Starting phenix.real_space_refine on Tue Mar 3 17:31:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l9o_62911/03_2026/9l9o_62911.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l9o_62911/03_2026/9l9o_62911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l9o_62911/03_2026/9l9o_62911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l9o_62911/03_2026/9l9o_62911.map" model { file = "/net/cci-nas-00/data/ceres_data/9l9o_62911/03_2026/9l9o_62911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l9o_62911/03_2026/9l9o_62911.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.068 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 38 5.16 5 C 4707 2.51 5 N 1223 2.21 5 O 1382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7350 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 921 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1632 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201} Chain: "B" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1642 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Chain breaks: 1 Chain: "A" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3155 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 14, 'TRANS': 381} Time building chain proxies: 1.45, per 1000 atoms: 0.20 Number of scatterers: 7350 At special positions: 0 Unit cell: (64.6941, 102.149, 145.562, 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 38 16.00 O 1382 8.00 N 1223 7.00 C 4707 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.04 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 210 " distance=2.04 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 178 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 282.7 milliseconds 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 37.3% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'D' and resid 87 through 91 removed outlier: 4.161A pdb=" N THR D 91 " --> pdb=" O PRO D 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 130 removed outlier: 3.651A pdb=" N LEU C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS C 128 " --> pdb=" O ASP C 124 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER C 129 " --> pdb=" O SER C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 189 Processing helix chain 'B' and resid 31 through 34 Processing helix chain 'B' and resid 107 through 112 removed outlier: 3.642A pdb=" N TRP B 111 " --> pdb=" O GLY B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'A' and resid 25 through 54 removed outlier: 3.507A pdb=" N ILE A 44 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 53 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N THR A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 removed outlier: 4.337A pdb=" N VAL A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 92 removed outlier: 3.766A pdb=" N LEU A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 131 removed outlier: 3.664A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.604A pdb=" N ILE A 139 " --> pdb=" O GLN A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 161 removed outlier: 4.106A pdb=" N VAL A 150 " --> pdb=" O CYS A 146 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 151 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 197 Processing helix chain 'A' and resid 197 through 219 Processing helix chain 'A' and resid 1002 through 1021 removed outlier: 3.628A pdb=" N LEU A1013 " --> pdb=" O ASN A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1045 removed outlier: 3.966A pdb=" N VAL A1029 " --> pdb=" O ASN A1025 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS A1045 " --> pdb=" O LEU A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1083 removed outlier: 3.645A pdb=" N PHE A1068 " --> pdb=" O PHE A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1095 Processing helix chain 'A' and resid 1096 through 1105 removed outlier: 4.009A pdb=" N THR A1100 " --> pdb=" O GLN A1096 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A1105 " --> pdb=" O ARG A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1116 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 232 through 256 removed outlier: 3.761A pdb=" N PHE A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET A 239 " --> pdb=" O ASN A 235 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 274 through 286 removed outlier: 4.271A pdb=" N ALA A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 297 removed outlier: 4.029A pdb=" N ILE A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYR A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 310 removed outlier: 3.658A pdb=" N ARG A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TRP A 306 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR A 307 " --> pdb=" O ARG A 303 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.630A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.084A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALA D 33 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.084A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE D 98 " --> pdb=" O TYR D 110 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TYR D 110 " --> pdb=" O ILE D 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 14 removed outlier: 6.422A pdb=" N VAL C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TYR C 50 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 14 removed outlier: 3.757A pdb=" N THR C 99 " --> pdb=" O GLN C 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 116 through 120 removed outlier: 5.824A pdb=" N TYR C 175 " --> pdb=" O ASN C 140 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 147 through 152 Processing sheet with id=AA9, first strand: chain 'B' and resid 6 through 10 Processing sheet with id=AB1, first strand: chain 'B' and resid 13 through 15 removed outlier: 6.674A pdb=" N LEU B 37 " --> pdb=" O TYR B 53 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR B 53 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TRP B 39 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR B 53 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER B 62 " --> pdb=" O TYR B 53 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 134 through 137 removed outlier: 5.922A pdb=" N TYR B 190 " --> pdb=" O ASP B 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 134 through 137 removed outlier: 5.922A pdb=" N TYR B 190 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 191 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 165 through 168 removed outlier: 4.084A pdb=" N TYR B 208 " --> pdb=" O VAL B 225 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1092 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: 1.17 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.53: 6945 1.53 - 1.85: 575 1.85 - 2.16: 0 2.16 - 2.48: 0 2.48 - 2.80: 2 Bond restraints: 7522 Sorted by residual: bond pdb=" C LEU A1116 " pdb=" N ASP A 227 " ideal model delta sigma weight residual 1.335 2.796 -1.461 1.38e-02 5.25e+03 1.12e+04 bond pdb=" C ARG A 219 " pdb=" N ARG A1001 " ideal model delta sigma weight residual 1.335 2.781 -1.446 1.38e-02 5.25e+03 1.10e+04 bond pdb=" CA TRP A 94 " pdb=" CB TRP A 94 " ideal model delta sigma weight residual 1.525 1.413 0.111 1.47e-02 4.63e+03 5.74e+01 bond pdb=" CZ TYR A 171 " pdb=" OH TYR A 171 " ideal model delta sigma weight residual 1.376 1.247 0.129 2.10e-02 2.27e+03 3.80e+01 bond pdb=" CD2 TYR A 171 " pdb=" CE2 TYR A 171 " ideal model delta sigma weight residual 1.382 1.240 0.142 3.00e-02 1.11e+03 2.23e+01 ... (remaining 7517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.02: 10196 5.02 - 10.04: 28 10.04 - 15.06: 5 15.06 - 20.08: 4 20.08 - 25.10: 3 Bond angle restraints: 10236 Sorted by residual: angle pdb=" N GLU A 170 " pdb=" CA GLU A 170 " pdb=" C GLU A 170 " ideal model delta sigma weight residual 107.73 127.92 -20.19 1.34e+00 5.57e-01 2.27e+02 angle pdb=" C LEU A1116 " pdb=" N ASP A 227 " pdb=" CA ASP A 227 " ideal model delta sigma weight residual 120.72 95.62 25.10 1.67e+00 3.59e-01 2.26e+02 angle pdb=" CA LEU A1116 " pdb=" C LEU A1116 " pdb=" N ASP A 227 " ideal model delta sigma weight residual 117.22 101.08 16.14 1.17e+00 7.31e-01 1.90e+02 angle pdb=" CA ARG A 219 " pdb=" C ARG A 219 " pdb=" N ARG A1001 " ideal model delta sigma weight residual 117.56 101.92 15.64 1.22e+00 6.72e-01 1.64e+02 angle pdb=" O LEU A1116 " pdb=" C LEU A1116 " pdb=" N ASP A 227 " ideal model delta sigma weight residual 122.12 135.63 -13.51 1.06e+00 8.90e-01 1.62e+02 ... (remaining 10231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 4090 17.14 - 34.27: 303 34.27 - 51.40: 57 51.40 - 68.54: 8 68.54 - 85.67: 11 Dihedral angle restraints: 4469 sinusoidal: 1704 harmonic: 2765 Sorted by residual: dihedral pdb=" CB CYS A 101 " pdb=" SG CYS A 101 " pdb=" SG CYS A 178 " pdb=" CB CYS A 178 " ideal model delta sinusoidal sigma weight residual -86.00 -135.79 49.79 1 1.00e+01 1.00e-02 3.40e+01 dihedral pdb=" CA ARG A 219 " pdb=" C ARG A 219 " pdb=" N ARG A1001 " pdb=" CA ARG A1001 " ideal model delta harmonic sigma weight residual -180.00 -159.81 -20.19 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA ILE A 169 " pdb=" C ILE A 169 " pdb=" N GLU A 170 " pdb=" CA GLU A 170 " ideal model delta harmonic sigma weight residual -180.00 -161.67 -18.33 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 4466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 939 0.055 - 0.110: 188 0.110 - 0.165: 32 0.165 - 0.220: 5 0.220 - 0.275: 1 Chirality restraints: 1165 Sorted by residual: chirality pdb=" CA LEU A 161 " pdb=" N LEU A 161 " pdb=" C LEU A 161 " pdb=" CB LEU A 161 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA GLU A 170 " pdb=" N GLU A 170 " pdb=" C GLU A 170 " pdb=" CB GLU A 170 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA TYR A 171 " pdb=" N TYR A 171 " pdb=" C TYR A 171 " pdb=" CB TYR A 171 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1162 not shown) Planarity restraints: 1291 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 219 " -0.053 2.00e-02 2.50e+03 1.01e-01 1.02e+02 pdb=" C ARG A 219 " 0.171 2.00e-02 2.50e+03 pdb=" O ARG A 219 " -0.087 2.00e-02 2.50e+03 pdb=" N ARG A1001 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 171 " 0.085 2.00e-02 2.50e+03 6.11e-02 7.46e+01 pdb=" CG TYR A 171 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR A 171 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 171 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR A 171 " -0.047 2.00e-02 2.50e+03 pdb=" CE2 TYR A 171 " -0.065 2.00e-02 2.50e+03 pdb=" CZ TYR A 171 " -0.029 2.00e-02 2.50e+03 pdb=" OH TYR A 171 " 0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 94 " -0.039 2.00e-02 2.50e+03 2.69e-02 1.81e+01 pdb=" CG TRP A 94 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP A 94 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 94 " -0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 94 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP A 94 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP A 94 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 94 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 94 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 94 " 0.001 2.00e-02 2.50e+03 ... (remaining 1288 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 230 2.72 - 3.26: 6779 3.26 - 3.81: 11228 3.81 - 4.35: 13448 4.35 - 4.90: 24018 Nonbonded interactions: 55703 Sorted by model distance: nonbonded pdb=" OD1 ASN A 184 " pdb=" ND2 ASN A 185 " model vdw 2.175 3.120 nonbonded pdb=" OG SER C 64 " pdb=" OG1 THR C 75 " model vdw 2.234 3.040 nonbonded pdb=" OG SER A1055 " pdb=" OD1 ASP A1057 " model vdw 2.244 3.040 nonbonded pdb=" OG SER C 66 " pdb=" OG1 THR C 73 " model vdw 2.258 3.040 nonbonded pdb=" O ILE D 29 " pdb=" NH2 ARG D 72 " model vdw 2.330 3.120 ... (remaining 55698 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.180 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.680 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 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 : 0.024 1.461 7528 Z= 1.734 Angle : 0.882 25.095 10248 Z= 0.526 Chirality : 0.046 0.275 1165 Planarity : 0.007 0.101 1291 Dihedral : 13.176 85.675 2675 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.28), residues: 932 helix: 1.19 (0.30), residues: 291 sheet: 1.53 (0.33), residues: 252 loop : -1.20 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A1001 TYR 0.115 0.002 TYR A 171 PHE 0.016 0.001 PHE A 236 TRP 0.073 0.002 TRP A 94 HIS 0.002 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.02422 ( 7522) covalent geometry : angle 0.88147 (10236) SS BOND : bond 0.00632 ( 6) SS BOND : angle 1.17975 ( 12) hydrogen bonds : bond 0.10889 ( 370) hydrogen bonds : angle 5.29067 ( 1092) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1864 Ramachandran restraints generated. 932 Oldfield, 0 Emsley, 932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 19 ARG cc_start: 0.7554 (ttp80) cc_final: 0.7333 (ttm170) REVERT: C 46 LYS cc_start: 0.8062 (mtmm) cc_final: 0.7483 (mttm) REVERT: C 71 ASP cc_start: 0.7972 (m-30) cc_final: 0.7677 (m-30) REVERT: C 102 GLN cc_start: 0.7050 (mm-40) cc_final: 0.6785 (mp10) REVERT: C 208 THR cc_start: 0.8569 (t) cc_final: 0.8341 (m) REVERT: B 24 SER cc_start: 0.8744 (m) cc_final: 0.8280 (p) REVERT: B 46 LYS cc_start: 0.7681 (mmtt) cc_final: 0.7469 (mppt) REVERT: A 182 TYR cc_start: 0.4942 (m-80) cc_final: 0.4165 (p90) REVERT: A 1061 MET cc_start: 0.5391 (mmm) cc_final: 0.5076 (mmm) REVERT: A 1083 ASN cc_start: 0.7189 (t0) cc_final: 0.6981 (t0) outliers start: 0 outliers final: 1 residues processed: 152 average time/residue: 0.5349 time to fit residues: 85.7876 Evaluate side-chains 97 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 0.2980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN A 185 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.230176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.174067 restraints weight = 7420.010| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 1.99 r_work: 0.3405 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7528 Z= 0.144 Angle : 0.591 7.380 10248 Z= 0.308 Chirality : 0.043 0.250 1165 Planarity : 0.005 0.052 1291 Dihedral : 4.592 33.492 1028 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.09 % Allowed : 9.41 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.28), residues: 936 helix: 1.69 (0.30), residues: 303 sheet: 1.47 (0.33), residues: 248 loop : -1.11 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 210 TYR 0.024 0.001 TYR A 171 PHE 0.020 0.002 PHE C 211 TRP 0.010 0.001 TRP B 117 HIS 0.004 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7522) covalent geometry : angle 0.59032 (10236) SS BOND : bond 0.00618 ( 6) SS BOND : angle 1.00745 ( 12) hydrogen bonds : bond 0.04350 ( 370) hydrogen bonds : angle 4.32669 ( 1092) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.182 Fit side-chains REVERT: D 19 ARG cc_start: 0.7485 (ttp80) cc_final: 0.7037 (ttm170) REVERT: D 109 ASP cc_start: 0.7527 (m-30) cc_final: 0.7312 (m-30) REVERT: C 46 LYS cc_start: 0.8228 (mtmm) cc_final: 0.7988 (mttm) REVERT: C 71 ASP cc_start: 0.8305 (m-30) cc_final: 0.8079 (m-30) REVERT: C 208 THR cc_start: 0.8566 (t) cc_final: 0.8158 (m) REVERT: B 46 LYS cc_start: 0.8239 (mmtt) cc_final: 0.8000 (mppt) REVERT: A 48 MET cc_start: 0.5784 (ptp) cc_final: 0.5249 (ppp) REVERT: A 75 MET cc_start: 0.6956 (mmm) cc_final: 0.6645 (mmp) REVERT: A 85 MET cc_start: 0.7590 (tmm) cc_final: 0.6586 (tmm) REVERT: A 1001 ARG cc_start: 0.6887 (mmm-85) cc_final: 0.6444 (ptp-110) REVERT: A 1007 GLU cc_start: 0.7526 (mp0) cc_final: 0.7041 (tm-30) REVERT: A 280 TYR cc_start: 0.5189 (OUTLIER) cc_final: 0.3646 (t80) outliers start: 25 outliers final: 14 residues processed: 108 average time/residue: 0.5470 time to fit residues: 62.3184 Evaluate side-chains 103 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 280 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 37 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 57 optimal weight: 0.0670 chunk 61 optimal weight: 0.0970 chunk 53 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 overall best weight: 0.4716 ------------------------------------------------------------------------------- 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 = 0.4498 r_free = 0.4498 target = 0.231633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.189817 restraints weight = 7269.868| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 1.80 r_work: 0.3533 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7528 Z= 0.120 Angle : 0.564 6.733 10248 Z= 0.290 Chirality : 0.042 0.192 1165 Planarity : 0.004 0.046 1291 Dihedral : 4.439 29.514 1026 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.09 % Allowed : 12.13 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.28), residues: 936 helix: 2.00 (0.30), residues: 304 sheet: 1.24 (0.32), residues: 261 loop : -0.87 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 302 TYR 0.013 0.001 TYR A 171 PHE 0.017 0.001 PHE A 236 TRP 0.009 0.001 TRP B 117 HIS 0.002 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7522) covalent geometry : angle 0.56378 (10236) SS BOND : bond 0.00538 ( 6) SS BOND : angle 0.85160 ( 12) hydrogen bonds : bond 0.03910 ( 370) hydrogen bonds : angle 4.17392 ( 1092) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.267 Fit side-chains REVERT: D 19 ARG cc_start: 0.7785 (ttp80) cc_final: 0.7286 (ttm170) REVERT: D 109 ASP cc_start: 0.7737 (m-30) cc_final: 0.7365 (m-30) REVERT: C 208 THR cc_start: 0.8512 (t) cc_final: 0.8116 (m) REVERT: B 46 LYS cc_start: 0.8306 (mmtt) cc_final: 0.7995 (mppt) REVERT: A 48 MET cc_start: 0.5689 (ptp) cc_final: 0.5158 (ppp) REVERT: A 103 MET cc_start: 0.6102 (tpp) cc_final: 0.5876 (mmt) REVERT: A 1001 ARG cc_start: 0.7102 (mmm-85) cc_final: 0.6569 (ptp-110) REVERT: A 1007 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7175 (tm-30) REVERT: A 1061 MET cc_start: 0.5254 (mmm) cc_final: 0.4638 (mmm) REVERT: A 228 ASN cc_start: 0.6986 (m-40) cc_final: 0.6349 (t0) REVERT: A 280 TYR cc_start: 0.4915 (OUTLIER) cc_final: 0.3282 (t80) REVERT: A 302 ARG cc_start: 0.6212 (ttp-110) cc_final: 0.5934 (ptm-80) outliers start: 25 outliers final: 14 residues processed: 103 average time/residue: 0.5794 time to fit residues: 63.0379 Evaluate side-chains 101 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 1007 GLU Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 280 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 62 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.224160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.177721 restraints weight = 7468.153| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.23 r_work: 0.3319 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 7528 Z= 0.284 Angle : 0.768 12.598 10248 Z= 0.392 Chirality : 0.050 0.209 1165 Planarity : 0.006 0.068 1291 Dihedral : 5.108 28.464 1026 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.59 % Favored : 95.30 % Rotamer: Outliers : 4.83 % Allowed : 12.87 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.28), residues: 936 helix: 1.64 (0.29), residues: 306 sheet: 1.14 (0.33), residues: 254 loop : -1.20 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1037 TYR 0.016 0.002 TYR C 87 PHE 0.017 0.002 PHE A 236 TRP 0.017 0.002 TRP B 102 HIS 0.006 0.002 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00705 ( 7522) covalent geometry : angle 0.76730 (10236) SS BOND : bond 0.00792 ( 6) SS BOND : angle 1.29678 ( 12) hydrogen bonds : bond 0.05913 ( 370) hydrogen bonds : angle 4.69796 ( 1092) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 96 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: C 171 LYS cc_start: 0.7682 (mmtm) cc_final: 0.7454 (mptt) REVERT: A 103 MET cc_start: 0.6343 (tpp) cc_final: 0.6053 (mmt) REVERT: A 126 ARG cc_start: 0.6556 (tpp-160) cc_final: 0.6071 (tpp-160) REVERT: A 1001 ARG cc_start: 0.7204 (mmm-85) cc_final: 0.6812 (ptp-110) REVERT: A 1011 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7281 (pt0) REVERT: A 1061 MET cc_start: 0.5311 (mmm) cc_final: 0.4626 (mmm) REVERT: A 228 ASN cc_start: 0.7338 (m-40) cc_final: 0.6607 (t0) REVERT: A 280 TYR cc_start: 0.5651 (OUTLIER) cc_final: 0.3833 (t80) outliers start: 39 outliers final: 23 residues processed: 118 average time/residue: 0.5440 time to fit residues: 67.8119 Evaluate side-chains 109 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 53 TYR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 287 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 41 optimal weight: 0.7980 chunk 70 optimal weight: 0.0770 chunk 82 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 1 optimal weight: 0.2980 overall best weight: 0.5140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.227758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.188061 restraints weight = 7366.350| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 1.84 r_work: 0.3483 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7528 Z= 0.125 Angle : 0.573 8.589 10248 Z= 0.294 Chirality : 0.042 0.175 1165 Planarity : 0.004 0.040 1291 Dihedral : 4.505 27.763 1026 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.59 % Allowed : 16.71 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.28), residues: 936 helix: 1.96 (0.30), residues: 306 sheet: 1.14 (0.33), residues: 258 loop : -0.98 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1037 TYR 0.010 0.001 TYR A 171 PHE 0.022 0.001 PHE A 206 TRP 0.011 0.001 TRP B 117 HIS 0.002 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 7522) covalent geometry : angle 0.57292 (10236) SS BOND : bond 0.00548 ( 6) SS BOND : angle 0.80154 ( 12) hydrogen bonds : bond 0.03970 ( 370) hydrogen bonds : angle 4.23690 ( 1092) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.266 Fit side-chains REVERT: D 19 ARG cc_start: 0.7490 (ttp80) cc_final: 0.7117 (ttm170) REVERT: D 109 ASP cc_start: 0.7401 (m-30) cc_final: 0.7119 (m-30) REVERT: A 103 MET cc_start: 0.6312 (tpp) cc_final: 0.5976 (mmt) REVERT: A 126 ARG cc_start: 0.6575 (tpp-160) cc_final: 0.6118 (tpp-160) REVERT: A 1011 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7169 (pt0) REVERT: A 1061 MET cc_start: 0.5273 (mmm) cc_final: 0.4707 (mmm) REVERT: A 228 ASN cc_start: 0.7347 (m-40) cc_final: 0.6644 (t0) REVERT: A 280 TYR cc_start: 0.5778 (OUTLIER) cc_final: 0.3950 (t80) outliers start: 29 outliers final: 17 residues processed: 111 average time/residue: 0.4974 time to fit residues: 58.7344 Evaluate side-chains 107 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 280 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 70 optimal weight: 0.0070 chunk 75 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 65 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** 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 = 0.4418 r_free = 0.4418 target = 0.223420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.160785 restraints weight = 7330.945| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.44 r_work: 0.3279 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7528 Z= 0.153 Angle : 0.598 7.350 10248 Z= 0.308 Chirality : 0.043 0.164 1165 Planarity : 0.004 0.037 1291 Dihedral : 4.484 27.070 1026 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.46 % Allowed : 16.83 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.28), residues: 936 helix: 2.00 (0.30), residues: 306 sheet: 1.09 (0.33), residues: 258 loop : -1.03 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1037 TYR 0.010 0.001 TYR B 98 PHE 0.016 0.002 PHE A 236 TRP 0.012 0.001 TRP B 117 HIS 0.003 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 7522) covalent geometry : angle 0.59783 (10236) SS BOND : bond 0.00634 ( 6) SS BOND : angle 0.93284 ( 12) hydrogen bonds : bond 0.04327 ( 370) hydrogen bonds : angle 4.26772 ( 1092) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 87 time to evaluate : 0.219 Fit side-chains REVERT: D 109 ASP cc_start: 0.7417 (m-30) cc_final: 0.6954 (m-30) REVERT: C 171 LYS cc_start: 0.7531 (mptt) cc_final: 0.6913 (mtmm) REVERT: B 22 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.6855 (mtm180) REVERT: A 126 ARG cc_start: 0.5762 (tpp-160) cc_final: 0.5367 (tpp-160) REVERT: A 171 TYR cc_start: 0.6835 (OUTLIER) cc_final: 0.6446 (m-80) REVERT: A 1011 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7123 (pt0) REVERT: A 1061 MET cc_start: 0.4826 (mmm) cc_final: 0.4367 (mmm) REVERT: A 228 ASN cc_start: 0.7078 (m-40) cc_final: 0.6313 (t0) REVERT: A 280 TYR cc_start: 0.4571 (OUTLIER) cc_final: 0.3094 (t80) outliers start: 36 outliers final: 21 residues processed: 109 average time/residue: 0.4942 time to fit residues: 57.0850 Evaluate side-chains 111 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 53 TYR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 280 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 77 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 185 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.221387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.171360 restraints weight = 7344.975| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.14 r_work: 0.3332 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7528 Z= 0.172 Angle : 0.625 7.992 10248 Z= 0.319 Chirality : 0.044 0.170 1165 Planarity : 0.004 0.039 1291 Dihedral : 4.561 26.742 1026 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 5.07 % Allowed : 16.21 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.28), residues: 936 helix: 1.90 (0.29), residues: 309 sheet: 1.01 (0.34), residues: 258 loop : -1.11 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1037 TYR 0.011 0.001 TYR B 98 PHE 0.016 0.002 PHE A 236 TRP 0.013 0.001 TRP B 117 HIS 0.003 0.001 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 7522) covalent geometry : angle 0.62478 (10236) SS BOND : bond 0.00668 ( 6) SS BOND : angle 0.96689 ( 12) hydrogen bonds : bond 0.04564 ( 370) hydrogen bonds : angle 4.35571 ( 1092) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 86 time to evaluate : 0.282 Fit side-chains REVERT: D 109 ASP cc_start: 0.7441 (m-30) cc_final: 0.7083 (m-30) REVERT: C 171 LYS cc_start: 0.7700 (mptt) cc_final: 0.7008 (mtmm) REVERT: B 22 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.6930 (mtm180) REVERT: A 126 ARG cc_start: 0.6656 (tpp-160) cc_final: 0.6180 (tpp-160) REVERT: A 1011 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7399 (pt0) REVERT: A 1061 MET cc_start: 0.5247 (mmm) cc_final: 0.4904 (mmm) REVERT: A 228 ASN cc_start: 0.7303 (m-40) cc_final: 0.6638 (t0) outliers start: 41 outliers final: 26 residues processed: 113 average time/residue: 0.5258 time to fit residues: 62.9441 Evaluate side-chains 111 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 53 TYR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 230 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.8980 chunk 91 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4431 r_free = 0.4431 target = 0.225178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.177861 restraints weight = 7505.551| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.14 r_work: 0.3374 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7528 Z= 0.159 Angle : 0.608 7.262 10248 Z= 0.312 Chirality : 0.043 0.179 1165 Planarity : 0.005 0.069 1291 Dihedral : 4.520 29.788 1026 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.96 % Allowed : 17.70 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.29), residues: 936 helix: 1.92 (0.30), residues: 307 sheet: 1.03 (0.34), residues: 258 loop : -1.11 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1111 TYR 0.021 0.001 TYR A 129 PHE 0.016 0.002 PHE A 236 TRP 0.013 0.001 TRP B 117 HIS 0.003 0.001 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 7522) covalent geometry : angle 0.60710 (10236) SS BOND : bond 0.00647 ( 6) SS BOND : angle 0.91020 ( 12) hydrogen bonds : bond 0.04394 ( 370) hydrogen bonds : angle 4.34185 ( 1092) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 88 time to evaluate : 0.269 Fit side-chains REVERT: D 109 ASP cc_start: 0.7371 (m-30) cc_final: 0.6995 (m-30) REVERT: C 171 LYS cc_start: 0.7650 (mptt) cc_final: 0.7051 (mtmm) REVERT: B 16 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8218 (mt0) REVERT: B 22 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.6824 (mtm180) REVERT: A 85 MET cc_start: 0.7344 (ttm) cc_final: 0.6976 (mtp) REVERT: A 126 ARG cc_start: 0.6536 (tpp-160) cc_final: 0.6043 (tpp-160) REVERT: A 1011 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7237 (pt0) REVERT: A 228 ASN cc_start: 0.7310 (m-40) cc_final: 0.6622 (t0) REVERT: A 280 TYR cc_start: 0.5668 (OUTLIER) cc_final: 0.3955 (t80) outliers start: 32 outliers final: 26 residues processed: 108 average time/residue: 0.5432 time to fit residues: 62.1767 Evaluate side-chains 113 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 83 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 53 TYR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 280 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 50 optimal weight: 0.0970 chunk 18 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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 = 0.4431 r_free = 0.4431 target = 0.225329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.172954 restraints weight = 7411.899| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 1.96 r_work: 0.3367 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7528 Z= 0.146 Angle : 0.607 8.347 10248 Z= 0.308 Chirality : 0.043 0.168 1165 Planarity : 0.004 0.038 1291 Dihedral : 4.464 28.405 1026 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.46 % Allowed : 17.45 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.29), residues: 936 helix: 1.89 (0.30), residues: 307 sheet: 1.06 (0.33), residues: 265 loop : -1.07 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1111 TYR 0.015 0.001 TYR A 165 PHE 0.016 0.001 PHE A 236 TRP 0.012 0.001 TRP B 117 HIS 0.002 0.001 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 7522) covalent geometry : angle 0.60708 (10236) SS BOND : bond 0.00602 ( 6) SS BOND : angle 0.85939 ( 12) hydrogen bonds : bond 0.04195 ( 370) hydrogen bonds : angle 4.31295 ( 1092) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 84 time to evaluate : 0.293 Fit side-chains REVERT: D 109 ASP cc_start: 0.7369 (m-30) cc_final: 0.6969 (m-30) REVERT: C 171 LYS cc_start: 0.7642 (mptt) cc_final: 0.7057 (mtmm) REVERT: B 16 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8219 (mt0) REVERT: B 22 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.6779 (mtm180) REVERT: B 130 THR cc_start: 0.8046 (OUTLIER) cc_final: 0.7827 (t) REVERT: A 126 ARG cc_start: 0.6459 (tpp-160) cc_final: 0.5973 (tpp-160) REVERT: A 1011 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7225 (pt0) REVERT: A 228 ASN cc_start: 0.7293 (m-40) cc_final: 0.6608 (t0) REVERT: A 253 ILE cc_start: 0.5561 (OUTLIER) cc_final: 0.5349 (mm) REVERT: A 280 TYR cc_start: 0.5615 (OUTLIER) cc_final: 0.3910 (t80) REVERT: A 305 TYR cc_start: 0.5241 (p90) cc_final: 0.3283 (m-10) outliers start: 36 outliers final: 25 residues processed: 107 average time/residue: 0.5285 time to fit residues: 59.8998 Evaluate side-chains 113 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 53 TYR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 280 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 82 optimal weight: 0.0170 chunk 25 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 = 0.4440 r_free = 0.4440 target = 0.226424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.170970 restraints weight = 7445.806| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.19 r_work: 0.3329 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7528 Z= 0.128 Angle : 0.583 9.504 10248 Z= 0.298 Chirality : 0.042 0.164 1165 Planarity : 0.004 0.035 1291 Dihedral : 4.344 27.674 1026 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.59 % Allowed : 18.07 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.29), residues: 936 helix: 2.04 (0.30), residues: 307 sheet: 1.11 (0.33), residues: 265 loop : -0.99 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1111 TYR 0.018 0.001 TYR A 165 PHE 0.016 0.001 PHE A 236 TRP 0.011 0.001 TRP B 117 HIS 0.002 0.001 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 7522) covalent geometry : angle 0.58301 (10236) SS BOND : bond 0.00549 ( 6) SS BOND : angle 0.75734 ( 12) hydrogen bonds : bond 0.03779 ( 370) hydrogen bonds : angle 4.18302 ( 1092) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: D 109 ASP cc_start: 0.7404 (m-30) cc_final: 0.6937 (m-30) REVERT: C 171 LYS cc_start: 0.7638 (mptt) cc_final: 0.7004 (mtmm) REVERT: B 16 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8242 (mt0) REVERT: B 22 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.6690 (mtm180) REVERT: B 46 LYS cc_start: 0.8371 (mptp) cc_final: 0.8013 (mppt) REVERT: B 130 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7857 (t) REVERT: A 126 ARG cc_start: 0.6307 (tpp-160) cc_final: 0.5827 (tpp-160) REVERT: A 1011 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7218 (pt0) REVERT: A 228 ASN cc_start: 0.7292 (m-40) cc_final: 0.6566 (t0) REVERT: A 280 TYR cc_start: 0.5462 (OUTLIER) cc_final: 0.3969 (t80) REVERT: A 305 TYR cc_start: 0.5378 (p90) cc_final: 0.3343 (m-10) outliers start: 29 outliers final: 20 residues processed: 106 average time/residue: 0.5412 time to fit residues: 60.7173 Evaluate side-chains 110 residues out of total 809 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 16 GLN Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 53 TYR Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 280 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.0670 chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 overall best weight: 1.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.222775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.175084 restraints weight = 7374.503| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.08 r_work: 0.3358 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7528 Z= 0.193 Angle : 0.668 9.149 10248 Z= 0.338 Chirality : 0.044 0.170 1165 Planarity : 0.005 0.041 1291 Dihedral : 4.623 27.280 1026 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.08 % Allowed : 18.44 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.29), residues: 936 helix: 1.88 (0.30), residues: 314 sheet: 1.04 (0.34), residues: 259 loop : -1.17 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A1111 TYR 0.023 0.002 TYR A 165 PHE 0.016 0.002 PHE A 236 TRP 0.012 0.001 TRP B 117 HIS 0.003 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 7522) covalent geometry : angle 0.66786 (10236) SS BOND : bond 0.00709 ( 6) SS BOND : angle 1.03089 ( 12) hydrogen bonds : bond 0.04706 ( 370) hydrogen bonds : angle 4.44376 ( 1092) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2591.48 seconds wall clock time: 44 minutes 48.04 seconds (2688.04 seconds total)