Starting phenix.real_space_refine on Tue Feb 3 21:34:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e51_47522/02_2026/9e51_47522.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e51_47522/02_2026/9e51_47522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e51_47522/02_2026/9e51_47522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e51_47522/02_2026/9e51_47522.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e51_47522/02_2026/9e51_47522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e51_47522/02_2026/9e51_47522.map" } resolution = 2.9 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= 0.005 sd= 0.022 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 48 5.16 5 C 4498 2.51 5 N 1162 2.21 5 O 1270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6978 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1729 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 5, 'TRP:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2568 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 394 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 2229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2229 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 271} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2, 'water': 2} Link IDs: {None: 3} Time building chain proxies: 1.53, per 1000 atoms: 0.22 Number of scatterers: 6978 At special positions: 0 Unit cell: (72, 101.25, 128.25, 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 48 16.00 O 1270 8.00 N 1162 7.00 C 4498 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 910 " - pdb=" SG CYS A 982 " distance=2.03 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: 0.52 Conformation dependent library (CDL) restraints added in 251.5 milliseconds 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1668 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 8 sheets defined 45.1% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'B' and resid 5 through 32 removed outlier: 3.970A pdb=" N THR B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TYR B 29 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B 32 " --> pdb=" O THR B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 87 through 92 removed outlier: 3.584A pdb=" N SER B 91 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 98 Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.618A pdb=" N GLU B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLN B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 171 through 185 Processing helix chain 'B' and resid 207 through 226 removed outlier: 4.069A pdb=" N ILE B 211 " --> pdb=" O ASN B 207 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG B 213 " --> pdb=" O ARG B 209 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 26 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 128 through 132 removed outlier: 4.010A pdb=" N ASN C 132 " --> pdb=" O ARG C 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 23 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'A' and resid 826 through 830 removed outlier: 3.711A pdb=" N ILE A 829 " --> pdb=" O ASN A 826 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 830 " --> pdb=" O PHE A 827 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 826 through 830' Processing helix chain 'A' and resid 842 through 872 removed outlier: 3.812A pdb=" N PHE A 872 " --> pdb=" O THR A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 876 removed outlier: 3.820A pdb=" N GLN A 876 " --> pdb=" O ARG A 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 873 through 876' Processing helix chain 'A' and resid 879 through 901 removed outlier: 3.631A pdb=" N ILE A 901 " --> pdb=" O PHE A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 940 removed outlier: 3.876A pdb=" N ILE A 912 " --> pdb=" O ILE A 908 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 932 " --> pdb=" O MET A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 972 Proline residue: A 961 - end of helix Processing helix chain 'A' and resid 991 through 1020 Proline residue: A 997 - end of helix Processing helix chain 'A' and resid 1028 through 1048 removed outlier: 3.607A pdb=" N ASN A1032 " --> pdb=" O SER A1028 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS A1045 " --> pdb=" O PHE A1041 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU A1046 " --> pdb=" O ALA A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1052 removed outlier: 3.640A pdb=" N SER A1052 " --> pdb=" O LEU A1049 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1049 through 1052' Processing helix chain 'A' and resid 1053 through 1057 Processing helix chain 'A' and resid 1062 through 1075 removed outlier: 4.185A pdb=" N ALA A1066 " --> pdb=" O THR A1062 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE A1075 " --> pdb=" O ILE A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1085 Processing helix chain 'A' and resid 1088 through 1098 Processing sheet with id=AA1, first strand: chain 'B' and resid 70 through 75 removed outlier: 6.843A pdb=" N LYS B 35 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LEU B 107 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU B 37 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU B 39 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N ASP B 111 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.549A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.636A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.987A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.631A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.852A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.886A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.873A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP C 303 " --> pdb=" O ASP C 298 " (cutoff:3.500A) 342 hydrogen bonds defined for protein. 978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.72 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2226 1.34 - 1.46: 1514 1.46 - 1.58: 3318 1.58 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 7124 Sorted by residual: bond pdb=" N HIS B 221 " pdb=" CA HIS B 221 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.28e-02 6.10e+03 8.09e+00 bond pdb=" N MET C 262 " pdb=" CA MET C 262 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 7.13e+00 bond pdb=" N THR C 263 " pdb=" CA THR C 263 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.23e-02 6.61e+03 7.00e+00 bond pdb=" N ILE C 123 " pdb=" CA ILE C 123 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.26e+00 bond pdb=" N LYS B 193 " pdb=" CA LYS B 193 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.29e-02 6.01e+03 5.93e+00 ... (remaining 7119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 9447 1.28 - 2.56: 156 2.56 - 3.84: 40 3.84 - 5.13: 9 5.13 - 6.41: 3 Bond angle restraints: 9655 Sorted by residual: angle pdb=" CA PHE B 165 " pdb=" CB PHE B 165 " pdb=" CG PHE B 165 " ideal model delta sigma weight residual 113.80 117.59 -3.79 1.00e+00 1.00e+00 1.44e+01 angle pdb=" CA PHE C 278 " pdb=" CB PHE C 278 " pdb=" CG PHE C 278 " ideal model delta sigma weight residual 113.80 117.13 -3.33 1.00e+00 1.00e+00 1.11e+01 angle pdb=" C LYS B 193 " pdb=" CA LYS B 193 " pdb=" CB LYS B 193 " ideal model delta sigma weight residual 109.52 114.37 -4.85 1.58e+00 4.01e-01 9.42e+00 angle pdb=" CA PHE B 165 " pdb=" C PHE B 165 " pdb=" O PHE B 165 " ideal model delta sigma weight residual 121.44 117.91 3.53 1.17e+00 7.31e-01 9.12e+00 angle pdb=" CA MET C 262 " pdb=" C MET C 262 " pdb=" O MET C 262 " ideal model delta sigma weight residual 120.99 118.08 2.91 1.12e+00 7.97e-01 6.75e+00 ... (remaining 9650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.19: 3747 15.19 - 30.38: 396 30.38 - 45.57: 120 45.57 - 60.76: 34 60.76 - 75.95: 10 Dihedral angle restraints: 4307 sinusoidal: 1736 harmonic: 2571 Sorted by residual: dihedral pdb=" CB CYS A 910 " pdb=" SG CYS A 910 " pdb=" SG CYS A 982 " pdb=" CB CYS A 982 " ideal model delta sinusoidal sigma weight residual -86.00 -122.99 36.99 1 1.00e+01 1.00e-02 1.93e+01 dihedral pdb=" N MET C 262 " pdb=" CA MET C 262 " pdb=" CB MET C 262 " pdb=" CG MET C 262 " ideal model delta sinusoidal sigma weight residual -60.00 -119.68 59.68 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET B 53 " pdb=" CG MET B 53 " pdb=" SD MET B 53 " pdb=" CE MET B 53 " ideal model delta sinusoidal sigma weight residual -180.00 -120.33 -59.67 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 688 0.031 - 0.063: 293 0.063 - 0.094: 85 0.094 - 0.125: 42 0.125 - 0.157: 4 Chirality restraints: 1112 Sorted by residual: chirality pdb=" C17 CLR A1202 " pdb=" C13 CLR A1202 " pdb=" C16 CLR A1202 " pdb=" C20 CLR A1202 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" C20 CLR A1202 " pdb=" C17 CLR A1202 " pdb=" C21 CLR A1202 " pdb=" C22 CLR A1202 " both_signs ideal model delta sigma weight residual False 2.59 2.44 0.16 2.00e-01 2.50e+01 6.03e-01 chirality pdb=" CA GLN B 230 " pdb=" N GLN B 230 " pdb=" C GLN B 230 " pdb=" CB GLN B 230 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.84e-01 ... (remaining 1109 not shown) Planarity restraints: 1205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " -0.040 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PRO C 236 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 996 " -0.023 5.00e-02 4.00e+02 3.53e-02 2.00e+00 pdb=" N PRO A 997 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 997 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 997 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 193 " 0.016 5.00e-02 4.00e+02 2.43e-02 9.47e-01 pdb=" N PRO C 194 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO C 194 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 194 " 0.014 5.00e-02 4.00e+02 ... (remaining 1202 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 225 2.72 - 3.26: 6523 3.26 - 3.81: 10691 3.81 - 4.35: 13580 4.35 - 4.90: 24147 Nonbonded interactions: 55166 Sorted by model distance: nonbonded pdb=" OG1 THR A 868 " pdb=" OH TYR A1095 " model vdw 2.172 3.040 nonbonded pdb=" OG SER B 112 " pdb=" O ASN B 144 " model vdw 2.249 3.040 nonbonded pdb=" O ALA B 41 " pdb=" OG SER B 44 " model vdw 2.282 3.040 nonbonded pdb=" OE2 GLU B 126 " pdb=" ND2 ASN B 130 " model vdw 2.286 3.120 nonbonded pdb=" OG SER B 105 " pdb=" OG SER B 138 " model vdw 2.331 3.040 ... (remaining 55161 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: 5.450 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.240 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:5.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 0.003 0.036 7125 Z= 0.150 Angle : 0.478 6.408 9657 Z= 0.270 Chirality : 0.041 0.157 1112 Planarity : 0.003 0.061 1205 Dihedral : 14.745 75.952 2636 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.40 % Allowed : 14.42 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.09 (0.29), residues: 872 helix: 2.18 (0.28), residues: 355 sheet: 1.08 (0.40), residues: 173 loop : -1.09 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 96 TYR 0.007 0.001 TYR C 59 PHE 0.016 0.001 PHE C 278 TRP 0.009 0.001 TRP A 992 HIS 0.003 0.001 HIS B 221 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7124) covalent geometry : angle 0.47826 ( 9655) SS BOND : bond 0.00119 ( 1) SS BOND : angle 0.52523 ( 2) hydrogen bonds : bond 0.17435 ( 342) hydrogen bonds : angle 5.59534 ( 978) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 0.266 Fit side-chains REVERT: B 150 GLU cc_start: 0.6849 (tm-30) cc_final: 0.6554 (tm-30) REVERT: B 204 ASN cc_start: 0.6910 (t0) cc_final: 0.6601 (t0) REVERT: D 21 MET cc_start: 0.6229 (mmm) cc_final: 0.5885 (ttp) REVERT: A 824 MET cc_start: 0.7954 (mtm) cc_final: 0.7727 (mtm) REVERT: A 1062 THR cc_start: 0.7802 (p) cc_final: 0.7385 (m) REVERT: A 1072 PHE cc_start: 0.8495 (m-80) cc_final: 0.8293 (m-10) outliers start: 3 outliers final: 1 residues processed: 114 average time/residue: 0.5650 time to fit residues: 67.2613 Evaluate side-chains 98 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.0870 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN B 198 HIS C 75 GLN C 155 ASN C 259 GLN C 293 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.115898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.092920 restraints weight = 11059.588| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.14 r_work: 0.3162 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7125 Z= 0.173 Angle : 0.547 5.778 9657 Z= 0.291 Chirality : 0.043 0.167 1112 Planarity : 0.004 0.059 1205 Dihedral : 6.172 54.164 1072 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.83 % Allowed : 16.44 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.06 (0.28), residues: 872 helix: 2.06 (0.28), residues: 359 sheet: 1.15 (0.39), residues: 168 loop : -1.05 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 879 TYR 0.009 0.002 TYR B 29 PHE 0.014 0.002 PHE A 920 TRP 0.013 0.002 TRP C 169 HIS 0.003 0.001 HIS A 833 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 7124) covalent geometry : angle 0.54665 ( 9655) SS BOND : bond 0.00031 ( 1) SS BOND : angle 0.68714 ( 2) hydrogen bonds : bond 0.06210 ( 342) hydrogen bonds : angle 4.33658 ( 978) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.262 Fit side-chains REVERT: B 150 GLU cc_start: 0.6844 (tm-30) cc_final: 0.6538 (tm-30) REVERT: D 21 MET cc_start: 0.6205 (mmm) cc_final: 0.5858 (ttp) outliers start: 21 outliers final: 12 residues processed: 106 average time/residue: 0.6067 time to fit residues: 67.4053 Evaluate side-chains 106 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1064 VAL Chi-restraints excluded: chain A residue 1082 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 33 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 47 optimal weight: 0.0470 chunk 46 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.116805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.093948 restraints weight = 11024.522| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.12 r_work: 0.3181 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7125 Z= 0.128 Angle : 0.479 5.571 9657 Z= 0.259 Chirality : 0.041 0.161 1112 Planarity : 0.003 0.057 1205 Dihedral : 5.572 48.265 1070 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.56 % Allowed : 17.25 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.21 (0.28), residues: 872 helix: 2.24 (0.28), residues: 359 sheet: 1.07 (0.39), residues: 172 loop : -0.97 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 188 TYR 0.007 0.001 TYR B 29 PHE 0.012 0.001 PHE C 199 TRP 0.011 0.001 TRP C 211 HIS 0.002 0.001 HIS A1019 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 7124) covalent geometry : angle 0.47915 ( 9655) SS BOND : bond 0.00075 ( 1) SS BOND : angle 0.65701 ( 2) hydrogen bonds : bond 0.05365 ( 342) hydrogen bonds : angle 4.06684 ( 978) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.237 Fit side-chains REVERT: B 150 GLU cc_start: 0.6877 (tm-30) cc_final: 0.6586 (tm-30) REVERT: B 214 ASP cc_start: 0.8349 (m-30) cc_final: 0.8146 (m-30) REVERT: D 21 MET cc_start: 0.6233 (mmm) cc_final: 0.5893 (ttp) REVERT: A 1062 THR cc_start: 0.7703 (p) cc_final: 0.7358 (m) outliers start: 19 outliers final: 9 residues processed: 115 average time/residue: 0.6348 time to fit residues: 76.4516 Evaluate side-chains 102 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1044 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 54 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 31 optimal weight: 0.0370 chunk 83 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 3 optimal weight: 0.0980 chunk 8 optimal weight: 0.6980 overall best weight: 0.4458 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.116937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.094290 restraints weight = 11099.575| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.06 r_work: 0.3206 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7125 Z= 0.116 Angle : 0.466 5.584 9657 Z= 0.252 Chirality : 0.041 0.166 1112 Planarity : 0.003 0.056 1205 Dihedral : 5.356 46.160 1070 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.70 % Allowed : 17.65 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.28 (0.29), residues: 872 helix: 2.31 (0.28), residues: 359 sheet: 1.13 (0.39), residues: 170 loop : -0.95 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 96 TYR 0.008 0.001 TYR B 29 PHE 0.013 0.001 PHE C 199 TRP 0.010 0.001 TRP C 211 HIS 0.002 0.001 HIS A1019 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 7124) covalent geometry : angle 0.46570 ( 9655) SS BOND : bond 0.00076 ( 1) SS BOND : angle 0.56722 ( 2) hydrogen bonds : bond 0.04995 ( 342) hydrogen bonds : angle 3.95146 ( 978) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.169 Fit side-chains REVERT: B 126 GLU cc_start: 0.6922 (tp30) cc_final: 0.6066 (tp30) REVERT: B 150 GLU cc_start: 0.6856 (tm-30) cc_final: 0.6567 (tm-30) REVERT: D 21 MET cc_start: 0.6187 (mmm) cc_final: 0.5866 (ttp) REVERT: A 1062 THR cc_start: 0.7653 (p) cc_final: 0.7320 (m) outliers start: 20 outliers final: 14 residues processed: 109 average time/residue: 0.5980 time to fit residues: 68.4836 Evaluate side-chains 108 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1064 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 64 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 0.1980 chunk 4 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 47 optimal weight: 0.0980 chunk 84 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.117106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.094350 restraints weight = 11015.532| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.12 r_work: 0.3189 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7125 Z= 0.118 Angle : 0.459 5.616 9657 Z= 0.249 Chirality : 0.041 0.168 1112 Planarity : 0.003 0.056 1205 Dihedral : 5.271 45.540 1070 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.29 % Allowed : 18.06 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.30 (0.29), residues: 872 helix: 2.33 (0.28), residues: 360 sheet: 1.02 (0.39), residues: 172 loop : -0.88 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 117 TYR 0.011 0.001 TYR A 973 PHE 0.012 0.001 PHE C 199 TRP 0.010 0.001 TRP C 211 HIS 0.002 0.001 HIS A 833 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 7124) covalent geometry : angle 0.45923 ( 9655) SS BOND : bond 0.00074 ( 1) SS BOND : angle 0.53845 ( 2) hydrogen bonds : bond 0.04964 ( 342) hydrogen bonds : angle 3.90535 ( 978) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.277 Fit side-chains REVERT: B 150 GLU cc_start: 0.6888 (tm-30) cc_final: 0.6605 (tm-30) REVERT: D 21 MET cc_start: 0.6206 (mmm) cc_final: 0.5887 (ttp) REVERT: A 1062 THR cc_start: 0.7663 (p) cc_final: 0.7335 (m) outliers start: 17 outliers final: 12 residues processed: 104 average time/residue: 0.5634 time to fit residues: 61.3493 Evaluate side-chains 105 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1064 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 35 optimal weight: 2.9990 chunk 67 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 6 optimal weight: 0.2980 chunk 60 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 47 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.116590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.093782 restraints weight = 11128.126| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.15 r_work: 0.3185 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7125 Z= 0.125 Angle : 0.471 5.754 9657 Z= 0.254 Chirality : 0.041 0.174 1112 Planarity : 0.003 0.055 1205 Dihedral : 5.244 45.771 1070 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.56 % Allowed : 18.33 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.30 (0.29), residues: 872 helix: 2.31 (0.28), residues: 360 sheet: 1.08 (0.39), residues: 170 loop : -0.89 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 96 TYR 0.009 0.001 TYR A1095 PHE 0.013 0.001 PHE C 199 TRP 0.010 0.001 TRP C 82 HIS 0.002 0.001 HIS A 833 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7124) covalent geometry : angle 0.47074 ( 9655) SS BOND : bond 0.00048 ( 1) SS BOND : angle 0.57725 ( 2) hydrogen bonds : bond 0.05077 ( 342) hydrogen bonds : angle 3.89049 ( 978) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.179 Fit side-chains REVERT: B 150 GLU cc_start: 0.6919 (tm-30) cc_final: 0.6627 (tm-30) REVERT: D 21 MET cc_start: 0.6195 (mmm) cc_final: 0.5874 (ttp) REVERT: A 1062 THR cc_start: 0.7656 (p) cc_final: 0.7336 (m) outliers start: 19 outliers final: 13 residues processed: 110 average time/residue: 0.5419 time to fit residues: 62.4767 Evaluate side-chains 107 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1064 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 12 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 0.0980 chunk 84 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 ASN B 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.116026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.093417 restraints weight = 10970.315| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.07 r_work: 0.3186 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7125 Z= 0.138 Angle : 0.493 5.893 9657 Z= 0.265 Chirality : 0.041 0.177 1112 Planarity : 0.003 0.056 1205 Dihedral : 5.320 46.930 1070 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.56 % Allowed : 18.87 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.24 (0.28), residues: 872 helix: 2.28 (0.28), residues: 359 sheet: 0.93 (0.39), residues: 172 loop : -0.86 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 96 TYR 0.011 0.001 TYR A 973 PHE 0.013 0.001 PHE C 199 TRP 0.011 0.002 TRP C 82 HIS 0.003 0.001 HIS A 833 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 7124) covalent geometry : angle 0.49324 ( 9655) SS BOND : bond 0.00033 ( 1) SS BOND : angle 0.64998 ( 2) hydrogen bonds : bond 0.05319 ( 342) hydrogen bonds : angle 3.92796 ( 978) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.195 Fit side-chains REVERT: B 150 GLU cc_start: 0.6955 (tm-30) cc_final: 0.6659 (tm-30) REVERT: D 21 MET cc_start: 0.6189 (mmm) cc_final: 0.5871 (ttp) REVERT: A 1062 THR cc_start: 0.7667 (p) cc_final: 0.7347 (m) outliers start: 19 outliers final: 14 residues processed: 109 average time/residue: 0.6154 time to fit residues: 70.1677 Evaluate side-chains 109 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1064 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 63 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 84 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 71 optimal weight: 0.0980 chunk 55 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 ASN B 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.116954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.094166 restraints weight = 11186.878| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.14 r_work: 0.3187 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7125 Z= 0.119 Angle : 0.471 6.572 9657 Z= 0.256 Chirality : 0.041 0.181 1112 Planarity : 0.003 0.056 1205 Dihedral : 5.070 44.745 1070 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.02 % Allowed : 19.14 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.31 (0.29), residues: 872 helix: 2.35 (0.28), residues: 360 sheet: 0.92 (0.39), residues: 172 loop : -0.82 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 96 TYR 0.008 0.001 TYR A1095 PHE 0.013 0.001 PHE C 199 TRP 0.011 0.001 TRP C 211 HIS 0.002 0.001 HIS A 833 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7124) covalent geometry : angle 0.47126 ( 9655) SS BOND : bond 0.00088 ( 1) SS BOND : angle 0.58671 ( 2) hydrogen bonds : bond 0.04909 ( 342) hydrogen bonds : angle 3.85941 ( 978) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.287 Fit side-chains REVERT: B 126 GLU cc_start: 0.6872 (tp30) cc_final: 0.6095 (tp30) REVERT: B 150 GLU cc_start: 0.7003 (tm-30) cc_final: 0.6712 (tm-30) REVERT: D 21 MET cc_start: 0.6192 (mmm) cc_final: 0.5876 (ttp) REVERT: A 1062 THR cc_start: 0.7659 (p) cc_final: 0.7346 (m) outliers start: 15 outliers final: 11 residues processed: 111 average time/residue: 0.5648 time to fit residues: 65.5956 Evaluate side-chains 106 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1064 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 18 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 59 optimal weight: 0.0770 chunk 60 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.120082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.097205 restraints weight = 11067.888| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.11 r_work: 0.3174 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7125 Z= 0.153 Angle : 0.516 6.067 9657 Z= 0.275 Chirality : 0.042 0.184 1112 Planarity : 0.004 0.056 1205 Dihedral : 5.373 48.142 1070 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.70 % Allowed : 19.14 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.22 (0.28), residues: 872 helix: 2.26 (0.28), residues: 359 sheet: 0.80 (0.38), residues: 173 loop : -0.80 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 96 TYR 0.010 0.001 TYR A1095 PHE 0.013 0.001 PHE C 199 TRP 0.011 0.002 TRP C 82 HIS 0.003 0.001 HIS A 833 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 7124) covalent geometry : angle 0.51586 ( 9655) SS BOND : bond 0.00033 ( 1) SS BOND : angle 0.81192 ( 2) hydrogen bonds : bond 0.05577 ( 342) hydrogen bonds : angle 3.96126 ( 978) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.170 Fit side-chains REVERT: B 126 GLU cc_start: 0.6913 (tp30) cc_final: 0.6192 (tp30) REVERT: B 150 GLU cc_start: 0.6947 (tm-30) cc_final: 0.6645 (tm-30) REVERT: D 21 MET cc_start: 0.6191 (mmm) cc_final: 0.5868 (ttp) REVERT: A 1062 THR cc_start: 0.7671 (p) cc_final: 0.7355 (m) outliers start: 20 outliers final: 15 residues processed: 107 average time/residue: 0.5344 time to fit residues: 59.9490 Evaluate side-chains 106 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain A residue 846 LEU Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1064 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 47 optimal weight: 0.0570 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 0.0370 chunk 72 optimal weight: 0.7980 chunk 67 optimal weight: 0.0470 chunk 31 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.3474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.122623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.100113 restraints weight = 10959.792| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.05 r_work: 0.3218 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7125 Z= 0.106 Angle : 0.456 5.606 9657 Z= 0.249 Chirality : 0.040 0.185 1112 Planarity : 0.003 0.056 1205 Dihedral : 4.824 42.315 1070 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.75 % Allowed : 19.95 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.38 (0.29), residues: 872 helix: 2.42 (0.28), residues: 361 sheet: 0.99 (0.39), residues: 170 loop : -0.82 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 96 TYR 0.008 0.001 TYR B 29 PHE 0.012 0.001 PHE C 199 TRP 0.011 0.001 TRP C 211 HIS 0.002 0.000 HIS A1019 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 7124) covalent geometry : angle 0.45565 ( 9655) SS BOND : bond 0.00098 ( 1) SS BOND : angle 0.64360 ( 2) hydrogen bonds : bond 0.04542 ( 342) hydrogen bonds : angle 3.79195 ( 978) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.208 Fit side-chains REVERT: B 150 GLU cc_start: 0.6926 (tm-30) cc_final: 0.6652 (tm-30) REVERT: B 204 ASN cc_start: 0.6913 (t0) cc_final: 0.6652 (t0) REVERT: D 21 MET cc_start: 0.6205 (mmm) cc_final: 0.5903 (ttp) REVERT: A 904 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8237 (m) REVERT: A 1062 THR cc_start: 0.7619 (p) cc_final: 0.7305 (m) outliers start: 13 outliers final: 10 residues processed: 104 average time/residue: 0.5673 time to fit residues: 61.8011 Evaluate side-chains 104 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1064 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.8343 > 50: distance: 68 - 74: 26.615 distance: 74 - 75: 27.466 distance: 75 - 76: 31.343 distance: 75 - 78: 23.724 distance: 76 - 77: 9.179 distance: 76 - 81: 53.767 distance: 78 - 79: 41.468 distance: 78 - 80: 20.629 distance: 81 - 82: 26.395 distance: 82 - 83: 9.855 distance: 82 - 85: 25.538 distance: 83 - 84: 23.583 distance: 83 - 90: 14.780 distance: 85 - 86: 12.862 distance: 86 - 87: 12.217 distance: 87 - 88: 17.798 distance: 87 - 89: 29.376 distance: 90 - 91: 22.303 distance: 91 - 92: 10.846 distance: 91 - 94: 10.513 distance: 92 - 93: 21.844 distance: 92 - 98: 34.590 distance: 94 - 95: 15.851 distance: 95 - 96: 29.617 distance: 95 - 97: 18.465 distance: 98 - 99: 31.071 distance: 99 - 100: 15.112 distance: 99 - 102: 40.680 distance: 100 - 101: 14.760 distance: 101 - 124: 33.250 distance: 103 - 104: 11.042 distance: 104 - 105: 31.480 distance: 104 - 107: 46.433 distance: 105 - 106: 28.567 distance: 105 - 108: 35.936 distance: 108 - 109: 21.549 distance: 109 - 110: 15.406 distance: 109 - 112: 35.531 distance: 110 - 111: 4.565 distance: 110 - 116: 35.260 distance: 111 - 146: 47.423 distance: 112 - 113: 41.913 distance: 113 - 114: 21.504 distance: 113 - 115: 41.026 distance: 116 - 117: 9.207 distance: 117 - 118: 25.407 distance: 117 - 120: 10.542 distance: 118 - 119: 29.684 distance: 118 - 124: 30.657 distance: 119 - 154: 25.620 distance: 120 - 121: 23.896 distance: 120 - 122: 22.831 distance: 121 - 123: 23.290 distance: 124 - 125: 22.249 distance: 125 - 126: 21.440 distance: 125 - 128: 21.605 distance: 126 - 127: 18.179 distance: 126 - 135: 8.155 distance: 127 - 161: 10.878 distance: 128 - 129: 30.104 distance: 129 - 130: 11.832 distance: 129 - 131: 18.786 distance: 130 - 132: 6.796 distance: 131 - 133: 15.422 distance: 132 - 134: 19.665 distance: 133 - 134: 14.478 distance: 135 - 136: 12.271 distance: 136 - 137: 17.081 distance: 136 - 139: 52.106 distance: 137 - 138: 40.742 distance: 137 - 146: 20.874 distance: 138 - 168: 31.699 distance: 139 - 140: 35.682 distance: 140 - 141: 36.166 distance: 141 - 142: 17.784 distance: 142 - 143: 16.572 distance: 143 - 144: 17.907 distance: 143 - 145: 25.954 distance: 146 - 147: 29.315 distance: 147 - 148: 14.615 distance: 147 - 150: 49.685 distance: 148 - 149: 46.560 distance: 148 - 154: 28.998 distance: 149 - 174: 25.683 distance: 150 - 151: 44.703 distance: 151 - 152: 37.686 distance: 151 - 153: 37.404