Starting phenix.real_space_refine on Sun Aug 24 09:25:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cl2_16710/08_2025/8cl2_16710.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cl2_16710/08_2025/8cl2_16710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cl2_16710/08_2025/8cl2_16710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cl2_16710/08_2025/8cl2_16710.map" model { file = "/net/cci-nas-00/data/ceres_data/8cl2_16710/08_2025/8cl2_16710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cl2_16710/08_2025/8cl2_16710.cif" } resolution = 3.45 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= 0.002 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6995 atoms to isotropic. 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 115 5.16 5 C 8400 2.51 5 N 2285 2.21 5 O 2535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13335 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 527 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 514 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "A" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1626 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'HIS:plan': 2, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 38 Restraints were copied for chains: D, G, J, M, E, H, K, N, F, I, L, O Time building chain proxies: 2.21, per 1000 atoms: 0.17 Number of scatterers: 13335 At special positions: 0 Unit cell: (159.96, 155.31, 93.93, 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 115 16.00 O 2535 8.00 N 2285 7.00 C 8400 6.00 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: 1.23 Conformation dependent library (CDL) restraints added in 698.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3250 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 5 sheets defined 75.4% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'B' and resid 160 through 175 removed outlier: 3.855A pdb=" N ALA B 174 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 193 removed outlier: 4.035A pdb=" N LEU B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 removed outlier: 3.559A pdb=" N ALA B 204 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 219 Processing helix chain 'C' and resid 160 through 175 removed outlier: 3.748A pdb=" N ALA C 174 " --> pdb=" O LYS C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 193 removed outlier: 4.245A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 204 removed outlier: 3.807A pdb=" N ALA C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 219 Processing helix chain 'A' and resid 16 through 30 removed outlier: 3.576A pdb=" N LYS A 30 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 57 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 145 removed outlier: 4.027A pdb=" N ARG A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 175 removed outlier: 3.564A pdb=" N ALA A 174 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.702A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 removed outlier: 3.724A pdb=" N LEU A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'D' and resid 160 through 175 removed outlier: 3.855A pdb=" N ALA D 174 " --> pdb=" O LYS D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.036A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.559A pdb=" N ALA D 204 " --> pdb=" O THR D 200 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY D 206 " --> pdb=" O LEU D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 219 Processing helix chain 'E' and resid 160 through 175 removed outlier: 3.749A pdb=" N ALA E 174 " --> pdb=" O LYS E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 193 removed outlier: 4.245A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 204 removed outlier: 3.807A pdb=" N ALA E 204 " --> pdb=" O THR E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 219 Processing helix chain 'F' and resid 16 through 30 removed outlier: 3.577A pdb=" N LYS F 30 " --> pdb=" O VAL F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 44 Processing helix chain 'F' and resid 48 through 57 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 145 removed outlier: 4.028A pdb=" N ARG F 132 " --> pdb=" O GLU F 128 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP F 133 " --> pdb=" O ILE F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 153 Processing helix chain 'F' and resid 160 through 175 removed outlier: 3.565A pdb=" N ALA F 174 " --> pdb=" O LYS F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 193 removed outlier: 3.702A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 205 removed outlier: 3.724A pdb=" N LEU F 205 " --> pdb=" O ILE F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 219 Processing helix chain 'G' and resid 160 through 175 removed outlier: 3.855A pdb=" N ALA G 174 " --> pdb=" O LYS G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 193 removed outlier: 4.036A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL G 191 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 removed outlier: 3.559A pdb=" N ALA G 204 " --> pdb=" O THR G 200 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU G 205 " --> pdb=" O ILE G 201 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY G 206 " --> pdb=" O LEU G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 219 Processing helix chain 'H' and resid 160 through 175 removed outlier: 3.748A pdb=" N ALA H 174 " --> pdb=" O LYS H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 193 removed outlier: 4.245A pdb=" N VAL H 191 " --> pdb=" O GLU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 204 removed outlier: 3.807A pdb=" N ALA H 204 " --> pdb=" O THR H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 219 Processing helix chain 'I' and resid 16 through 30 removed outlier: 3.576A pdb=" N LYS I 30 " --> pdb=" O VAL I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 44 Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 62 through 84 Processing helix chain 'I' and resid 100 through 105 Processing helix chain 'I' and resid 110 through 120 Processing helix chain 'I' and resid 125 through 145 removed outlier: 4.028A pdb=" N ARG I 132 " --> pdb=" O GLU I 128 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP I 133 " --> pdb=" O ILE I 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 153 Processing helix chain 'I' and resid 160 through 175 removed outlier: 3.564A pdb=" N ALA I 174 " --> pdb=" O LYS I 170 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 193 removed outlier: 3.703A pdb=" N VAL I 191 " --> pdb=" O GLU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 205 removed outlier: 3.724A pdb=" N LEU I 205 " --> pdb=" O ILE I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 219 Processing helix chain 'J' and resid 160 through 175 removed outlier: 3.855A pdb=" N ALA J 174 " --> pdb=" O LYS J 170 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 193 removed outlier: 4.035A pdb=" N LEU J 190 " --> pdb=" O THR J 186 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL J 191 " --> pdb=" O GLU J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 206 removed outlier: 3.559A pdb=" N ALA J 204 " --> pdb=" O THR J 200 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU J 205 " --> pdb=" O ILE J 201 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY J 206 " --> pdb=" O LEU J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 219 Processing helix chain 'K' and resid 160 through 175 removed outlier: 3.748A pdb=" N ALA K 174 " --> pdb=" O LYS K 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 193 removed outlier: 4.246A pdb=" N VAL K 191 " --> pdb=" O GLU K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 204 removed outlier: 3.807A pdb=" N ALA K 204 " --> pdb=" O THR K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 219 Processing helix chain 'L' and resid 16 through 30 removed outlier: 3.576A pdb=" N LYS L 30 " --> pdb=" O VAL L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 44 Processing helix chain 'L' and resid 48 through 57 Processing helix chain 'L' and resid 62 through 84 Processing helix chain 'L' and resid 100 through 105 Processing helix chain 'L' and resid 110 through 120 Processing helix chain 'L' and resid 125 through 145 removed outlier: 4.027A pdb=" N ARG L 132 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP L 133 " --> pdb=" O ILE L 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 153 Processing helix chain 'L' and resid 160 through 175 removed outlier: 3.565A pdb=" N ALA L 174 " --> pdb=" O LYS L 170 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 193 removed outlier: 3.703A pdb=" N VAL L 191 " --> pdb=" O GLU L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 205 removed outlier: 3.724A pdb=" N LEU L 205 " --> pdb=" O ILE L 201 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 219 Processing helix chain 'M' and resid 160 through 175 removed outlier: 3.855A pdb=" N ALA M 174 " --> pdb=" O LYS M 170 " (cutoff:3.500A) Processing helix chain 'M' and resid 178 through 193 removed outlier: 4.036A pdb=" N LEU M 190 " --> pdb=" O THR M 186 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL M 191 " --> pdb=" O GLU M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 206 removed outlier: 3.559A pdb=" N ALA M 204 " --> pdb=" O THR M 200 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU M 205 " --> pdb=" O ILE M 201 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY M 206 " --> pdb=" O LEU M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 219 Processing helix chain 'N' and resid 160 through 175 removed outlier: 3.748A pdb=" N ALA N 174 " --> pdb=" O LYS N 170 " (cutoff:3.500A) Processing helix chain 'N' and resid 178 through 193 removed outlier: 4.245A pdb=" N VAL N 191 " --> pdb=" O GLU N 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 204 removed outlier: 3.807A pdb=" N ALA N 204 " --> pdb=" O THR N 200 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 219 Processing helix chain 'O' and resid 16 through 30 removed outlier: 3.576A pdb=" N LYS O 30 " --> pdb=" O VAL O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 44 Processing helix chain 'O' and resid 48 through 57 Processing helix chain 'O' and resid 62 through 84 Processing helix chain 'O' and resid 100 through 105 Processing helix chain 'O' and resid 110 through 120 Processing helix chain 'O' and resid 125 through 145 removed outlier: 4.027A pdb=" N ARG O 132 " --> pdb=" O GLU O 128 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP O 133 " --> pdb=" O ILE O 129 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 153 Processing helix chain 'O' and resid 160 through 175 removed outlier: 3.565A pdb=" N ALA O 174 " --> pdb=" O LYS O 170 " (cutoff:3.500A) Processing helix chain 'O' and resid 178 through 193 removed outlier: 3.703A pdb=" N VAL O 191 " --> pdb=" O GLU O 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 205 removed outlier: 3.724A pdb=" N LEU O 205 " --> pdb=" O ILE O 201 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 219 Processing sheet with id=1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=2, first strand: chain 'F' and resid 2 through 4 Processing sheet with id=3, first strand: chain 'I' and resid 2 through 4 Processing sheet with id=4, first strand: chain 'L' and resid 2 through 4 Processing sheet with id=5, first strand: chain 'O' and resid 2 through 4 840 hydrogen bonds defined for protein. 2490 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: 2.07 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4410 1.34 - 1.46: 1422 1.46 - 1.57: 7563 1.57 - 1.69: 0 1.69 - 1.81: 200 Bond restraints: 13595 Sorted by residual: bond pdb=" CB PRO I 1 " pdb=" CG PRO I 1 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.58e+00 bond pdb=" CB PRO O 1 " pdb=" CG PRO O 1 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.57e+00 bond pdb=" CB PRO F 1 " pdb=" CG PRO F 1 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.57e+00 bond pdb=" CB PRO L 1 " pdb=" CG PRO L 1 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.57e+00 bond pdb=" CB PRO A 1 " pdb=" CG PRO A 1 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.56e+00 ... (remaining 13590 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 15646 1.03 - 2.06: 2240 2.06 - 3.09: 384 3.09 - 4.12: 140 4.12 - 5.14: 30 Bond angle restraints: 18440 Sorted by residual: angle pdb=" N ALA O 177 " pdb=" CA ALA O 177 " pdb=" C ALA O 177 " ideal model delta sigma weight residual 110.24 114.10 -3.86 1.47e+00 4.63e-01 6.89e+00 angle pdb=" N ALA A 177 " pdb=" CA ALA A 177 " pdb=" C ALA A 177 " ideal model delta sigma weight residual 110.24 114.08 -3.84 1.47e+00 4.63e-01 6.84e+00 angle pdb=" N ALA I 177 " pdb=" CA ALA I 177 " pdb=" C ALA I 177 " ideal model delta sigma weight residual 110.24 114.08 -3.84 1.47e+00 4.63e-01 6.84e+00 angle pdb=" N ALA F 177 " pdb=" CA ALA F 177 " pdb=" C ALA F 177 " ideal model delta sigma weight residual 110.24 114.08 -3.84 1.47e+00 4.63e-01 6.81e+00 angle pdb=" N ALA L 177 " pdb=" CA ALA L 177 " pdb=" C ALA L 177 " ideal model delta sigma weight residual 110.24 114.07 -3.83 1.47e+00 4.63e-01 6.78e+00 ... (remaining 18435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.68: 7740 15.68 - 31.37: 450 31.37 - 47.05: 120 47.05 - 62.74: 30 62.74 - 78.42: 20 Dihedral angle restraints: 8360 sinusoidal: 3365 harmonic: 4995 Sorted by residual: dihedral pdb=" CA GLU H 175 " pdb=" C GLU H 175 " pdb=" N GLN H 176 " pdb=" CA GLN H 176 " ideal model delta harmonic sigma weight residual -180.00 -150.43 -29.57 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA GLU E 175 " pdb=" C GLU E 175 " pdb=" N GLN E 176 " pdb=" CA GLN E 176 " ideal model delta harmonic sigma weight residual -180.00 -150.44 -29.56 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA GLU C 175 " pdb=" C GLU C 175 " pdb=" N GLN C 176 " pdb=" CA GLN C 176 " ideal model delta harmonic sigma weight residual -180.00 -150.45 -29.55 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 8357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1129 0.033 - 0.065: 610 0.065 - 0.098: 226 0.098 - 0.131: 97 0.131 - 0.164: 23 Chirality restraints: 2085 Sorted by residual: chirality pdb=" CA LYS I 30 " pdb=" N LYS I 30 " pdb=" C LYS I 30 " pdb=" CB LYS I 30 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CA LYS A 30 " pdb=" N LYS A 30 " pdb=" C LYS A 30 " pdb=" CB LYS A 30 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.60e-01 chirality pdb=" CA LYS L 30 " pdb=" N LYS L 30 " pdb=" C LYS L 30 " pdb=" CB LYS L 30 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.51e-01 ... (remaining 2082 not shown) Planarity restraints: 2390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR L 186 " 0.024 2.00e-02 2.50e+03 4.74e-02 2.25e+01 pdb=" C THR L 186 " -0.082 2.00e-02 2.50e+03 pdb=" O THR L 186 " 0.031 2.00e-02 2.50e+03 pdb=" N GLU L 187 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR I 186 " 0.024 2.00e-02 2.50e+03 4.74e-02 2.24e+01 pdb=" C THR I 186 " -0.082 2.00e-02 2.50e+03 pdb=" O THR I 186 " 0.031 2.00e-02 2.50e+03 pdb=" N GLU I 187 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 186 " -0.024 2.00e-02 2.50e+03 4.74e-02 2.24e+01 pdb=" C THR A 186 " 0.082 2.00e-02 2.50e+03 pdb=" O THR A 186 " -0.031 2.00e-02 2.50e+03 pdb=" N GLU A 187 " -0.028 2.00e-02 2.50e+03 ... (remaining 2387 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 788 2.73 - 3.28: 14664 3.28 - 3.82: 21424 3.82 - 4.36: 26734 4.36 - 4.90: 43361 Nonbonded interactions: 106971 Sorted by model distance: nonbonded pdb=" NH1 ARG I 173 " pdb=" OE1 GLU L 28 " model vdw 2.192 3.120 nonbonded pdb=" NH1 ARG F 173 " pdb=" OE1 GLU I 28 " model vdw 2.193 3.120 nonbonded pdb=" NH1 ARG A 173 " pdb=" OE1 GLU F 28 " model vdw 2.193 3.120 nonbonded pdb=" OE1 GLU A 28 " pdb=" NH1 ARG O 173 " model vdw 2.193 3.120 nonbonded pdb=" NH1 ARG L 173 " pdb=" OE1 GLU O 28 " model vdw 2.193 3.120 ... (remaining 106966 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: 0.05 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' } 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: 5.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.620 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:1.400 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 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 0.080 13595 Z= 0.227 Angle : 0.824 5.144 18440 Z= 0.497 Chirality : 0.048 0.164 2085 Planarity : 0.009 0.086 2390 Dihedral : 12.071 78.424 5110 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: -0.83 (0.18), residues: 1685 helix: -0.79 (0.13), residues: 1145 sheet: -2.23 (0.57), residues: 45 loop : 0.82 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG L 18 TYR 0.014 0.004 TYR O 169 PHE 0.024 0.003 PHE A 40 TRP 0.017 0.004 TRP O 117 HIS 0.007 0.003 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00447 (13595) covalent geometry : angle 0.82357 (18440) hydrogen bonds : bond 0.12089 ( 840) hydrogen bonds : angle 6.27745 ( 2490) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 681 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 LYS cc_start: 0.8710 (tttm) cc_final: 0.8427 (tppt) REVERT: C 166 ASP cc_start: 0.7844 (m-30) cc_final: 0.7479 (m-30) REVERT: C 183 ASN cc_start: 0.8349 (m-40) cc_final: 0.8040 (m-40) REVERT: C 213 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7483 (mt-10) REVERT: A 41 SER cc_start: 0.9001 (t) cc_final: 0.8262 (p) REVERT: A 117 TRP cc_start: 0.8103 (m-10) cc_final: 0.7749 (m-90) REVERT: A 167 ARG cc_start: 0.7978 (mtp180) cc_final: 0.7727 (mtm-85) REVERT: A 183 ASN cc_start: 0.8615 (m-40) cc_final: 0.8405 (m-40) REVERT: A 192 GLN cc_start: 0.8591 (tp40) cc_final: 0.8216 (tm-30) REVERT: D 159 GLU cc_start: 0.8502 (tt0) cc_final: 0.8102 (tt0) REVERT: D 170 LYS cc_start: 0.8690 (tttm) cc_final: 0.8471 (tppt) REVERT: E 166 ASP cc_start: 0.7870 (m-30) cc_final: 0.7594 (m-30) REVERT: E 168 PHE cc_start: 0.8949 (t80) cc_final: 0.8661 (t80) REVERT: E 213 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7498 (mt-10) REVERT: F 39 MET cc_start: 0.8466 (mtt) cc_final: 0.8230 (mtm) REVERT: F 41 SER cc_start: 0.9200 (t) cc_final: 0.8547 (p) REVERT: F 70 LYS cc_start: 0.8720 (mmmm) cc_final: 0.8518 (mptt) REVERT: F 192 GLN cc_start: 0.8575 (tp40) cc_final: 0.8171 (tm-30) REVERT: G 170 LYS cc_start: 0.8634 (tttm) cc_final: 0.8417 (tppt) REVERT: I 41 SER cc_start: 0.9176 (t) cc_final: 0.8552 (p) REVERT: I 68 MET cc_start: 0.8790 (mtp) cc_final: 0.8313 (mtp) REVERT: I 183 ASN cc_start: 0.8494 (m-40) cc_final: 0.8254 (m-40) REVERT: I 192 GLN cc_start: 0.8506 (tp40) cc_final: 0.8209 (tm-30) REVERT: J 159 GLU cc_start: 0.8524 (tt0) cc_final: 0.8207 (tt0) REVERT: J 170 LYS cc_start: 0.8632 (tttm) cc_final: 0.8365 (tppt) REVERT: K 182 LYS cc_start: 0.8494 (mttt) cc_final: 0.8166 (mttp) REVERT: K 183 ASN cc_start: 0.8337 (m-40) cc_final: 0.7921 (m-40) REVERT: K 192 GLN cc_start: 0.8343 (mt0) cc_final: 0.8085 (tt0) REVERT: K 213 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7486 (mt-10) REVERT: L 25 LYS cc_start: 0.8326 (mttt) cc_final: 0.8102 (mtmt) REVERT: L 41 SER cc_start: 0.9112 (t) cc_final: 0.8401 (p) REVERT: L 183 ASN cc_start: 0.8512 (m-40) cc_final: 0.8091 (m-40) REVERT: L 192 GLN cc_start: 0.8518 (tp40) cc_final: 0.8110 (tm-30) REVERT: L 195 ASN cc_start: 0.8522 (p0) cc_final: 0.8064 (p0) REVERT: L 215 MET cc_start: 0.8794 (mtp) cc_final: 0.8589 (mtm) REVERT: M 170 LYS cc_start: 0.8660 (tttm) cc_final: 0.8402 (tppt) REVERT: N 213 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7530 (mt-10) REVERT: O 39 MET cc_start: 0.8458 (mtt) cc_final: 0.8178 (mtp) REVERT: O 41 SER cc_start: 0.9124 (t) cc_final: 0.8407 (p) REVERT: O 117 TRP cc_start: 0.8111 (m-10) cc_final: 0.7518 (m-90) REVERT: O 183 ASN cc_start: 0.8599 (m-40) cc_final: 0.8372 (m-40) REVERT: O 192 GLN cc_start: 0.8636 (tp40) cc_final: 0.8299 (tm-30) REVERT: O 214 MET cc_start: 0.9045 (mtp) cc_final: 0.8842 (mtm) outliers start: 0 outliers final: 0 residues processed: 681 average time/residue: 0.1462 time to fit residues: 136.3773 Evaluate side-chains 495 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 495 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.0570 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN F 50 GLN I 120 HIS M 179 GLN M 219 GLN O 50 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.132602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.100083 restraints weight = 22862.026| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.55 r_work: 0.3134 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13595 Z= 0.140 Angle : 0.621 9.846 18440 Z= 0.324 Chirality : 0.041 0.152 2085 Planarity : 0.005 0.037 2390 Dihedral : 5.147 26.273 1820 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer: Outliers : 2.39 % Allowed : 11.69 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 1.33 (0.19), residues: 1685 helix: 0.89 (0.14), residues: 1160 sheet: -1.88 (0.64), residues: 45 loop : 1.58 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 82 TYR 0.016 0.002 TYR H 164 PHE 0.013 0.001 PHE L 40 TRP 0.009 0.001 TRP O 184 HIS 0.003 0.000 HIS I 120 Details of bonding type rmsd covalent geometry : bond 0.00326 (13595) covalent geometry : angle 0.62132 (18440) hydrogen bonds : bond 0.04552 ( 840) hydrogen bonds : angle 4.44282 ( 2490) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 555 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8690 (tp30) cc_final: 0.8375 (tp30) REVERT: C 166 ASP cc_start: 0.7931 (m-30) cc_final: 0.7539 (m-30) REVERT: C 168 PHE cc_start: 0.8809 (t80) cc_final: 0.8266 (t80) REVERT: C 200 THR cc_start: 0.8789 (m) cc_final: 0.8485 (p) REVERT: C 213 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8033 (mt-10) REVERT: A 154 ARG cc_start: 0.8604 (mtp85) cc_final: 0.8237 (mtp85) REVERT: A 199 LYS cc_start: 0.8908 (tttt) cc_final: 0.8629 (ttmt) REVERT: A 210 THR cc_start: 0.9333 (p) cc_final: 0.9123 (p) REVERT: D 159 GLU cc_start: 0.8614 (tt0) cc_final: 0.8043 (tt0) REVERT: D 167 ARG cc_start: 0.8656 (mtm-85) cc_final: 0.8175 (mtm180) REVERT: D 170 LYS cc_start: 0.8870 (tttm) cc_final: 0.8542 (tppt) REVERT: D 198 CYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8420 (m) REVERT: E 166 ASP cc_start: 0.8190 (m-30) cc_final: 0.7919 (m-30) REVERT: E 200 THR cc_start: 0.8737 (m) cc_final: 0.8493 (p) REVERT: E 213 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7940 (mt-10) REVERT: F 3 VAL cc_start: 0.9070 (t) cc_final: 0.8856 (m) REVERT: F 70 LYS cc_start: 0.8869 (mmmm) cc_final: 0.8430 (mptt) REVERT: F 130 TYR cc_start: 0.9304 (t80) cc_final: 0.8954 (t80) REVERT: F 199 LYS cc_start: 0.8903 (tttt) cc_final: 0.8666 (ttmt) REVERT: G 170 LYS cc_start: 0.8866 (tttm) cc_final: 0.8638 (tptt) REVERT: H 183 ASN cc_start: 0.8285 (m-40) cc_final: 0.8077 (m-40) REVERT: H 200 THR cc_start: 0.8790 (m) cc_final: 0.8575 (p) REVERT: H 213 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7950 (mt-10) REVERT: I 210 THR cc_start: 0.9343 (p) cc_final: 0.9125 (p) REVERT: J 170 LYS cc_start: 0.8883 (tttm) cc_final: 0.8630 (tppt) REVERT: K 166 ASP cc_start: 0.7969 (m-30) cc_final: 0.7681 (m-30) REVERT: K 167 ARG cc_start: 0.8324 (mtp85) cc_final: 0.8046 (mtp85) REVERT: K 192 GLN cc_start: 0.8375 (mt0) cc_final: 0.8132 (tt0) REVERT: K 200 THR cc_start: 0.8853 (m) cc_final: 0.8610 (p) REVERT: K 213 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8057 (mt-10) REVERT: L 179 GLN cc_start: 0.9168 (tp40) cc_final: 0.8739 (tp40) REVERT: L 183 ASN cc_start: 0.8658 (m-40) cc_final: 0.8391 (m-40) REVERT: L 192 GLN cc_start: 0.8776 (tp40) cc_final: 0.8355 (tm-30) REVERT: L 195 ASN cc_start: 0.8554 (p0) cc_final: 0.8243 (p0) REVERT: L 213 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8338 (mp0) REVERT: M 170 LYS cc_start: 0.8894 (tttm) cc_final: 0.8607 (tppt) REVERT: N 168 PHE cc_start: 0.8947 (t80) cc_final: 0.8742 (t80) REVERT: N 170 LYS cc_start: 0.8725 (ttpp) cc_final: 0.8429 (ttmm) REVERT: N 200 THR cc_start: 0.8827 (m) cc_final: 0.8601 (p) REVERT: N 213 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7992 (mt-10) REVERT: O 3 VAL cc_start: 0.9048 (t) cc_final: 0.8847 (m) REVERT: O 183 ASN cc_start: 0.8695 (m-40) cc_final: 0.8488 (m-40) outliers start: 34 outliers final: 14 residues processed: 579 average time/residue: 0.1457 time to fit residues: 116.0226 Evaluate side-chains 501 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 486 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 178 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 100 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 134 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 156 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 GLN ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 219 GLN 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 = 0.131812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.099043 restraints weight = 22704.362| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.43 r_work: 0.3079 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13595 Z= 0.128 Angle : 0.576 9.521 18440 Z= 0.301 Chirality : 0.041 0.159 2085 Planarity : 0.005 0.041 2390 Dihedral : 4.713 19.857 1820 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.54 % Allowed : 14.79 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 1.52 (0.20), residues: 1685 helix: 1.01 (0.15), residues: 1180 sheet: -1.77 (0.68), residues: 45 loop : 1.76 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 132 TYR 0.018 0.001 TYR C 164 PHE 0.020 0.001 PHE E 168 TRP 0.009 0.001 TRP O 184 HIS 0.003 0.000 HIS I 120 Details of bonding type rmsd covalent geometry : bond 0.00292 (13595) covalent geometry : angle 0.57616 (18440) hydrogen bonds : bond 0.04094 ( 840) hydrogen bonds : angle 4.18028 ( 2490) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 503 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8690 (tp30) cc_final: 0.8404 (tp30) REVERT: C 166 ASP cc_start: 0.7877 (m-30) cc_final: 0.7524 (m-30) REVERT: C 168 PHE cc_start: 0.8533 (t80) cc_final: 0.8280 (t80) REVERT: C 200 THR cc_start: 0.8710 (m) cc_final: 0.8452 (p) REVERT: C 213 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7934 (mt-10) REVERT: A 68 MET cc_start: 0.8595 (mtp) cc_final: 0.8364 (mtm) REVERT: D 170 LYS cc_start: 0.8815 (tttm) cc_final: 0.8554 (tppt) REVERT: E 166 ASP cc_start: 0.7763 (m-30) cc_final: 0.7491 (m-30) REVERT: E 168 PHE cc_start: 0.8324 (t80) cc_final: 0.7928 (t80) REVERT: E 200 THR cc_start: 0.8681 (m) cc_final: 0.8471 (p) REVERT: E 213 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8027 (mp0) REVERT: F 3 VAL cc_start: 0.9068 (t) cc_final: 0.8846 (m) REVERT: F 70 LYS cc_start: 0.8859 (mmmm) cc_final: 0.8511 (mptt) REVERT: G 176 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7651 (mm-40) REVERT: H 183 ASN cc_start: 0.8289 (m-40) cc_final: 0.8051 (m-40) REVERT: H 213 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7914 (mt-10) REVERT: K 200 THR cc_start: 0.8829 (m) cc_final: 0.8589 (p) REVERT: K 213 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8071 (mt-10) REVERT: L 192 GLN cc_start: 0.8741 (tp40) cc_final: 0.8412 (tm-30) REVERT: M 170 LYS cc_start: 0.8851 (tttm) cc_final: 0.8630 (tppt) REVERT: M 199 LYS cc_start: 0.9055 (ttmm) cc_final: 0.8850 (ttmt) REVERT: N 170 LYS cc_start: 0.8723 (ttpp) cc_final: 0.8490 (ttmm) REVERT: N 213 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8012 (mt-10) REVERT: N 214 MET cc_start: 0.8925 (mtm) cc_final: 0.8698 (ttm) REVERT: O 192 GLN cc_start: 0.8650 (tp40) cc_final: 0.8310 (tm-30) outliers start: 36 outliers final: 23 residues processed: 519 average time/residue: 0.1440 time to fit residues: 102.9631 Evaluate side-chains 479 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 456 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain O residue 178 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 65 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 114 optimal weight: 0.0870 chunk 76 optimal weight: 0.0170 chunk 38 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 159 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 GLN A 183 ASN L 179 GLN L 183 ASN L 193 ASN M 155 GLN M 219 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.133431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.099419 restraints weight = 22728.271| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.61 r_work: 0.3114 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13595 Z= 0.151 Angle : 0.579 7.502 18440 Z= 0.304 Chirality : 0.041 0.168 2085 Planarity : 0.005 0.042 2390 Dihedral : 4.604 21.323 1820 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.68 % Allowed : 16.76 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 1.50 (0.20), residues: 1685 helix: 1.06 (0.15), residues: 1185 sheet: -1.68 (0.69), residues: 45 loop : 1.52 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 82 TYR 0.009 0.001 TYR E 164 PHE 0.016 0.001 PHE E 168 TRP 0.009 0.001 TRP O 184 HIS 0.001 0.000 HIS L 12 Details of bonding type rmsd covalent geometry : bond 0.00363 (13595) covalent geometry : angle 0.57919 (18440) hydrogen bonds : bond 0.03944 ( 840) hydrogen bonds : angle 4.23902 ( 2490) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 464 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8736 (tp30) cc_final: 0.8464 (tp30) REVERT: C 166 ASP cc_start: 0.7858 (m-30) cc_final: 0.7533 (m-30) REVERT: C 168 PHE cc_start: 0.8572 (t80) cc_final: 0.8311 (t80) REVERT: C 200 THR cc_start: 0.8736 (m) cc_final: 0.8483 (p) REVERT: C 201 ILE cc_start: 0.9010 (mm) cc_final: 0.8791 (mm) REVERT: A 68 MET cc_start: 0.8592 (mtp) cc_final: 0.8359 (mtm) REVERT: A 199 LYS cc_start: 0.8976 (ttmt) cc_final: 0.8758 (ttmt) REVERT: D 157 PRO cc_start: 0.8521 (Cg_endo) cc_final: 0.8297 (Cg_exo) REVERT: D 170 LYS cc_start: 0.8845 (tttm) cc_final: 0.8597 (tppt) REVERT: E 166 ASP cc_start: 0.7946 (m-30) cc_final: 0.7708 (m-30) REVERT: E 213 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8090 (mp0) REVERT: F 3 VAL cc_start: 0.9036 (t) cc_final: 0.8791 (m) REVERT: F 70 LYS cc_start: 0.8919 (mmmm) cc_final: 0.8537 (mmtm) REVERT: H 168 PHE cc_start: 0.8237 (t80) cc_final: 0.7954 (t80) REVERT: H 171 THR cc_start: 0.8832 (m) cc_final: 0.8624 (p) REVERT: H 213 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8024 (mt-10) REVERT: K 200 THR cc_start: 0.8825 (m) cc_final: 0.8601 (p) REVERT: K 203 LYS cc_start: 0.8741 (mmtt) cc_final: 0.8476 (mmtp) REVERT: K 213 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8163 (mt-10) REVERT: K 215 MET cc_start: 0.8431 (mtp) cc_final: 0.8167 (mtp) REVERT: L 192 GLN cc_start: 0.8887 (tp40) cc_final: 0.8353 (tm-30) REVERT: M 170 LYS cc_start: 0.8836 (tttm) cc_final: 0.8619 (tppt) REVERT: M 199 LYS cc_start: 0.8863 (ttmm) cc_final: 0.8611 (ttmt) REVERT: N 170 LYS cc_start: 0.8723 (ttpp) cc_final: 0.8466 (ttmm) REVERT: N 213 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8101 (mt-10) REVERT: O 192 GLN cc_start: 0.8739 (tp40) cc_final: 0.8293 (tm-30) outliers start: 38 outliers final: 23 residues processed: 482 average time/residue: 0.1387 time to fit residues: 93.1617 Evaluate side-chains 457 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 434 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 124 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 86 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.134205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.100434 restraints weight = 22684.344| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.61 r_work: 0.3130 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13595 Z= 0.131 Angle : 0.552 7.156 18440 Z= 0.289 Chirality : 0.041 0.161 2085 Planarity : 0.005 0.042 2390 Dihedral : 4.466 20.851 1820 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.68 % Allowed : 17.32 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 1.60 (0.20), residues: 1685 helix: 1.13 (0.15), residues: 1185 sheet: -1.59 (0.70), residues: 45 loop : 1.56 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 82 TYR 0.010 0.001 TYR E 164 PHE 0.016 0.001 PHE N 168 TRP 0.009 0.001 TRP O 184 HIS 0.001 0.000 HIS F 12 Details of bonding type rmsd covalent geometry : bond 0.00307 (13595) covalent geometry : angle 0.55152 (18440) hydrogen bonds : bond 0.03802 ( 840) hydrogen bonds : angle 4.17026 ( 2490) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 458 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8737 (tp30) cc_final: 0.8486 (tp30) REVERT: C 166 ASP cc_start: 0.7350 (m-30) cc_final: 0.7016 (m-30) REVERT: C 200 THR cc_start: 0.8777 (m) cc_final: 0.8552 (p) REVERT: C 201 ILE cc_start: 0.9031 (mm) cc_final: 0.8808 (mm) REVERT: C 213 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7954 (mt-10) REVERT: A 68 MET cc_start: 0.8569 (mtp) cc_final: 0.8329 (mtm) REVERT: A 176 GLN cc_start: 0.8372 (tt0) cc_final: 0.8086 (tp40) REVERT: A 199 LYS cc_start: 0.9012 (ttmt) cc_final: 0.8792 (ttmt) REVERT: D 170 LYS cc_start: 0.8817 (tttm) cc_final: 0.8585 (tppt) REVERT: D 203 LYS cc_start: 0.8457 (mtpp) cc_final: 0.8118 (mtmt) REVERT: E 166 ASP cc_start: 0.7752 (m-30) cc_final: 0.7488 (m-30) REVERT: E 213 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8029 (mp0) REVERT: F 3 VAL cc_start: 0.9037 (t) cc_final: 0.8806 (m) REVERT: F 70 LYS cc_start: 0.8919 (mmmm) cc_final: 0.8544 (mmtm) REVERT: G 158 LYS cc_start: 0.8661 (mmtm) cc_final: 0.8335 (tppt) REVERT: H 168 PHE cc_start: 0.7935 (t80) cc_final: 0.7609 (t80) REVERT: H 171 THR cc_start: 0.8851 (m) cc_final: 0.8580 (p) REVERT: H 183 ASN cc_start: 0.8206 (m-40) cc_final: 0.7949 (m-40) REVERT: H 213 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8000 (mp0) REVERT: J 158 LYS cc_start: 0.8433 (mmtm) cc_final: 0.8229 (tppt) REVERT: K 200 THR cc_start: 0.8783 (m) cc_final: 0.8572 (p) REVERT: K 213 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8147 (mt-10) REVERT: M 167 ARG cc_start: 0.8693 (ttp80) cc_final: 0.8439 (ttp-170) REVERT: M 199 LYS cc_start: 0.8799 (ttmm) cc_final: 0.8539 (ttmt) REVERT: N 213 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8171 (mp0) REVERT: O 111 LEU cc_start: 0.8633 (tp) cc_final: 0.8416 (mp) REVERT: O 192 GLN cc_start: 0.8659 (tp40) cc_final: 0.8302 (tm-30) outliers start: 38 outliers final: 20 residues processed: 474 average time/residue: 0.1374 time to fit residues: 91.1370 Evaluate side-chains 452 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 432 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain M residue 221 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 119 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 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 193 ASN O 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.134971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.101297 restraints weight = 22534.719| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.60 r_work: 0.3140 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13595 Z= 0.130 Angle : 0.565 10.507 18440 Z= 0.296 Chirality : 0.040 0.161 2085 Planarity : 0.005 0.041 2390 Dihedral : 4.379 20.867 1820 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.46 % Allowed : 18.45 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 1.66 (0.20), residues: 1685 helix: 1.19 (0.15), residues: 1175 sheet: -1.30 (0.70), residues: 45 loop : 1.52 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 82 TYR 0.010 0.001 TYR E 164 PHE 0.011 0.001 PHE H 168 TRP 0.009 0.001 TRP O 184 HIS 0.001 0.000 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00306 (13595) covalent geometry : angle 0.56485 (18440) hydrogen bonds : bond 0.03719 ( 840) hydrogen bonds : angle 4.21154 ( 2490) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 454 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8697 (tp30) cc_final: 0.8495 (tp30) REVERT: C 166 ASP cc_start: 0.7340 (m-30) cc_final: 0.7039 (m-30) REVERT: C 213 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8114 (mp0) REVERT: A 68 MET cc_start: 0.8564 (mtp) cc_final: 0.8325 (mtm) REVERT: A 176 GLN cc_start: 0.8318 (tt0) cc_final: 0.8065 (tp40) REVERT: A 192 GLN cc_start: 0.8875 (tp40) cc_final: 0.8391 (tm-30) REVERT: A 199 LYS cc_start: 0.9050 (ttmt) cc_final: 0.8769 (ttmt) REVERT: D 170 LYS cc_start: 0.8817 (tttm) cc_final: 0.8592 (tppt) REVERT: E 166 ASP cc_start: 0.7734 (m-30) cc_final: 0.7495 (m-30) REVERT: E 213 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8019 (mp0) REVERT: F 70 LYS cc_start: 0.8929 (mmmm) cc_final: 0.8592 (mmtm) REVERT: G 158 LYS cc_start: 0.8684 (mmtm) cc_final: 0.8335 (tppt) REVERT: H 168 PHE cc_start: 0.8073 (t80) cc_final: 0.7782 (t80) REVERT: H 171 THR cc_start: 0.8826 (m) cc_final: 0.8583 (p) REVERT: H 183 ASN cc_start: 0.8125 (m-40) cc_final: 0.7896 (m-40) REVERT: H 213 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7971 (mp0) REVERT: J 158 LYS cc_start: 0.8384 (mmtm) cc_final: 0.8133 (tppt) REVERT: K 167 ARG cc_start: 0.8335 (mtp85) cc_final: 0.7982 (mtm-85) REVERT: K 213 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8105 (mt-10) REVERT: M 199 LYS cc_start: 0.8799 (ttmm) cc_final: 0.8560 (ttpt) REVERT: N 166 ASP cc_start: 0.7663 (m-30) cc_final: 0.7206 (m-30) REVERT: N 168 PHE cc_start: 0.8345 (t80) cc_final: 0.7906 (t80) REVERT: N 213 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8028 (mt-10) REVERT: O 70 LYS cc_start: 0.8668 (mptt) cc_final: 0.8369 (mptt) REVERT: O 192 GLN cc_start: 0.8667 (tp40) cc_final: 0.8324 (tm-30) outliers start: 35 outliers final: 24 residues processed: 468 average time/residue: 0.1352 time to fit residues: 89.0155 Evaluate side-chains 449 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 425 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 218 CYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain M residue 218 CYS Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain O residue 124 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 140 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 137 optimal weight: 0.0870 chunk 67 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 overall best weight: 0.9360 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.133056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.100375 restraints weight = 22569.046| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.50 r_work: 0.3147 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13595 Z= 0.136 Angle : 0.565 11.230 18440 Z= 0.297 Chirality : 0.041 0.163 2085 Planarity : 0.005 0.041 2390 Dihedral : 4.357 21.198 1820 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.68 % Allowed : 19.65 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 1.65 (0.20), residues: 1685 helix: 1.16 (0.15), residues: 1175 sheet: -1.22 (0.69), residues: 45 loop : 1.58 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 82 TYR 0.011 0.001 TYR E 164 PHE 0.012 0.001 PHE H 168 TRP 0.012 0.001 TRP N 184 HIS 0.001 0.000 HIS F 12 Details of bonding type rmsd covalent geometry : bond 0.00321 (13595) covalent geometry : angle 0.56474 (18440) hydrogen bonds : bond 0.03761 ( 840) hydrogen bonds : angle 4.30763 ( 2490) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 441 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8702 (tp30) cc_final: 0.8480 (tp30) REVERT: C 166 ASP cc_start: 0.7350 (m-30) cc_final: 0.7041 (m-30) REVERT: C 213 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8043 (mp0) REVERT: A 192 GLN cc_start: 0.8842 (tp40) cc_final: 0.8364 (tm-30) REVERT: A 199 LYS cc_start: 0.9075 (ttmt) cc_final: 0.8804 (ttmt) REVERT: E 166 ASP cc_start: 0.7886 (m-30) cc_final: 0.7667 (m-30) REVERT: E 213 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8018 (mp0) REVERT: F 70 LYS cc_start: 0.8934 (mmmm) cc_final: 0.8602 (mmtm) REVERT: G 158 LYS cc_start: 0.8711 (mmtm) cc_final: 0.8345 (tppt) REVERT: H 168 PHE cc_start: 0.8169 (t80) cc_final: 0.7886 (t80) REVERT: H 171 THR cc_start: 0.8852 (m) cc_final: 0.8601 (p) REVERT: H 183 ASN cc_start: 0.8199 (m-40) cc_final: 0.7785 (m-40) REVERT: H 213 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7972 (mp0) REVERT: K 175 GLU cc_start: 0.5099 (mt-10) cc_final: 0.4875 (mt-10) REVERT: K 213 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8064 (mt-10) REVERT: L 195 ASN cc_start: 0.8368 (p0) cc_final: 0.7591 (p0) REVERT: N 166 ASP cc_start: 0.7919 (m-30) cc_final: 0.7458 (m-30) REVERT: N 213 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7976 (mt-10) REVERT: O 192 GLN cc_start: 0.8654 (tp40) cc_final: 0.8404 (tm-30) outliers start: 38 outliers final: 31 residues processed: 458 average time/residue: 0.1366 time to fit residues: 88.1778 Evaluate side-chains 445 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 414 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain H residue 215 MET Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 218 CYS Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain O residue 124 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 18 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 156 optimal weight: 0.5980 chunk 121 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 179 GLN I 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.135375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.101578 restraints weight = 22458.523| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.61 r_work: 0.3154 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13595 Z= 0.132 Angle : 0.571 10.782 18440 Z= 0.302 Chirality : 0.041 0.175 2085 Planarity : 0.005 0.041 2390 Dihedral : 4.310 21.515 1820 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.68 % Allowed : 20.07 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 1.69 (0.20), residues: 1685 helix: 1.19 (0.15), residues: 1175 sheet: -1.14 (0.69), residues: 45 loop : 1.59 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 82 TYR 0.009 0.001 TYR E 164 PHE 0.034 0.001 PHE C 168 TRP 0.010 0.001 TRP F 184 HIS 0.001 0.000 HIS F 12 Details of bonding type rmsd covalent geometry : bond 0.00311 (13595) covalent geometry : angle 0.57060 (18440) hydrogen bonds : bond 0.03792 ( 840) hydrogen bonds : angle 4.37289 ( 2490) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 430 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8682 (tp30) cc_final: 0.8464 (tp30) REVERT: C 166 ASP cc_start: 0.7367 (m-30) cc_final: 0.7039 (m-30) REVERT: C 213 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8046 (mp0) REVERT: A 68 MET cc_start: 0.8566 (mtp) cc_final: 0.8285 (mtm) REVERT: A 199 LYS cc_start: 0.9040 (ttmt) cc_final: 0.8777 (ttmt) REVERT: E 166 ASP cc_start: 0.7899 (m-30) cc_final: 0.7672 (m-30) REVERT: E 213 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8016 (mp0) REVERT: F 70 LYS cc_start: 0.8962 (mmmm) cc_final: 0.8614 (mmtm) REVERT: G 158 LYS cc_start: 0.8633 (mmtm) cc_final: 0.8336 (tppt) REVERT: G 183 ASN cc_start: 0.8239 (m-40) cc_final: 0.8038 (m-40) REVERT: H 168 PHE cc_start: 0.8189 (t80) cc_final: 0.7889 (t80) REVERT: H 171 THR cc_start: 0.8822 (m) cc_final: 0.8583 (p) REVERT: H 183 ASN cc_start: 0.8095 (m-40) cc_final: 0.7859 (m-40) REVERT: H 213 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7898 (mt-10) REVERT: I 152 ASP cc_start: 0.8974 (m-30) cc_final: 0.8712 (m-30) REVERT: K 213 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8102 (mt-10) REVERT: L 152 ASP cc_start: 0.8942 (m-30) cc_final: 0.8652 (m-30) REVERT: L 195 ASN cc_start: 0.8288 (p0) cc_final: 0.8029 (p0) REVERT: M 199 LYS cc_start: 0.8560 (ttmt) cc_final: 0.8165 (ttmt) REVERT: N 213 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7933 (mt-10) REVERT: O 39 MET cc_start: 0.8860 (mtm) cc_final: 0.8530 (mtm) outliers start: 38 outliers final: 33 residues processed: 448 average time/residue: 0.1360 time to fit residues: 85.8688 Evaluate side-chains 441 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 408 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain H residue 215 MET Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 218 CYS Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain M residue 218 CYS Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain O residue 18 ARG Chi-restraints excluded: chain O residue 111 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 13 optimal weight: 0.0770 chunk 76 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 146 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 63 GLN L 193 ASN O 50 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.133854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.099785 restraints weight = 22768.864| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.62 r_work: 0.3130 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13595 Z= 0.155 Angle : 0.609 11.406 18440 Z= 0.322 Chirality : 0.043 0.167 2085 Planarity : 0.005 0.041 2390 Dihedral : 4.368 22.115 1820 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.61 % Allowed : 21.34 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 1.54 (0.20), residues: 1685 helix: 1.07 (0.15), residues: 1175 sheet: -1.11 (0.70), residues: 45 loop : 1.53 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 82 TYR 0.010 0.001 TYR E 164 PHE 0.032 0.001 PHE C 168 TRP 0.011 0.001 TRP F 184 HIS 0.006 0.001 HIS I 120 Details of bonding type rmsd covalent geometry : bond 0.00377 (13595) covalent geometry : angle 0.60880 (18440) hydrogen bonds : bond 0.03886 ( 840) hydrogen bonds : angle 4.53755 ( 2490) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 415 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8728 (tp30) cc_final: 0.8516 (tp30) REVERT: C 166 ASP cc_start: 0.7381 (m-30) cc_final: 0.7052 (m-30) REVERT: C 213 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8000 (mp0) REVERT: A 70 LYS cc_start: 0.8621 (mptt) cc_final: 0.8349 (mptt) REVERT: E 166 ASP cc_start: 0.7900 (m-30) cc_final: 0.7690 (m-30) REVERT: E 213 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8024 (mp0) REVERT: F 70 LYS cc_start: 0.8973 (mmmm) cc_final: 0.8637 (mmtm) REVERT: H 168 PHE cc_start: 0.8281 (t80) cc_final: 0.7984 (t80) REVERT: H 171 THR cc_start: 0.8858 (m) cc_final: 0.8599 (p) REVERT: H 213 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8009 (mp0) REVERT: I 152 ASP cc_start: 0.8977 (m-30) cc_final: 0.8652 (m-30) REVERT: K 175 GLU cc_start: 0.4125 (mt-10) cc_final: 0.3900 (mt-10) REVERT: K 199 LYS cc_start: 0.8683 (ttpt) cc_final: 0.8459 (mttt) REVERT: M 199 LYS cc_start: 0.8573 (ttmt) cc_final: 0.8362 (ttpt) REVERT: N 167 ARG cc_start: 0.8218 (mtp180) cc_final: 0.7922 (mtp180) REVERT: N 213 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8082 (mp0) outliers start: 37 outliers final: 31 residues processed: 436 average time/residue: 0.1321 time to fit residues: 81.6528 Evaluate side-chains 437 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 406 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain H residue 215 MET Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 218 CYS Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain M residue 218 CYS Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain O residue 18 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 41 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 157 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 113 optimal weight: 0.6980 chunk 46 optimal weight: 0.0870 chunk 57 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 176 GLN O 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.135996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.101952 restraints weight = 22559.210| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.62 r_work: 0.3159 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13595 Z= 0.133 Angle : 0.600 11.237 18440 Z= 0.320 Chirality : 0.042 0.169 2085 Planarity : 0.005 0.042 2390 Dihedral : 4.318 21.618 1820 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.04 % Allowed : 21.69 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 1.61 (0.20), residues: 1685 helix: 1.09 (0.15), residues: 1170 sheet: -0.96 (0.70), residues: 45 loop : 1.63 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 132 TYR 0.009 0.001 TYR K 164 PHE 0.027 0.001 PHE C 168 TRP 0.012 0.001 TRP C 184 HIS 0.005 0.001 HIS I 120 Details of bonding type rmsd covalent geometry : bond 0.00314 (13595) covalent geometry : angle 0.60045 (18440) hydrogen bonds : bond 0.03833 ( 840) hydrogen bonds : angle 4.53350 ( 2490) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 413 time to evaluate : 0.556 Fit side-chains REVERT: B 172 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8620 (tp) REVERT: C 166 ASP cc_start: 0.7379 (m-30) cc_final: 0.7052 (m-30) REVERT: C 175 GLU cc_start: 0.4193 (mt-10) cc_final: 0.3990 (mt-10) REVERT: C 213 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7946 (mp0) REVERT: A 68 MET cc_start: 0.8533 (mtp) cc_final: 0.8227 (mtm) REVERT: E 166 ASP cc_start: 0.7918 (m-30) cc_final: 0.7718 (m-30) REVERT: E 213 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8006 (mp0) REVERT: F 70 LYS cc_start: 0.8981 (mmmm) cc_final: 0.8649 (mmtm) REVERT: F 130 TYR cc_start: 0.9298 (t80) cc_final: 0.9051 (t80) REVERT: H 168 PHE cc_start: 0.8232 (t80) cc_final: 0.7928 (t80) REVERT: H 171 THR cc_start: 0.8834 (m) cc_final: 0.8597 (p) REVERT: H 213 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7876 (mt-10) REVERT: I 70 LYS cc_start: 0.8574 (mptt) cc_final: 0.8251 (mmtt) REVERT: I 143 ARG cc_start: 0.8854 (ttp-110) cc_final: 0.8634 (ttp-170) REVERT: I 152 ASP cc_start: 0.8982 (m-30) cc_final: 0.8714 (m-30) REVERT: K 199 LYS cc_start: 0.8668 (ttpt) cc_final: 0.8461 (mttt) REVERT: K 213 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8033 (mt-10) REVERT: M 199 LYS cc_start: 0.8564 (ttmt) cc_final: 0.8362 (ttpt) REVERT: N 164 TYR cc_start: 0.7936 (t80) cc_final: 0.7736 (t80) REVERT: N 213 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8055 (mp0) outliers start: 29 outliers final: 27 residues processed: 429 average time/residue: 0.1308 time to fit residues: 79.5929 Evaluate side-chains 430 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 402 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain H residue 215 MET Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 218 CYS Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain M residue 218 CYS Chi-restraints excluded: chain O residue 18 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 116 optimal weight: 0.8980 chunk 136 optimal weight: 0.5980 chunk 133 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 71 optimal weight: 0.0970 chunk 70 optimal weight: 4.9990 chunk 31 optimal weight: 0.0970 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.136439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.103713 restraints weight = 22514.058| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.54 r_work: 0.3210 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13595 Z= 0.126 Angle : 0.594 10.873 18440 Z= 0.316 Chirality : 0.042 0.171 2085 Planarity : 0.005 0.043 2390 Dihedral : 4.245 22.011 1820 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.90 % Allowed : 22.39 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 aren not related in a simple way. whole: 1.72 (0.20), residues: 1685 helix: 1.17 (0.15), residues: 1165 sheet: -0.76 (0.72), residues: 45 loop : 1.65 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 82 TYR 0.009 0.001 TYR K 164 PHE 0.027 0.001 PHE C 168 TRP 0.011 0.001 TRP O 184 HIS 0.005 0.000 HIS I 120 Details of bonding type rmsd covalent geometry : bond 0.00296 (13595) covalent geometry : angle 0.59412 (18440) hydrogen bonds : bond 0.03725 ( 840) hydrogen bonds : angle 4.51012 ( 2490) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4037.22 seconds wall clock time: 69 minutes 59.58 seconds (4199.58 seconds total)