Starting phenix.real_space_refine on Sat May 10 03:26:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mmv_48404/05_2025/9mmv_48404.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mmv_48404/05_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_48404/05_2025/9mmv_48404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mmv_48404/05_2025/9mmv_48404.map" model { file = "/net/cci-nas-00/data/ceres_data/9mmv_48404/05_2025/9mmv_48404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mmv_48404/05_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-5687/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: 3.71, per 1000 atoms: 0.75 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: 1.39 Conformation dependent library (CDL) restraints added in 757.2 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: 0.97 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: 1.55 Time building geometry restraints manager: 1.61 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: 0.380 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: 0.040 Set scattering table: 0.050 Process input model: 16.960 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: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.580 ------------------------------------------------------------------------------- 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 : 0.634 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: 0.2036 time to fit residues: 36.6621 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 : 0.633 ------------------------------------------------------------------------------- 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 = 0.068297 restraints weight = 12865.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.069864 restraints weight = 7448.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.071017 restraints weight = 5135.224| |-----------------------------------------------------------------------------| r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 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 : 0.623 Fit side-chains REVERT: H 6 GLU cc_start: 0.8194 (mp0) cc_final: 0.7965 (mp0) REVERT: H 76 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8218 (tmtt) REVERT: L 16 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8228 (tm-30) REVERT: L 101 THR cc_start: 0.8883 (m) cc_final: 0.8550 (p) outliers start: 21 outliers final: 9 residues processed: 156 average time/residue: 0.1814 time to fit residues: 34.9862 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 : 0.533 ------------------------------------------------------------------------------- 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: 50.0000 chunk 60 optimal weight: 50.0000 chunk 12 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 80 optimal weight: 40.0000 chunk 50 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 overall best weight: 3.9200 ------------------------------------------------------------------------------- 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 = 0.3089 r_free = 0.3089 target = 0.080967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.067192 restraints weight = 13048.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.068820 restraints weight = 7493.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.069971 restraints weight = 5172.893| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5045 Z= 0.168 Angle : 0.567 6.703 6682 Z= 0.311 Chirality : 0.043 0.159 522 Planarity : 0.004 0.059 995 Dihedral : 4.484 19.850 876 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.41 % Favored : 96.47 % Rotamer: Outliers : 4.58 % Allowed : 31.00 % 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: 1.27 (0.30), residues: 821 helix: 1.57 (1.48), residues: 16 sheet: 1.58 (0.26), residues: 366 loop : 0.22 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 47 HIS 0.005 0.003 HIS H 35 PHE 0.023 0.002 PHE N 94 TYR 0.015 0.002 TYR L 47 ARG 0.005 0.001 ARG M 16 Details of bonding type rmsd hydrogen bonds : bond 0.03156 ( 244) hydrogen bonds : angle 5.17807 ( 708) SS BOND : bond 0.00714 ( 4) SS BOND : angle 1.81058 ( 8) covalent geometry : bond 0.00363 ( 5041) covalent geometry : angle 0.56346 ( 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 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 Fit side-chains REVERT: H 76 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8238 (tmtt) REVERT: L 16 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8223 (tm-30) REVERT: L 101 THR cc_start: 0.8911 (m) cc_final: 0.8586 (p) outliers start: 17 outliers final: 10 residues processed: 152 average time/residue: 0.1802 time to fit residues: 33.9849 Evaluate side-chains 155 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 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 2 ILE Chi-restraints excluded: chain L residue 30 TYR 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 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: 6.9990 chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 73 optimal weight: 50.0000 chunk 5 optimal weight: 8.9990 chunk 61 optimal weight: 40.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- 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 = 0.3023 r_free = 0.3023 target = 0.077861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.063529 restraints weight = 13466.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.065220 restraints weight = 7622.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.066377 restraints weight = 5153.249| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 5045 Z= 0.313 Angle : 0.703 10.506 6682 Z= 0.386 Chirality : 0.047 0.206 522 Planarity : 0.005 0.057 995 Dihedral : 5.196 20.002 875 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.36 % Favored : 94.52 % Rotamer: Outliers : 7.28 % Allowed : 30.73 % Favored : 61.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.29), residues: 821 helix: 0.82 (1.44), residues: 16 sheet: 1.38 (0.26), residues: 363 loop : -0.07 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP M 47 HIS 0.006 0.004 HIS H 35 PHE 0.026 0.003 PHE N 94 TYR 0.028 0.003 TYR M 112 ARG 0.005 0.001 ARG M 16 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 244) hydrogen bonds : angle 5.61733 ( 708) SS BOND : bond 0.01060 ( 4) SS BOND : angle 2.27478 ( 8) covalent geometry : bond 0.00680 ( 5041) covalent geometry : angle 0.69898 ( 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 173 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.608 Fit side-chains REVERT: H 76 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8282 (tmtt) REVERT: L 16 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8221 (tm-30) REVERT: N 50 ASP cc_start: 0.7796 (m-30) cc_final: 0.7399 (m-30) outliers start: 27 outliers final: 16 residues processed: 156 average time/residue: 0.1941 time to fit residues: 37.4668 Evaluate side-chains 159 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 L residue 6 GLN 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 53 SER Chi-restraints excluded: chain M residue 75 ASP 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 5 THR 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: 6.9990 chunk 68 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 78 optimal weight: 30.0000 chunk 45 optimal weight: 4.9990 chunk 81 optimal weight: 50.0000 chunk 80 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 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 = 0.3059 r_free = 0.3059 target = 0.079489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.064988 restraints weight = 13276.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.066781 restraints weight = 7530.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.067980 restraints weight = 5129.039| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5045 Z= 0.191 Angle : 0.597 7.442 6682 Z= 0.329 Chirality : 0.043 0.178 522 Planarity : 0.005 0.056 995 Dihedral : 4.726 18.122 875 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.14 % Favored : 95.74 % Rotamer: Outliers : 5.66 % Allowed : 31.54 % 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: 0.88 (0.29), residues: 821 helix: 1.03 (1.45), residues: 16 sheet: 1.31 (0.26), residues: 362 loop : -0.01 (0.30), residues: 443 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 0.019 0.003 PHE H 68 TYR 0.027 0.002 TYR M 112 ARG 0.005 0.001 ARG M 16 Details of bonding type rmsd hydrogen bonds : bond 0.03163 ( 244) hydrogen bonds : angle 5.12863 ( 708) SS BOND : bond 0.00762 ( 4) SS BOND : angle 1.80733 ( 8) covalent geometry : bond 0.00413 ( 5041) covalent geometry : angle 0.59391 ( 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 170 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: H 76 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8256 (tmtt) REVERT: L 16 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8303 (tm-30) outliers start: 21 outliers final: 14 residues processed: 157 average time/residue: 0.1956 time to fit residues: 38.0866 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 : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 85 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 2 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 13 optimal weight: 50.0000 chunk 38 optimal weight: 50.0000 chunk 69 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 48 optimal weight: 0.1980 chunk 71 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 35 optimal weight: 50.0000 overall best weight: 5.8390 ------------------------------------------------------------------------------- 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 = 0.3044 r_free = 0.3044 target = 0.078781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.064405 restraints weight = 13359.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.066048 restraints weight = 7607.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.067244 restraints weight = 5203.798| |-----------------------------------------------------------------------------| r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5045 Z= 0.231 Angle : 0.624 7.572 6682 Z= 0.344 Chirality : 0.044 0.187 522 Planarity : 0.005 0.057 995 Dihedral : 4.845 18.495 875 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.99 % Favored : 94.88 % Rotamer: Outliers : 5.93 % Allowed : 31.00 % 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: 0.80 (0.29), residues: 821 helix: 1.02 (1.46), residues: 16 sheet: 1.23 (0.26), residues: 362 loop : -0.05 (0.31), residues: 443 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 0.027 0.003 PHE H 68 TYR 0.018 0.002 TYR L 47 ARG 0.006 0.001 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.03315 ( 244) hydrogen bonds : angle 5.16791 ( 708) SS BOND : bond 0.00925 ( 4) SS BOND : angle 2.06434 ( 8) covalent geometry : bond 0.00501 ( 5041) covalent geometry : angle 0.62056 ( 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 168 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.539 Fit side-chains REVERT: H 76 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8257 (tmtt) REVERT: L 16 GLN cc_start: 0.8755 (tm-30) cc_final: 0.8325 (tm-30) REVERT: N 4 MET cc_start: 0.8413 (mmm) cc_final: 0.8133 (mmm) outliers start: 22 outliers final: 17 residues processed: 155 average time/residue: 0.1795 time to fit residues: 34.6016 Evaluate side-chains 162 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 85 MET 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: 3.9990 chunk 23 optimal weight: 8.9990 chunk 59 optimal weight: 0.5980 chunk 50 optimal weight: 6.9990 chunk 15 optimal weight: 0.0000 chunk 62 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 overall best weight: 3.5190 ------------------------------------------------------------------------------- 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 = 0.3069 r_free = 0.3069 target = 0.080057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.065628 restraints weight = 13128.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.067318 restraints weight = 7481.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.068532 restraints weight = 5142.697| |-----------------------------------------------------------------------------| r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 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 : 0.004 0.038 5045 Z= 0.162 Angle : 0.584 6.469 6682 Z= 0.318 Chirality : 0.043 0.166 522 Planarity : 0.004 0.056 995 Dihedral : 4.533 17.638 875 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.14 % Favored : 95.62 % Rotamer: Outliers : 5.66 % Allowed : 32.08 % 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: 0.85 (0.30), residues: 821 helix: 1.24 (1.48), residues: 16 sheet: 1.21 (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 0.026 0.002 PHE H 68 TYR 0.015 0.002 TYR M 112 ARG 0.005 0.001 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.02924 ( 244) hydrogen bonds : angle 4.88314 ( 708) SS BOND : bond 0.00743 ( 4) SS BOND : angle 1.89857 ( 8) covalent geometry : bond 0.00354 ( 5041) covalent geometry : angle 0.58034 ( 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 171 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.641 Fit side-chains REVERT: H 76 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8251 (tmtt) REVERT: L 16 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8335 (tm-30) REVERT: N 4 MET cc_start: 0.8439 (mmm) cc_final: 0.8236 (tpp) outliers start: 21 outliers final: 17 residues processed: 158 average time/residue: 0.2015 time to fit residues: 39.4027 Evaluate side-chains 167 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 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 78 LYS Chi-restraints excluded: chain M residue 85 MET Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 78 optimal weight: 40.0000 chunk 68 optimal weight: 9.9990 chunk 56 optimal weight: 40.0000 chunk 38 optimal weight: 0.1980 chunk 52 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 76 optimal weight: 30.0000 chunk 73 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 9 optimal weight: 0.7980 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 = 0.3039 r_free = 0.3039 target = 0.078688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.064279 restraints weight = 13512.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.065992 restraints weight = 7604.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.067197 restraints weight = 5157.853| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2068 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= 0.245 Angle : 0.653 7.915 6682 Z= 0.357 Chirality : 0.045 0.193 522 Planarity : 0.005 0.060 995 Dihedral : 4.881 18.618 875 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.24 % Favored : 94.52 % Rotamer: Outliers : 5.93 % Allowed : 32.08 % Favored : 61.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.73 (0.30), residues: 821 helix: 1.10 (1.47), residues: 16 sheet: 1.19 (0.26), residues: 362 loop : -0.10 (0.31), residues: 443 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 0.033 0.004 PHE H 68 TYR 0.031 0.002 TYR M 112 ARG 0.005 0.001 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.03356 ( 244) hydrogen bonds : angle 5.13542 ( 708) SS BOND : bond 0.00927 ( 4) SS BOND : angle 2.07908 ( 8) covalent geometry : bond 0.00538 ( 5041) covalent geometry : angle 0.64899 ( 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 171 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.587 Fit side-chains REVERT: H 76 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8279 (tmtt) REVERT: L 16 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8334 (tm-30) REVERT: N 4 MET cc_start: 0.8465 (mmm) cc_final: 0.8247 (mmm) outliers start: 22 outliers final: 20 residues processed: 158 average time/residue: 0.1802 time to fit residues: 35.3880 Evaluate side-chains 165 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 116 VAL Chi-restraints excluded: chain N residue 5 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 78 optimal weight: 40.0000 chunk 51 optimal weight: 8.9990 chunk 55 optimal weight: 40.0000 chunk 58 optimal weight: 20.0000 chunk 20 optimal weight: 50.0000 chunk 23 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 50.0000 chunk 70 optimal weight: 8.9990 overall best weight: 5.9992 ------------------------------------------------------------------------------- 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 = 0.3038 r_free = 0.3038 target = 0.078567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.064354 restraints weight = 13180.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.066040 restraints weight = 7446.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.067217 restraints weight = 5097.892| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2134 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= 0.239 Angle : 0.662 7.821 6682 Z= 0.362 Chirality : 0.045 0.192 522 Planarity : 0.005 0.060 995 Dihedral : 4.894 18.399 875 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.38 % Favored : 95.37 % Rotamer: Outliers : 6.47 % Allowed : 32.08 % 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: 0.71 (0.30), residues: 821 helix: 1.13 (1.48), residues: 16 sheet: 1.14 (0.26), residues: 369 loop : -0.10 (0.31), residues: 436 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 0.041 0.004 PHE N 49 TYR 0.039 0.002 TYR M 112 ARG 0.007 0.001 ARG M 19 Details of bonding type rmsd hydrogen bonds : bond 0.03329 ( 244) hydrogen bonds : angle 5.11201 ( 708) SS BOND : bond 0.00935 ( 4) SS BOND : angle 2.06832 ( 8) covalent geometry : bond 0.00524 ( 5041) covalent geometry : angle 0.65899 ( 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: 24 poor density : 146 time to evaluate : 0.588 Fit side-chains REVERT: H 76 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8304 (tmtt) REVERT: L 16 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8308 (tm-30) REVERT: L 101 THR cc_start: 0.8899 (m) cc_final: 0.8564 (p) REVERT: N 4 MET cc_start: 0.8475 (mmm) cc_final: 0.8231 (mmm) outliers start: 24 outliers final: 21 residues processed: 156 average time/residue: 0.1881 time to fit residues: 36.4018 Evaluate side-chains 169 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 78 LYS Chi-restraints excluded: chain M residue 85 MET Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 48 ILE 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: 6.9990 chunk 56 optimal weight: 10.0000 chunk 53 optimal weight: 30.0000 chunk 16 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 78 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- 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 = 0.3056 r_free = 0.3056 target = 0.079498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.065008 restraints weight = 13239.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.066689 restraints weight = 7527.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.067892 restraints weight = 5141.430| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 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 : 0.004 0.037 5045 Z= 0.193 Angle : 0.630 7.066 6682 Z= 0.342 Chirality : 0.044 0.178 522 Planarity : 0.005 0.058 995 Dihedral : 4.689 18.134 875 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.12 % Favored : 94.64 % Rotamer: Outliers : 5.93 % Allowed : 32.08 % Favored : 61.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.74 (0.30), residues: 821 helix: 1.25 (1.49), residues: 16 sheet: 1.12 (0.26), residues: 372 loop : -0.05 (0.31), 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 0.038 0.003 PHE N 49 TYR 0.034 0.002 TYR M 112 ARG 0.007 0.001 ARG M 19 Details of bonding type rmsd hydrogen bonds : bond 0.03050 ( 244) hydrogen bonds : angle 4.91853 ( 708) SS BOND : bond 0.00828 ( 4) SS BOND : angle 1.92736 ( 8) covalent geometry : bond 0.00427 ( 5041) covalent geometry : angle 0.62638 ( 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 170 residues out of total 709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.559 Fit side-chains REVERT: H 76 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8255 (tmtt) REVERT: L 16 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8302 (tm-30) REVERT: L 101 THR cc_start: 0.8884 (m) cc_final: 0.8559 (p) REVERT: N 4 MET cc_start: 0.8470 (mmm) cc_final: 0.8220 (mmm) outliers start: 22 outliers final: 20 residues processed: 155 average time/residue: 0.1894 time to fit residues: 36.5117 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 : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 69 THR 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 78 LYS Chi-restraints excluded: chain M residue 85 MET Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 48 ILE 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: 3.9990 chunk 37 optimal weight: 50.0000 chunk 80 optimal weight: 40.0000 chunk 36 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 13 optimal weight: 50.0000 chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 30.0000 chunk 28 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.078857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.064691 restraints weight = 13390.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.066289 restraints weight = 7770.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.067448 restraints weight = 5383.822| |-----------------------------------------------------------------------------| r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5045 Z= 0.221 Angle : 0.647 7.328 6682 Z= 0.353 Chirality : 0.045 0.187 522 Planarity : 0.005 0.060 995 Dihedral : 4.796 18.394 875 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.87 % Favored : 95.01 % Rotamer: Outliers : 5.93 % Allowed : 32.08 % Favored : 61.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.70 (0.30), residues: 821 helix: 1.21 (1.49), residues: 16 sheet: 1.11 (0.26), residues: 369 loop : -0.10 (0.31), residues: 436 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 0.033 0.003 PHE N 49 TYR 0.037 0.002 TYR M 112 ARG 0.008 0.001 ARG M 19 Details of bonding type rmsd hydrogen bonds : bond 0.03210 ( 244) hydrogen bonds : angle 4.99821 ( 708) SS BOND : bond 0.00892 ( 4) SS BOND : angle 2.03608 ( 8) covalent geometry : bond 0.00487 ( 5041) covalent geometry : angle 0.64396 ( 6674) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1903.44 seconds wall clock time: 34 minutes 30.00 seconds (2070.00 seconds total)