Starting phenix.real_space_refine on Wed Jun 18 13:48:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g6m_29774/06_2025/8g6m_29774.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g6m_29774/06_2025/8g6m_29774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g6m_29774/06_2025/8g6m_29774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g6m_29774/06_2025/8g6m_29774.map" model { file = "/net/cci-nas-00/data/ceres_data/8g6m_29774/06_2025/8g6m_29774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g6m_29774/06_2025/8g6m_29774.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians S 80 5.16 5 C 6803 2.51 5 N 1872 2.21 5 O 2026 1.98 5 H 10657 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21438 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3112 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2704 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 159} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 3279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3279 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3107 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3115 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 3067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3067 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3054 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 11.25, per 1000 atoms: 0.52 Number of scatterers: 21438 At special positions: 0 Unit cell: (113.1, 135.2, 127.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 O 2026 8.00 N 1872 7.00 C 6803 6.00 H 10657 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 5.49 Conformation dependent library (CDL) restraints added in 1.6 seconds 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2592 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 1 sheets defined 77.2% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 176 removed outlier: 3.554A pdb=" N GLN A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.154A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.945A pdb=" N ILE A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 217 Processing helix chain 'B' and resid 16 through 31 removed outlier: 3.505A pdb=" N ALA B 31 " --> pdb=" O VAL B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 48 through 58 Processing helix chain 'B' and resid 62 through 84 Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 110 through 119 Processing helix chain 'B' and resid 125 through 146 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 160 through 176 Processing helix chain 'B' and resid 178 through 193 removed outlier: 4.411A pdb=" N LEU B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VAL B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 30 Processing helix chain 'C' and resid 35 through 44 Processing helix chain 'C' and resid 48 through 60 removed outlier: 4.027A pdb=" N THR C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL C 59 " --> pdb=" O MET C 55 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 84 removed outlier: 3.698A pdb=" N LEU C 83 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 125 through 145 Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.591A pdb=" N ILE C 153 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 178 through 194 removed outlier: 4.269A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 removed outlier: 4.335A pdb=" N ILE C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'D' and resid 16 through 31 Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 59 removed outlier: 3.909A pdb=" N VAL D 59 " --> pdb=" O MET D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 84 Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 110 through 116 Processing helix chain 'D' and resid 125 through 146 Processing helix chain 'D' and resid 160 through 174 Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.171A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.866A pdb=" N ILE D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 218 Processing helix chain 'E' and resid 16 through 31 Processing helix chain 'E' and resid 35 through 44 Processing helix chain 'E' and resid 48 through 58 Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 110 through 120 Processing helix chain 'E' and resid 125 through 146 removed outlier: 3.609A pdb=" N TRP E 133 " --> pdb=" O ILE E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 160 through 176 removed outlier: 3.647A pdb=" N ALA E 174 " --> pdb=" O LYS E 170 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN E 176 " --> pdb=" O LEU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 194 removed outlier: 4.476A pdb=" N LEU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.969A pdb=" N ILE E 201 " --> pdb=" O ASP E 197 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY E 206 " --> pdb=" O LEU E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 218 Processing helix chain 'F' and resid 16 through 30 Processing helix chain 'F' and resid 35 through 44 Processing helix chain 'F' and resid 48 through 58 Processing helix chain 'F' and resid 62 through 84 Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 110 through 120 Processing helix chain 'F' and resid 125 through 146 Processing helix chain 'F' and resid 149 through 153 Processing helix chain 'F' and resid 160 through 176 removed outlier: 3.586A pdb=" N GLN F 176 " --> pdb=" O LEU F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 193 removed outlier: 4.571A pdb=" N TRP F 184 " --> pdb=" O GLU F 180 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET F 185 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LEU F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 206 removed outlier: 4.509A pdb=" N ILE F 201 " --> pdb=" O ASP F 197 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA F 204 " --> pdb=" O THR F 200 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY F 206 " --> pdb=" O LEU F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 219 Processing helix chain 'G' and resid 16 through 29 Processing helix chain 'G' and resid 35 through 44 Processing helix chain 'G' and resid 48 through 58 Processing helix chain 'G' and resid 62 through 84 Processing helix chain 'G' and resid 100 through 106 Processing helix chain 'G' and resid 110 through 120 Processing helix chain 'G' and resid 125 through 146 Processing helix chain 'G' and resid 160 through 176 Processing helix chain 'G' and resid 178 through 193 removed outlier: 4.757A pdb=" N TRP G 184 " --> pdb=" O GLU G 180 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET G 185 " --> pdb=" O VAL G 181 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL G 191 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 removed outlier: 4.423A pdb=" N ILE G 201 " --> pdb=" O ASP G 197 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY G 206 " --> pdb=" O LEU G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 219 Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 4 712 hydrogen bonds defined for protein. 2109 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: 7.41 Time building geometry restraints manager: 6.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 10645 1.02 - 1.22: 16 1.22 - 1.42: 4408 1.42 - 1.62: 6458 1.62 - 1.82: 148 Bond restraints: 21675 Sorted by residual: bond pdb=" C GLU A 98 " pdb=" N PRO A 99 " ideal model delta sigma weight residual 1.335 1.353 -0.018 8.70e-03 1.32e+04 4.16e+00 bond pdb=" CG ASN G 57 " pdb=" ND2 ASN G 57 " ideal model delta sigma weight residual 1.328 1.289 0.039 2.10e-02 2.27e+03 3.50e+00 bond pdb=" N HIS G 12 " pdb=" CA HIS G 12 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N HIS F 12 " pdb=" CA HIS F 12 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.80e+00 bond pdb=" CD GLN D 63 " pdb=" OE1 GLN D 63 " ideal model delta sigma weight residual 1.231 1.200 0.031 1.90e-02 2.77e+03 2.72e+00 ... (remaining 21670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 37310 1.46 - 2.92: 1716 2.92 - 4.38: 202 4.38 - 5.84: 50 5.84 - 7.30: 10 Bond angle restraints: 39288 Sorted by residual: angle pdb=" CA LYS G 30 " pdb=" CB LYS G 30 " pdb=" CG LYS G 30 " ideal model delta sigma weight residual 114.10 106.85 7.25 2.00e+00 2.50e-01 1.31e+01 angle pdb=" CA ASN G 57 " pdb=" CB ASN G 57 " pdb=" CG ASN G 57 " ideal model delta sigma weight residual 112.60 115.45 -2.85 1.00e+00 1.00e+00 8.11e+00 angle pdb=" CB LYS G 30 " pdb=" CG LYS G 30 " pdb=" CD LYS G 30 " ideal model delta sigma weight residual 111.30 117.57 -6.27 2.30e+00 1.89e-01 7.44e+00 angle pdb=" C ASN G 57 " pdb=" CA ASN G 57 " pdb=" CB ASN G 57 " ideal model delta sigma weight residual 110.79 106.67 4.12 1.66e+00 3.63e-01 6.16e+00 angle pdb=" CA GLY E 61 " pdb=" C GLY E 61 " pdb=" O GLY E 61 " ideal model delta sigma weight residual 122.59 120.15 2.44 1.04e+00 9.25e-01 5.50e+00 ... (remaining 39283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 9159 17.62 - 35.23: 722 35.23 - 52.85: 266 52.85 - 70.47: 76 70.47 - 88.08: 17 Dihedral angle restraints: 10240 sinusoidal: 5702 harmonic: 4538 Sorted by residual: dihedral pdb=" CA ILE D 115 " pdb=" C ILE D 115 " pdb=" N GLY D 116 " pdb=" CA GLY D 116 " ideal model delta harmonic sigma weight residual 180.00 161.52 18.48 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ILE B 15 " pdb=" C ILE B 15 " pdb=" N SER B 16 " pdb=" CA SER B 16 " ideal model delta harmonic sigma weight residual -180.00 -163.57 -16.43 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CB GLU D 29 " pdb=" CG GLU D 29 " pdb=" CD GLU D 29 " pdb=" OE1 GLU D 29 " ideal model delta sinusoidal sigma weight residual 0.00 -87.17 87.17 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 10237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1149 0.035 - 0.070: 386 0.070 - 0.105: 110 0.105 - 0.140: 28 0.140 - 0.175: 5 Chirality restraints: 1678 Sorted by residual: chirality pdb=" CA ILE A 124 " pdb=" N ILE A 124 " pdb=" C ILE A 124 " pdb=" CB ILE A 124 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CA ILE C 124 " pdb=" N ILE C 124 " pdb=" C ILE C 124 " pdb=" CB ILE C 124 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CA ILE F 124 " pdb=" N ILE F 124 " pdb=" C ILE F 124 " pdb=" CB ILE F 124 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 1675 not shown) Planarity restraints: 3206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 57 " -0.010 2.00e-02 2.50e+03 1.61e-02 3.91e+00 pdb=" CG ASN G 57 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN G 57 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN G 57 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN G 57 " -0.004 2.00e-02 2.50e+03 pdb="HD22 ASN G 57 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE F 124 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO F 125 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO F 125 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 125 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A 185 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.49e+00 pdb=" C MET A 185 " 0.027 2.00e-02 2.50e+03 pdb=" O MET A 185 " -0.010 2.00e-02 2.50e+03 pdb=" N THR A 186 " -0.009 2.00e-02 2.50e+03 ... (remaining 3203 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 2683 2.26 - 2.85: 48270 2.85 - 3.43: 57753 3.43 - 4.02: 75240 4.02 - 4.60: 117710 Nonbonded interactions: 301656 Sorted by model distance: nonbonded pdb=" OE2 GLU D 128 " pdb=" HZ3 LYS D 131 " model vdw 1.680 2.450 nonbonded pdb=" O GLY G 156 " pdb="HD22 ASN G 195 " model vdw 1.702 2.450 nonbonded pdb=" O ASN A 57 " pdb="HH22 ARG D 173 " model vdw 1.712 2.450 nonbonded pdb=" H ASN C 5 " pdb=" O GLN C 9 " model vdw 1.715 2.450 nonbonded pdb=" OE1 GLU F 35 " pdb=" H GLU F 35 " model vdw 1.718 2.450 ... (remaining 301651 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 85 or (resid 96 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 97 through 99 or (resid \ 100 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 101 through 111 or (resid 112 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name OE1 or name NE2)) or resid 113 thro \ ugh 119 or (resid 120 and (name N or name CA or name C or name O or name CB or n \ ame CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or n \ ame HB2 or name HB3 or name HD2 or name HE1)) or resid 121 through 157 or (resid \ 158 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 159 through 161 or (resid 162 and (name N or name CA or name C or na \ me O or name CB or name H or name HA )) or resid 163 through 181 or (resid 182 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 183 through 193)) selection = (chain 'B' and ((resid 12 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or resid 13 throug \ h 59 or (resid 60 and (name N or name CA or name C or name O )) or resid 61 thro \ ugh 85 or (resid 96 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 97 through 99 or (resid 100 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 101 through 111 or \ (resid 112 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name OE1 or name NE2)) or resid 113 through 119 or (resid 120 and (na \ me N or name CA or name C or name O or name CB or name CG or name ND1 or name CD \ 2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name H \ D2 or name HE1)) or resid 121 through 157 or (resid 158 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 159 through 193)) \ selection = (chain 'C' and (resid 12 through 59 or (resid 60 and (name N or name CA or name \ C or name O )) or resid 61 through 85 or (resid 96 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 97 through 99 or (resi \ d 100 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 101 through 111 or (resid 112 and (name N or name CA or name C or n \ ame O or name CB or name CG or name CD or name OE1 or name NE2)) or resid 113 th \ rough 119 or (resid 120 and (name N or name CA or name C or name O or name CB or \ name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or \ name HB2 or name HB3 or name HD2 or name HE1)) or resid 121 through 157 or (res \ id 158 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 159 through 181 or (resid 182 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 183 through 186 or (resid 187 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 188 through 193)) selection = (chain 'D' and ((resid 12 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or resid 13 throug \ h 59 or (resid 60 and (name N or name CA or name C or name O )) or resid 61 thro \ ugh 83 or (resid 84 and (name N or name CA or name C or name O or name CB or nam \ e CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or nam \ e HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or resid 85 through 99 o \ r (resid 100 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 101 through 119 or (resid 120 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or res \ id 121 through 157 or (resid 158 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 159 through 161 or (resid 162 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 163 \ through 181 or (resid 182 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 183 through 186 or (resid 187 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 188 throu \ gh 193)) selection = (chain 'E' and ((resid 12 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or resid 13 throug \ h 59 or (resid 60 and (name N or name CA or name C or name O )) or resid 61 thro \ ugh 85 or (resid 96 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 97 through 99 or (resid 100 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 101 through 111 or \ (resid 112 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name OE1 or name NE2)) or resid 113 through 119 or (resid 120 and (na \ me N or name CA or name C or name O or name CB or name CG or name ND1 or name CD \ 2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name H \ D2 or name HE1)) or resid 121 through 157 or (resid 158 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 159 through 161 o \ r (resid 162 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 163 through 181 or (resid 182 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 183 through 193)) selection = (chain 'F' and (resid 12 through 59 or (resid 60 and (name N or name CA or name \ C or name O )) or resid 61 through 85 or (resid 96 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 97 through 111 or (res \ id 112 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name NE2)) or resid 113 through 119 or (resid 120 and (name N \ or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 or \ name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or \ name HE1)) or resid 121 through 161 or (resid 162 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 163 through 193)) selection = (chain 'G' and (resid 12 through 59 or (resid 60 and (name N or name CA or name \ C or name O )) or resid 61 through 85 or (resid 96 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 97 through 111 or (res \ id 112 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name NE2)) or resid 113 through 119 or (resid 120 and (name N \ or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 or \ name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or \ name HE1)) or resid 121 through 161 or (resid 162 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 163 through 193)) } 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: 3.190 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: 0.380 Extract box with map and model: 0.850 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 46.810 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11018 Z= 0.186 Angle : 0.709 7.305 14971 Z= 0.360 Chirality : 0.040 0.175 1678 Planarity : 0.005 0.051 1940 Dihedral : 13.634 87.173 4136 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.43 % Allowed : 4.98 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.23), residues: 1351 helix: 0.90 (0.16), residues: 988 sheet: -2.28 (1.30), residues: 9 loop : -0.01 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 184 HIS 0.009 0.001 HIS D 120 PHE 0.009 0.001 PHE G 32 TYR 0.013 0.002 TYR D 169 ARG 0.007 0.001 ARG A 162 Details of bonding type rmsd hydrogen bonds : bond 0.09360 ( 712) hydrogen bonds : angle 4.53314 ( 2109) covalent geometry : bond 0.00424 (11018) covalent geometry : angle 0.70937 (14971) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 223 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 218 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7383 (pt0) cc_final: 0.7154 (pt0) REVERT: A 55 MET cc_start: 0.9276 (mtp) cc_final: 0.9017 (mtp) REVERT: A 66 MET cc_start: 0.9362 (mmp) cc_final: 0.9154 (mmt) REVERT: B 121 ASN cc_start: 0.7177 (m110) cc_final: 0.6850 (t0) REVERT: C 215 MET cc_start: 0.8202 (mtm) cc_final: 0.7865 (mtp) REVERT: E 66 MET cc_start: 0.8222 (mmm) cc_final: 0.7900 (mmp) REVERT: F 35 GLU cc_start: 0.6759 (pm20) cc_final: 0.6491 (pm20) REVERT: F 121 ASN cc_start: 0.2951 (m-40) cc_final: 0.2425 (t0) REVERT: F 161 PHE cc_start: 0.6765 (t80) cc_final: 0.6523 (t80) REVERT: G 96 MET cc_start: 0.2476 (ppp) cc_final: 0.0836 (ttp) REVERT: G 219 GLN cc_start: 0.7337 (pt0) cc_final: 0.7111 (pp30) outliers start: 5 outliers final: 2 residues processed: 221 average time/residue: 0.6700 time to fit residues: 195.0636 Evaluate side-chains 148 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain E residue 103 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 GLN F 13 GLN F 192 GLN F 193 ASN F 195 ASN G 57 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.136883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.104884 restraints weight = 55638.049| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.06 r_work: 0.3320 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 11018 Z= 0.241 Angle : 0.603 7.331 14971 Z= 0.316 Chirality : 0.042 0.158 1678 Planarity : 0.005 0.050 1940 Dihedral : 4.827 47.612 1463 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.03 % Allowed : 7.04 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.22), residues: 1351 helix: 0.74 (0.16), residues: 1013 sheet: -2.21 (1.09), residues: 9 loop : -0.46 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 184 HIS 0.005 0.001 HIS E 84 PHE 0.010 0.002 PHE C 32 TYR 0.016 0.002 TYR D 169 ARG 0.009 0.001 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.04926 ( 712) hydrogen bonds : angle 4.39823 ( 2109) covalent geometry : bond 0.00570 (11018) covalent geometry : angle 0.60262 (14971) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.7650 (mtm) cc_final: 0.7286 (mtm) REVERT: B 121 ASN cc_start: 0.7110 (m110) cc_final: 0.6874 (t0) REVERT: C 66 MET cc_start: 0.9122 (tpt) cc_final: 0.8872 (tpt) REVERT: E 66 MET cc_start: 0.8175 (mmm) cc_final: 0.7856 (mmp) REVERT: F 121 ASN cc_start: 0.2406 (m-40) cc_final: 0.1599 (t0) REVERT: F 144 MET cc_start: 0.7255 (tpt) cc_final: 0.6937 (tpt) REVERT: F 214 MET cc_start: 0.8196 (mtp) cc_final: 0.7991 (mtp) REVERT: G 96 MET cc_start: 0.1793 (ppp) cc_final: 0.0299 (ttp) REVERT: G 219 GLN cc_start: 0.8065 (pt0) cc_final: 0.7457 (pp30) outliers start: 12 outliers final: 7 residues processed: 152 average time/residue: 0.5642 time to fit residues: 119.9330 Evaluate side-chains 143 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 188 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 59 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 37 optimal weight: 0.0980 chunk 108 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 176 GLN F 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.139255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.107788 restraints weight = 55314.323| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.04 r_work: 0.3375 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11018 Z= 0.110 Angle : 0.495 4.940 14971 Z= 0.251 Chirality : 0.037 0.147 1678 Planarity : 0.004 0.044 1940 Dihedral : 4.404 50.028 1463 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.69 % Allowed : 7.99 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.23), residues: 1351 helix: 1.25 (0.16), residues: 1007 sheet: -1.73 (1.07), residues: 9 loop : -0.25 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 184 HIS 0.004 0.001 HIS E 84 PHE 0.006 0.001 PHE F 40 TYR 0.012 0.001 TYR D 169 ARG 0.002 0.000 ARG B 97 Details of bonding type rmsd hydrogen bonds : bond 0.03990 ( 712) hydrogen bonds : angle 3.97025 ( 2109) covalent geometry : bond 0.00245 (11018) covalent geometry : angle 0.49484 (14971) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.9114 (mtp) cc_final: 0.8829 (mtp) REVERT: A 66 MET cc_start: 0.9237 (mmt) cc_final: 0.8956 (mmt) REVERT: B 121 ASN cc_start: 0.7092 (m110) cc_final: 0.6716 (t0) REVERT: C 66 MET cc_start: 0.9073 (tpt) cc_final: 0.8671 (tpt) REVERT: E 45 GLU cc_start: 0.7253 (tm-30) cc_final: 0.6722 (tm-30) REVERT: E 66 MET cc_start: 0.8235 (mmm) cc_final: 0.7939 (mmp) REVERT: F 121 ASN cc_start: 0.2215 (m-40) cc_final: 0.1931 (t0) REVERT: F 144 MET cc_start: 0.7037 (tpt) cc_final: 0.6705 (tpt) REVERT: G 219 GLN cc_start: 0.7958 (pt0) cc_final: 0.7397 (pp30) outliers start: 8 outliers final: 7 residues processed: 152 average time/residue: 0.5556 time to fit residues: 116.3760 Evaluate side-chains 149 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 142 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain E residue 103 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 61 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 104 optimal weight: 0.0980 chunk 100 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.137964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.105692 restraints weight = 56100.831| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.15 r_work: 0.3335 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11018 Z= 0.158 Angle : 0.519 5.946 14971 Z= 0.266 Chirality : 0.038 0.147 1678 Planarity : 0.005 0.044 1940 Dihedral : 4.401 51.714 1463 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.12 % Allowed : 8.68 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.23), residues: 1351 helix: 1.22 (0.16), residues: 1007 sheet: -1.81 (1.08), residues: 9 loop : -0.32 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 184 HIS 0.003 0.001 HIS F 12 PHE 0.006 0.001 PHE D 32 TYR 0.016 0.002 TYR D 169 ARG 0.004 0.000 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 712) hydrogen bonds : angle 4.04130 ( 2109) covalent geometry : bond 0.00371 (11018) covalent geometry : angle 0.51873 (14971) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.9150 (mtp) cc_final: 0.8832 (mtp) REVERT: B 121 ASN cc_start: 0.7083 (m110) cc_final: 0.6742 (t0) REVERT: C 66 MET cc_start: 0.9119 (tpt) cc_final: 0.8742 (tpt) REVERT: E 66 MET cc_start: 0.8314 (mmm) cc_final: 0.8082 (mmp) REVERT: F 121 ASN cc_start: 0.2394 (m-40) cc_final: 0.2057 (t0) REVERT: F 144 MET cc_start: 0.7022 (tpt) cc_final: 0.6654 (tpt) REVERT: G 219 GLN cc_start: 0.7979 (pt0) cc_final: 0.7395 (pp30) outliers start: 13 outliers final: 10 residues processed: 157 average time/residue: 0.5374 time to fit residues: 117.6681 Evaluate side-chains 152 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain G residue 188 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 123 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 126 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.139277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.107114 restraints weight = 55762.608| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.01 r_work: 0.3366 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11018 Z= 0.109 Angle : 0.483 5.136 14971 Z= 0.243 Chirality : 0.037 0.165 1678 Planarity : 0.004 0.045 1940 Dihedral : 4.217 51.492 1463 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.95 % Allowed : 9.36 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.23), residues: 1351 helix: 1.50 (0.17), residues: 1009 sheet: -1.73 (1.08), residues: 9 loop : -0.22 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 117 HIS 0.003 0.001 HIS F 12 PHE 0.005 0.001 PHE D 32 TYR 0.014 0.001 TYR D 169 ARG 0.003 0.000 ARG D 167 Details of bonding type rmsd hydrogen bonds : bond 0.03743 ( 712) hydrogen bonds : angle 3.87805 ( 2109) covalent geometry : bond 0.00246 (11018) covalent geometry : angle 0.48252 (14971) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.9104 (mtp) cc_final: 0.8732 (mtp) REVERT: B 96 MET cc_start: 0.2599 (ppp) cc_final: 0.2209 (ppp) REVERT: B 121 ASN cc_start: 0.6956 (m110) cc_final: 0.6597 (t0) REVERT: F 121 ASN cc_start: 0.2521 (m-40) cc_final: 0.2163 (t0) REVERT: F 144 MET cc_start: 0.7113 (tpt) cc_final: 0.6705 (tpt) REVERT: G 219 GLN cc_start: 0.7931 (pt0) cc_final: 0.7389 (pp30) outliers start: 11 outliers final: 9 residues processed: 154 average time/residue: 0.5765 time to fit residues: 122.4206 Evaluate side-chains 151 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 215 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 64 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 117 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.139571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.108352 restraints weight = 55670.323| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.09 r_work: 0.3372 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11018 Z= 0.106 Angle : 0.478 4.803 14971 Z= 0.240 Chirality : 0.036 0.141 1678 Planarity : 0.004 0.043 1940 Dihedral : 4.114 51.843 1463 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.95 % Allowed : 9.45 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.23), residues: 1351 helix: 1.65 (0.17), residues: 1004 sheet: -1.74 (1.08), residues: 9 loop : -0.09 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 184 HIS 0.002 0.001 HIS F 12 PHE 0.005 0.001 PHE E 161 TYR 0.014 0.001 TYR D 169 ARG 0.002 0.000 ARG F 143 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 712) hydrogen bonds : angle 3.83538 ( 2109) covalent geometry : bond 0.00243 (11018) covalent geometry : angle 0.47754 (14971) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.9081 (mtp) cc_final: 0.8708 (mtp) REVERT: B 96 MET cc_start: 0.2712 (ppp) cc_final: 0.2265 (ppp) REVERT: B 121 ASN cc_start: 0.6938 (m110) cc_final: 0.6587 (t0) REVERT: F 121 ASN cc_start: 0.2514 (m-40) cc_final: 0.2174 (t0) REVERT: F 144 MET cc_start: 0.6925 (tpt) cc_final: 0.6581 (tpt) REVERT: F 164 TYR cc_start: 0.6511 (t80) cc_final: 0.5722 (t80) REVERT: G 219 GLN cc_start: 0.7859 (pt0) cc_final: 0.7366 (pp30) outliers start: 11 outliers final: 10 residues processed: 156 average time/residue: 0.5164 time to fit residues: 113.2111 Evaluate side-chains 147 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 137 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 215 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 103 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 12 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.139449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.107724 restraints weight = 55738.083| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.97 r_work: 0.3364 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11018 Z= 0.111 Angle : 0.481 4.848 14971 Z= 0.242 Chirality : 0.037 0.149 1678 Planarity : 0.004 0.044 1940 Dihedral : 4.068 51.708 1463 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.29 % Allowed : 9.28 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.23), residues: 1351 helix: 1.71 (0.17), residues: 1004 sheet: -1.64 (1.07), residues: 9 loop : -0.02 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 184 HIS 0.002 0.001 HIS F 12 PHE 0.006 0.001 PHE D 32 TYR 0.014 0.001 TYR D 169 ARG 0.002 0.000 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 712) hydrogen bonds : angle 3.85763 ( 2109) covalent geometry : bond 0.00256 (11018) covalent geometry : angle 0.48058 (14971) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7604 (pt0) REVERT: A 55 MET cc_start: 0.9077 (mtp) cc_final: 0.8707 (mtp) REVERT: B 96 MET cc_start: 0.2724 (ppp) cc_final: 0.2258 (ppp) REVERT: B 121 ASN cc_start: 0.6928 (m110) cc_final: 0.6580 (t0) REVERT: F 121 ASN cc_start: 0.2731 (m-40) cc_final: 0.2398 (t0) REVERT: F 144 MET cc_start: 0.7154 (tpt) cc_final: 0.6830 (tpt) REVERT: F 164 TYR cc_start: 0.6504 (t80) cc_final: 0.5686 (t80) REVERT: G 219 GLN cc_start: 0.8003 (pt0) cc_final: 0.7361 (pp30) outliers start: 15 outliers final: 12 residues processed: 153 average time/residue: 0.4924 time to fit residues: 108.2145 Evaluate side-chains 150 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 197 ASP Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 215 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.8585 > 50: distance: 195 - 246: 24.548 distance: 209 - 265: 23.682 distance: 219 - 234: 11.197 distance: 220 - 279: 8.749 distance: 234 - 235: 26.707 distance: 234 - 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