints weight = 13403.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.067633 restraints weight = 7739.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.068827 restraints weight = 5325.528| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2051 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= 0.145 Angle : 0.574 7.186 6682 Z= 0.315 Chirality : 0.042 0.162 522 Planarity : 0.004 0.058 995 Dihedral : 4.518 17.305 875 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.02 % Favored : 95.74 % 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 (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: 1.20 (1.45), residues: 16 sheet: 1.20 (0.26), residues: 363 loop : 0.00 (0.31), residues: 442 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 0.020 0.002 PHE H 68 TYR 0.018 0.002 TYR M 112 ARG 0.005 0.001 ARG M 16 Details of bonding type rmsd hydrogen bonds : bond 0.02857 ( 244) hydrogen bonds : angle 4.84785 ( 708) SS BOND : bond 0.00712 ( 4) SS BOND : angle 1.55085 ( 8) covalent geometry : bond 0.00315 ( 5041) covalent geometry : angle 0.57233 ( 6674) *********************** 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 174 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.584 Fit side-chains REVERT: H 76 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8215 (tmtt) REVERT: L 16 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8326 (tm-30) outliers start: 23 outliers final: 16 residues processed: 160 average time/residue: 0.1843 time to fit residues: 36.6063 Evaluate side-chains 169 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 78 optimal weight: 40.0000 chunk 51 optimal weight: 10.0000 chunk 55 optimal weight: 30.0000 chunk 58 optimal weight: 30.0000 chunk 20 optimal weight: 50.0000 chunk 23 optimal weight: 9.9990 chunk 40 optimal weight: 0.0070 chunk 5 optimal weight: 8.9990 chunk 25 optimal weight: 0.3980 chunk 19 optimal weight: 50.0000 chunk 70 optimal weight: 2.9990 overall best weight: 4.4804 ------------------------------------------------------------------------------- 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 = 0.3059 r_free = 0.3059 target = 0.079439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.065162 restraints weight = 13102.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.066820 restraints weight = 7485.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.068030 restraints weight = 5089.313| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 0.041 5045 Z= 0.192 Angle : 0.616 7.237 6682 Z= 0.336 Chirality : 0.043 0.176 522 Planarity : 0.005 0.059 995 Dihedral : 4.634 17.647 875 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.87 % Favored : 94.88 % Rotamer: Outliers : 5.66 % Allowed : 31.81 % 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: 0.80 (0.30), residues: 821 helix: 1.20 (1.45), residues: 16 sheet: 1.18 (0.26), residues: 365 loop : -0.00 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 47 HIS 0.003 0.002 HIS H 35 PHE 0.028 0.003 PHE H 68 TYR 0.019 0.002 TYR M 112 ARG 0.008 0.001 ARG M 16 Details of bonding type rmsd hydrogen bonds : bond 0.03052 ( 244) hydrogen bonds : angle 4.94199 ( 708) SS BOND : bond 0.00822 ( 4) SS BOND : angle 1.92506 ( 8) covalent geometry : bond 0.00422 ( 5041) covalent geometry : angle 0.61273 ( 6674) *********************** 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 170 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.471 Fit side-chains REVERT: H 76 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8272 (tmtt) REVERT: L 16 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8325 (tm-30) REVERT: L 101 THR cc_start: 0.8871 (m) cc_final: 0.8535 (p) outliers start: 21 outliers final: 16 residues processed: 156 average time/residue: 0.1849 time to fit residues: 35.9085 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 : 0.604 ------------------------------------------------------------------------------- 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 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 85 MET Chi-restraints excluded: chain M residue 99 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 27 optimal weight: 4.9990 chunk 56 optimal weight: 40.0000 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 0.0030 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 78 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 40.0000 chunk 45 optimal weight: 5.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- 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 = 0.3097 r_free = 0.3097 target = 0.081181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.066629 restraints weight = 12989.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.068294 restraints weight = 7562.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.069383 restraints weight = 5254.642| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5045 Z= 0.145 Angle : 0.581 7.099 6682 Z= 0.316 Chirality : 0.043 0.165 522 Planarity : 0.004 0.057 995 Dihedral : 4.384 17.343 875 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.02 % Favored : 95.86 % Rotamer: Outliers : 5.39 % Allowed : 31.00 % Favored : 63.61 % 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: 0.86 (0.30), residues: 821 helix: 1.48 (1.47), residues: 16 sheet: 1.16 (0.26), residues: 366 loop : 0.08 (0.31), residues: 439 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 0.022 0.002 PHE H 68 TYR 0.017 0.002 TYR M 112 ARG 0.006 0.001 ARG M 19 Details of bonding type rmsd hydrogen bonds : bond 0.02749 ( 244) hydrogen bonds : angle 4.71320 ( 708) SS BOND : bond 0.00682 ( 4) SS BOND : angle 1.72848 ( 8) covalent geometry : bond 0.00322 ( 5041) covalent geometry : angle 0.57871 ( 6674) ********************** 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 171 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.602 Fit side-chains REVERT: H 76 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8242 (tmtt) REVERT: L 16 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8329 (tm-30) REVERT: L 81 GLU cc_start: 0.8144 (pm20) cc_final: 0.7844 (pm20) REVERT: L 101 THR cc_start: 0.8853 (m) cc_final: 0.8536 (p) outliers start: 20 outliers final: 16 residues processed: 156 average time/residue: 0.1944 time to fit residues: 37.5420 Evaluate side-chains 164 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 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 85 MET 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: 30.0000 chunk 37 optimal weight: 50.0000 chunk 80 optimal weight: 30.0000 chunk 36 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 50.0000 chunk 25 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 107 ASN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.079213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.064908 restraints weight = 13317.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.066556 restraints weight = 7505.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.067798 restraints weight = 5114.759| |-----------------------------------------------------------------------------| r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 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 : 0.005 0.049 5045 Z= 0.209 Angle : 0.624 7.072 6682 Z= 0.341 Chirality : 0.045 0.188 522 Planarity : 0.005 0.060 995 Dihedral : 4.658 17.762 875 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.12 % Favored : 94.76 % Rotamer: Outliers : 5.93 % Allowed : 32.61 % 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: 0.80 (0.30), residues: 821 helix: 1.35 (1.46), residues: 16 sheet: 1.13 (0.26), residues: 366 loop : 0.03 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 47 HIS 0.003 0.002 HIS H 35 PHE 0.030 0.003 PHE H 68 TYR 0.022 0.002 TYR M 112 ARG 0.006 0.001 ARG N 103 Details of bonding type rmsd hydrogen bonds : bond 0.03108 ( 244) hydrogen bonds : angle 4.93645 ( 708) SS BOND : bond 0.00837 ( 4) SS BOND : angle 1.91144 ( 8) covalent geometry : bond 0.00462 ( 5041) covalent geometry : angle 0.62052 ( 6674) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2564.51 seconds wall clock time: 46 minutes 8.52 seconds (2768.52 seconds total)