Starting phenix.real_space_refine on Sun Aug 24 09:25:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cl4_16712/08_2025/8cl4_16712.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cl4_16712/08_2025/8cl4_16712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cl4_16712/08_2025/8cl4_16712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cl4_16712/08_2025/8cl4_16712.map" model { file = "/net/cci-nas-00/data/ceres_data/8cl4_16712/08_2025/8cl4_16712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cl4_16712/08_2025/8cl4_16712.cif" } resolution = 3.14 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: 1.98, per 1000 atoms: 0.15 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: 1.20 Conformation dependent library (CDL) restraints added in 702.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.41 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: 1.70 Time building geometry restraints manager: 1.46 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: 5.560 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: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.380 Find NCS groups from input model: 0.110 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 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 : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 166 ASP cc_start: 0.7780 (m-30) cc_final: 0.7438 (m-30) REVERT: C 183 ASN cc_start: 0.8263 (m-40) cc_final: 0.8010 (m-40) REVERT: C 213 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7316 (mt-10) REVERT: A 41 SER cc_start: 0.8854 (t) cc_final: 0.8203 (p) REVERT: A 117 TRP cc_start: 0.7838 (m-10) cc_final: 0.7626 (m-90) REVERT: A 183 ASN cc_start: 0.8226 (m-40) cc_final: 0.8026 (m-40) REVERT: D 159 GLU cc_start: 0.8455 (tt0) cc_final: 0.8138 (tt0) REVERT: E 166 ASP cc_start: 0.7808 (m-30) cc_final: 0.7544 (m-30) REVERT: E 168 PHE cc_start: 0.8860 (t80) cc_final: 0.8620 (t80) REVERT: E 213 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7367 (mt-10) REVERT: F 41 SER cc_start: 0.9051 (t) cc_final: 0.8514 (p) REVERT: I 25 LYS cc_start: 0.8235 (mttt) cc_final: 0.8009 (mtmt) REVERT: I 41 SER cc_start: 0.9003 (t) cc_final: 0.8500 (p) REVERT: I 68 MET cc_start: 0.8488 (mtp) cc_final: 0.7987 (mtp) REVERT: I 183 ASN cc_start: 0.8099 (m-40) cc_final: 0.7892 (m-40) REVERT: J 159 GLU cc_start: 0.8496 (tt0) cc_final: 0.8203 (tt0) REVERT: K 182 LYS cc_start: 0.8377 (mttt) cc_final: 0.8091 (mttp) REVERT: K 183 ASN cc_start: 0.8252 (m-40) cc_final: 0.7885 (m-40) REVERT: K 213 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7342 (mt-10) REVERT: L 25 LYS cc_start: 0.8204 (mttt) cc_final: 0.7974 (mtmt) REVERT: L 41 SER cc_start: 0.8927 (t) cc_final: 0.8401 (p) REVERT: L 183 ASN cc_start: 0.8055 (m-40) cc_final: 0.7679 (m-40) REVERT: L 195 ASN cc_start: 0.8189 (p0) cc_final: 0.7778 (p0) REVERT: N 213 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7350 (mt-10) REVERT: O 41 SER cc_start: 0.8938 (t) cc_final: 0.8359 (p) REVERT: O 117 TRP cc_start: 0.7806 (m-10) cc_final: 0.7417 (m-90) REVERT: O 183 ASN cc_start: 0.8214 (m-40) cc_final: 0.7989 (m-40) outliers start: 0 outliers final: 0 residues processed: 681 average time/residue: 0.1309 time to fit residues: 122.6515 Evaluate side-chains 491 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 491 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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: 0.6980 chunk 149 optimal weight: 1.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.132495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.100010 restraints weight = 22796.427| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.67 r_work: 0.3260 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13595 Z= 0.139 Angle : 0.619 9.692 18440 Z= 0.324 Chirality : 0.041 0.152 2085 Planarity : 0.005 0.037 2390 Dihedral : 5.130 26.057 1820 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer: Outliers : 2.61 % Allowed : 11.55 % Favored : 85.85 % 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: 1.30 (0.20), residues: 1685 helix: 0.88 (0.14), residues: 1170 sheet: -1.88 (0.64), residues: 45 loop : 1.56 (0.28), residues: 470 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 F 40 TRP 0.010 0.001 TRP O 184 HIS 0.003 0.000 HIS I 120 Details of bonding type rmsd covalent geometry : bond 0.00319 (13595) covalent geometry : angle 0.61930 (18440) hydrogen bonds : bond 0.04550 ( 840) hydrogen bonds : angle 4.40254 ( 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 593 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 556 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8538 (tp30) cc_final: 0.8215 (tp30) REVERT: C 166 ASP cc_start: 0.7858 (m-30) cc_final: 0.7510 (m-30) REVERT: C 168 PHE cc_start: 0.8730 (t80) cc_final: 0.8139 (t80) REVERT: C 171 THR cc_start: 0.8531 (m) cc_final: 0.8320 (p) REVERT: C 200 THR cc_start: 0.8750 (m) cc_final: 0.8435 (p) REVERT: C 213 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7927 (mt-10) REVERT: D 159 GLU cc_start: 0.8671 (tt0) cc_final: 0.7998 (tt0) REVERT: D 167 ARG cc_start: 0.8581 (mtm-85) cc_final: 0.8106 (mtm180) REVERT: D 216 THR cc_start: 0.9232 (m) cc_final: 0.9031 (p) REVERT: E 166 ASP cc_start: 0.8092 (m-30) cc_final: 0.7822 (m-30) REVERT: E 168 PHE cc_start: 0.8841 (t80) cc_final: 0.8415 (t80) REVERT: E 171 THR cc_start: 0.8632 (m) cc_final: 0.8260 (p) REVERT: E 200 THR cc_start: 0.8685 (m) cc_final: 0.8448 (p) REVERT: E 213 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7898 (mt-10) REVERT: F 3 VAL cc_start: 0.8834 (t) cc_final: 0.8603 (m) REVERT: F 66 MET cc_start: 0.8947 (tpt) cc_final: 0.8716 (tpt) REVERT: H 183 ASN cc_start: 0.8112 (m-40) cc_final: 0.7893 (m-40) REVERT: H 200 THR cc_start: 0.8730 (m) cc_final: 0.8504 (p) REVERT: H 213 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7874 (mt-10) REVERT: I 183 ASN cc_start: 0.8575 (m-40) cc_final: 0.8339 (m-40) REVERT: J 167 ARG cc_start: 0.8639 (mtm-85) cc_final: 0.8407 (ttp80) REVERT: J 216 THR cc_start: 0.9283 (m) cc_final: 0.9057 (p) REVERT: K 166 ASP cc_start: 0.7881 (m-30) cc_final: 0.7639 (m-30) REVERT: K 167 ARG cc_start: 0.8254 (mtp85) cc_final: 0.7984 (mtp85) REVERT: K 171 THR cc_start: 0.8621 (m) cc_final: 0.8262 (p) REVERT: K 182 LYS cc_start: 0.8336 (mttt) cc_final: 0.8029 (mttp) REVERT: K 200 THR cc_start: 0.8794 (m) cc_final: 0.8554 (p) REVERT: K 213 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8032 (mt-10) REVERT: L 179 GLN cc_start: 0.8966 (tp40) cc_final: 0.8471 (tp40) REVERT: L 183 ASN cc_start: 0.8525 (m-40) cc_final: 0.8200 (m-40) REVERT: L 192 GLN cc_start: 0.8448 (tm-30) cc_final: 0.8074 (tm-30) REVERT: L 195 ASN cc_start: 0.8123 (p0) cc_final: 0.7823 (p0) REVERT: L 210 THR cc_start: 0.8976 (p) cc_final: 0.8558 (p) REVERT: L 213 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8175 (mp0) REVERT: M 179 GLN cc_start: 0.6946 (mm-40) cc_final: 0.6685 (tt0) REVERT: M 183 ASN cc_start: 0.8402 (m-40) cc_final: 0.8162 (m-40) REVERT: M 198 CYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8148 (m) REVERT: N 168 PHE cc_start: 0.8829 (t80) cc_final: 0.8625 (t80) REVERT: N 170 LYS cc_start: 0.8544 (ttpp) cc_final: 0.8256 (ttmm) REVERT: N 200 THR cc_start: 0.8783 (m) cc_final: 0.8560 (p) REVERT: N 213 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7885 (mt-10) REVERT: O 183 ASN cc_start: 0.8581 (m-40) cc_final: 0.8330 (m-40) outliers start: 37 outliers final: 16 residues processed: 579 average time/residue: 0.1340 time to fit residues: 107.1615 Evaluate side-chains 499 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 482 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 178 SER 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 I residue 58 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 L residue 149 SER Chi-restraints excluded: chain M residue 198 CYS Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 178 SER Chi-restraints excluded: chain O residue 188 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 100 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 I 120 HIS ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.127985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.092359 restraints weight = 22770.823| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.87 r_work: 0.3064 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13595 Z= 0.171 Angle : 0.607 9.150 18440 Z= 0.316 Chirality : 0.043 0.154 2085 Planarity : 0.005 0.040 2390 Dihedral : 4.801 21.527 1820 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.75 % Allowed : 14.65 % Favored : 82.61 % 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: 1.35 (0.20), residues: 1685 helix: 0.92 (0.14), residues: 1185 sheet: -1.87 (0.65), residues: 45 loop : 1.58 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 132 TYR 0.018 0.001 TYR C 164 PHE 0.022 0.002 PHE H 168 TRP 0.009 0.001 TRP O 184 HIS 0.003 0.001 HIS I 120 Details of bonding type rmsd covalent geometry : bond 0.00415 (13595) covalent geometry : angle 0.60713 (18440) hydrogen bonds : bond 0.04312 ( 840) hydrogen bonds : angle 4.33941 ( 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 544 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 505 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8313 (tp30) cc_final: 0.8040 (tp30) REVERT: C 166 ASP cc_start: 0.7763 (m-30) cc_final: 0.7476 (m-30) REVERT: C 168 PHE cc_start: 0.8643 (t80) cc_final: 0.7960 (t80) REVERT: C 200 THR cc_start: 0.8648 (m) cc_final: 0.8388 (p) REVERT: C 213 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8163 (mm-30) REVERT: A 178 SER cc_start: 0.7892 (OUTLIER) cc_final: 0.7530 (p) REVERT: A 180 GLU cc_start: 0.8465 (pm20) cc_final: 0.8167 (mp0) REVERT: A 192 GLN cc_start: 0.8444 (tm-30) cc_final: 0.7678 (tm-30) REVERT: D 159 GLU cc_start: 0.8786 (tt0) cc_final: 0.8516 (tt0) REVERT: E 200 THR cc_start: 0.8579 (m) cc_final: 0.8353 (p) REVERT: E 213 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8099 (mp0) REVERT: F 3 VAL cc_start: 0.8603 (t) cc_final: 0.8333 (m) REVERT: F 66 MET cc_start: 0.8838 (tpt) cc_final: 0.8527 (tpt) REVERT: F 152 ASP cc_start: 0.8914 (m-30) cc_final: 0.8703 (m-30) REVERT: F 167 ARG cc_start: 0.8337 (mtm-85) cc_final: 0.8129 (ttp80) REVERT: H 200 THR cc_start: 0.8761 (m) cc_final: 0.8545 (p) REVERT: H 213 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8003 (mt-10) REVERT: I 183 ASN cc_start: 0.8442 (m-40) cc_final: 0.8149 (m-40) REVERT: K 200 THR cc_start: 0.8744 (m) cc_final: 0.8518 (p) REVERT: K 203 LYS cc_start: 0.8675 (mmtt) cc_final: 0.8473 (mmtp) REVERT: K 213 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8092 (mt-10) REVERT: L 179 GLN cc_start: 0.8689 (tp40) cc_final: 0.8453 (tp40) REVERT: L 183 ASN cc_start: 0.8322 (m-40) cc_final: 0.7955 (m-40) REVERT: L 192 GLN cc_start: 0.8361 (tm-30) cc_final: 0.7815 (tm-30) REVERT: M 179 GLN cc_start: 0.7229 (mm-40) cc_final: 0.6796 (tt0) REVERT: M 183 ASN cc_start: 0.7899 (m-40) cc_final: 0.7632 (m-40) REVERT: M 199 LYS cc_start: 0.8108 (ttmm) cc_final: 0.7695 (ttmt) REVERT: N 170 LYS cc_start: 0.8352 (ttpp) cc_final: 0.8114 (ttmm) REVERT: N 200 THR cc_start: 0.8724 (m) cc_final: 0.8507 (p) REVERT: N 213 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7975 (mt-10) REVERT: O 192 GLN cc_start: 0.8284 (tm-30) cc_final: 0.7470 (tm-30) outliers start: 39 outliers final: 28 residues processed: 527 average time/residue: 0.1300 time to fit residues: 94.5511 Evaluate side-chains 485 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 456 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 ASP 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 110 THR Chi-restraints excluded: chain A residue 178 SER 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 F residue 178 SER Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain I residue 63 GLN Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain M residue 198 CYS Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain O residue 2 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 65 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 114 optimal weight: 0.0030 chunk 76 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- 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 G 193 ASN ** J 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 219 GLN O 50 GLN O 176 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.131145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.098140 restraints weight = 23036.252| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.64 r_work: 0.3270 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13595 Z= 0.174 Angle : 0.600 8.056 18440 Z= 0.314 Chirality : 0.043 0.171 2085 Planarity : 0.005 0.041 2390 Dihedral : 4.647 23.476 1820 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.68 % Allowed : 16.55 % Favored : 80.77 % 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: 1.36 (0.20), residues: 1685 helix: 1.00 (0.15), residues: 1175 sheet: -1.74 (0.66), residues: 45 loop : 1.32 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 82 TYR 0.016 0.001 TYR E 164 PHE 0.022 0.001 PHE H 168 TRP 0.010 0.001 TRP F 184 HIS 0.001 0.000 HIS I 12 Details of bonding type rmsd covalent geometry : bond 0.00419 (13595) covalent geometry : angle 0.60040 (18440) hydrogen bonds : bond 0.04153 ( 840) hydrogen bonds : angle 4.34061 ( 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 504 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 466 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: B 210 THR cc_start: 0.9161 (p) cc_final: 0.7952 (p) REVERT: C 166 ASP cc_start: 0.7833 (m-30) cc_final: 0.7534 (m-30) REVERT: C 168 PHE cc_start: 0.8536 (t80) cc_final: 0.8298 (t80) REVERT: C 200 THR cc_start: 0.8743 (m) cc_final: 0.8491 (p) REVERT: C 213 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8116 (mp0) REVERT: A 192 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8316 (tm-30) REVERT: D 157 PRO cc_start: 0.8612 (Cg_endo) cc_final: 0.8400 (Cg_exo) REVERT: E 200 THR cc_start: 0.8663 (m) cc_final: 0.8462 (p) REVERT: E 213 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8081 (mp0) REVERT: F 66 MET cc_start: 0.8989 (tpt) cc_final: 0.8729 (tpt) REVERT: G 157 PRO cc_start: 0.8480 (Cg_endo) cc_final: 0.8271 (Cg_exo) REVERT: H 183 ASN cc_start: 0.8124 (m-40) cc_final: 0.7920 (m-40) REVERT: H 213 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8073 (mp0) REVERT: I 183 ASN cc_start: 0.8532 (m-40) cc_final: 0.8294 (m-40) REVERT: K 203 LYS cc_start: 0.8730 (mmtt) cc_final: 0.8473 (mmtp) REVERT: K 213 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8051 (mt-10) REVERT: M 179 GLN cc_start: 0.7433 (mm-40) cc_final: 0.7187 (tt0) REVERT: M 183 ASN cc_start: 0.8388 (m-40) cc_final: 0.8133 (m-40) REVERT: N 170 LYS cc_start: 0.8614 (ttpp) cc_final: 0.8351 (ttmm) REVERT: N 213 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8006 (mt-10) REVERT: N 214 MET cc_start: 0.8816 (mtm) cc_final: 0.8539 (mtp) REVERT: O 70 LYS cc_start: 0.8475 (mptt) cc_final: 0.8275 (mptt) outliers start: 38 outliers final: 25 residues processed: 483 average time/residue: 0.1248 time to fit residues: 84.1682 Evaluate side-chains 460 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 435 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 ASP 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 178 SER Chi-restraints excluded: chain F residue 2 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 H residue 191 VAL Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 110 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 71 GLU Chi-restraints excluded: chain M residue 198 CYS Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 111 LEU Chi-restraints excluded: chain O residue 176 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 86 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 GLN J 155 GLN L 179 GLN L 183 ASN M 219 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.132487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.099439 restraints weight = 22757.090| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.69 r_work: 0.3237 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4357 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= 0.133 Angle : 0.563 8.880 18440 Z= 0.295 Chirality : 0.041 0.163 2085 Planarity : 0.005 0.041 2390 Dihedral : 4.483 23.818 1820 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.17 % Allowed : 17.39 % Favored : 79.44 % 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: 1.13 (0.15), residues: 1175 sheet: -1.62 (0.67), residues: 45 loop : 1.36 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 82 TYR 0.013 0.001 TYR E 164 PHE 0.018 0.001 PHE H 168 TRP 0.011 0.001 TRP K 184 HIS 0.001 0.000 HIS F 12 Details of bonding type rmsd covalent geometry : bond 0.00310 (13595) covalent geometry : angle 0.56311 (18440) hydrogen bonds : bond 0.03873 ( 840) hydrogen bonds : angle 4.18490 ( 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 515 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 470 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8643 (tp30) cc_final: 0.8312 (tp30) REVERT: C 166 ASP cc_start: 0.7306 (m-30) cc_final: 0.7028 (m-30) REVERT: C 200 THR cc_start: 0.8715 (m) cc_final: 0.8478 (p) REVERT: C 213 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8052 (mp0) REVERT: E 213 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8089 (mp0) REVERT: F 66 MET cc_start: 0.8931 (tpt) cc_final: 0.8671 (tpt) REVERT: F 195 ASN cc_start: 0.8414 (p0) cc_final: 0.8175 (p0) REVERT: H 168 PHE cc_start: 0.8506 (t80) cc_final: 0.8000 (t80) REVERT: H 171 THR cc_start: 0.8701 (m) cc_final: 0.8469 (p) REVERT: I 152 ASP cc_start: 0.8982 (m-30) cc_final: 0.8760 (m-30) REVERT: I 179 GLN cc_start: 0.9072 (tp40) cc_final: 0.8837 (tp40) REVERT: I 183 ASN cc_start: 0.8557 (m-40) cc_final: 0.8204 (m-40) REVERT: I 192 GLN cc_start: 0.8670 (tm-30) cc_final: 0.7798 (tm-30) REVERT: K 213 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8045 (mt-10) REVERT: L 192 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8135 (tm-30) REVERT: M 167 ARG cc_start: 0.8684 (ttp80) cc_final: 0.8453 (ttp-170) REVERT: M 179 GLN cc_start: 0.7527 (mm-40) cc_final: 0.7202 (tt0) REVERT: M 183 ASN cc_start: 0.8272 (m-40) cc_final: 0.8018 (m-40) REVERT: N 214 MET cc_start: 0.8939 (mtm) cc_final: 0.8516 (mtp) REVERT: O 192 GLN cc_start: 0.8604 (tm-30) cc_final: 0.7704 (tm-30) outliers start: 45 outliers final: 28 residues processed: 483 average time/residue: 0.1211 time to fit residues: 82.6695 Evaluate side-chains 468 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 440 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 ASP 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 124 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain E residue 189 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 I residue 2 ILE Chi-restraints excluded: chain I residue 63 GLN Chi-restraints excluded: chain I residue 124 ILE 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 71 GLU Chi-restraints excluded: chain M residue 198 CYS Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 176 GLN 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: 4.9990 chunk 62 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 15 optimal weight: 0.0980 chunk 47 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN M 219 GLN O 50 GLN O 179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.134144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.101441 restraints weight = 22651.025| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.65 r_work: 0.3264 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4639 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= 0.131 Angle : 0.573 10.209 18440 Z= 0.299 Chirality : 0.041 0.163 2085 Planarity : 0.005 0.042 2390 Dihedral : 4.372 21.612 1820 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.66 % Allowed : 18.59 % Favored : 77.75 % 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: 1.17 (0.15), residues: 1175 sheet: -1.35 (0.67), residues: 45 loop : 1.43 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 82 TYR 0.008 0.001 TYR E 164 PHE 0.018 0.001 PHE H 168 TRP 0.010 0.001 TRP K 184 HIS 0.001 0.000 HIS I 62 Details of bonding type rmsd covalent geometry : bond 0.00306 (13595) covalent geometry : angle 0.57337 (18440) hydrogen bonds : bond 0.03778 ( 840) hydrogen bonds : angle 4.21649 ( 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 499 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 447 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8579 (tp30) cc_final: 0.8275 (tp30) REVERT: C 166 ASP cc_start: 0.7284 (m-30) cc_final: 0.6979 (m-30) REVERT: C 213 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8014 (mp0) REVERT: A 195 ASN cc_start: 0.8494 (OUTLIER) cc_final: 0.8231 (p0) REVERT: E 213 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8056 (mp0) REVERT: F 66 MET cc_start: 0.8916 (tpt) cc_final: 0.8699 (tpt) REVERT: F 152 ASP cc_start: 0.8896 (m-30) cc_final: 0.8593 (m-30) REVERT: H 168 PHE cc_start: 0.8523 (t80) cc_final: 0.7935 (t80) REVERT: H 171 THR cc_start: 0.8708 (m) cc_final: 0.8456 (p) REVERT: I 152 ASP cc_start: 0.8943 (m-30) cc_final: 0.8729 (m-30) REVERT: I 183 ASN cc_start: 0.8512 (m-40) cc_final: 0.8280 (m-40) REVERT: K 213 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7978 (mt-10) REVERT: L 185 MET cc_start: 0.8761 (mtm) cc_final: 0.8551 (mtp) REVERT: M 179 GLN cc_start: 0.7630 (mm-40) cc_final: 0.7294 (tt0) REVERT: M 183 ASN cc_start: 0.8296 (m-40) cc_final: 0.8068 (m-40) REVERT: N 168 PHE cc_start: 0.7769 (t80) cc_final: 0.7481 (t80) REVERT: N 213 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8084 (mp0) REVERT: O 192 GLN cc_start: 0.8546 (tm-30) cc_final: 0.8220 (tm-30) outliers start: 52 outliers final: 32 residues processed: 468 average time/residue: 0.1163 time to fit residues: 76.9014 Evaluate side-chains 449 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 416 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 197 ASP 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 18 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain G residue 195 ASN 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 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 18 ARG Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain M residue 198 CYS Chi-restraints excluded: chain M residue 218 CYS Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 210 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 140 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 137 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 193 ASN ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.134238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.101316 restraints weight = 22747.074| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.69 r_work: 0.3261 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4715 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= 0.134 Angle : 0.571 11.426 18440 Z= 0.299 Chirality : 0.041 0.164 2085 Planarity : 0.005 0.042 2390 Dihedral : 4.331 22.650 1820 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.31 % Allowed : 20.21 % Favored : 76.48 % 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: 1.57 (0.20), residues: 1685 helix: 1.13 (0.15), residues: 1175 sheet: -1.16 (0.68), residues: 45 loop : 1.44 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 143 TYR 0.008 0.001 TYR N 164 PHE 0.016 0.001 PHE H 168 TRP 0.011 0.001 TRP N 184 HIS 0.001 0.000 HIS I 62 Details of bonding type rmsd covalent geometry : bond 0.00315 (13595) covalent geometry : angle 0.57142 (18440) hydrogen bonds : bond 0.03796 ( 840) hydrogen bonds : angle 4.32257 ( 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 490 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 443 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8557 (tp30) cc_final: 0.8337 (tp30) REVERT: C 166 ASP cc_start: 0.7284 (m-30) cc_final: 0.7004 (m-30) REVERT: C 213 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8018 (mp0) REVERT: E 213 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8044 (mp0) REVERT: F 66 MET cc_start: 0.8904 (tpt) cc_final: 0.8671 (tpt) REVERT: F 152 ASP cc_start: 0.8917 (m-30) cc_final: 0.8601 (m-30) REVERT: H 168 PHE cc_start: 0.8628 (t80) cc_final: 0.8116 (t80) REVERT: H 171 THR cc_start: 0.8702 (m) cc_final: 0.8438 (p) REVERT: H 192 GLN cc_start: 0.7532 (tt0) cc_final: 0.7047 (tt0) REVERT: H 199 LYS cc_start: 0.8812 (ttpt) cc_final: 0.8498 (ttmt) REVERT: I 152 ASP cc_start: 0.8938 (m-30) cc_final: 0.8717 (m-30) REVERT: I 183 ASN cc_start: 0.8518 (m-40) cc_final: 0.8297 (m-40) REVERT: K 167 ARG cc_start: 0.8348 (mtp85) cc_final: 0.8105 (ttp-110) REVERT: L 185 MET cc_start: 0.8735 (mtm) cc_final: 0.8509 (mtp) REVERT: M 179 GLN cc_start: 0.7673 (mm-40) cc_final: 0.7279 (tt0) REVERT: M 183 ASN cc_start: 0.8365 (m-40) cc_final: 0.8119 (m-40) REVERT: M 203 LYS cc_start: 0.8419 (mtpp) cc_final: 0.8189 (mtmt) REVERT: N 213 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8137 (mp0) REVERT: O 192 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8285 (tm-30) outliers start: 47 outliers final: 37 residues processed: 461 average time/residue: 0.1234 time to fit residues: 80.1905 Evaluate side-chains 454 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 417 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 197 ASP 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 18 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain E residue 189 LEU 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 195 ASN 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 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 198 CYS Chi-restraints excluded: chain M residue 218 CYS Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 18 ARG Chi-restraints excluded: chain O residue 210 THR 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: 0.7980 chunk 89 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN D 193 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.134412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.101317 restraints weight = 22509.131| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.75 r_work: 0.3254 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4846 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= 0.134 Angle : 0.581 10.795 18440 Z= 0.307 Chirality : 0.042 0.169 2085 Planarity : 0.005 0.042 2390 Dihedral : 4.308 22.255 1820 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 3.31 % Allowed : 21.27 % Favored : 75.42 % 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: 1.10 (0.15), residues: 1175 sheet: -1.01 (0.68), residues: 45 loop : 1.44 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 143 TYR 0.008 0.001 TYR N 164 PHE 0.017 0.001 PHE H 168 TRP 0.011 0.001 TRP N 184 HIS 0.001 0.000 HIS F 12 Details of bonding type rmsd covalent geometry : bond 0.00315 (13595) covalent geometry : angle 0.58141 (18440) hydrogen bonds : bond 0.03804 ( 840) hydrogen bonds : angle 4.38048 ( 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 474 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 427 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8589 (tp30) cc_final: 0.8352 (tp30) REVERT: C 166 ASP cc_start: 0.7541 (m-30) cc_final: 0.7255 (m-30) REVERT: C 213 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8003 (mp0) REVERT: A 167 ARG cc_start: 0.8596 (mtm-85) cc_final: 0.8390 (mtm-85) REVERT: A 195 ASN cc_start: 0.8390 (OUTLIER) cc_final: 0.8078 (p0) REVERT: E 213 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7844 (mt-10) REVERT: F 66 MET cc_start: 0.8885 (tpt) cc_final: 0.8681 (tpt) REVERT: F 152 ASP cc_start: 0.8911 (m-30) cc_final: 0.8653 (m-30) REVERT: H 168 PHE cc_start: 0.8553 (t80) cc_final: 0.8054 (t80) REVERT: H 171 THR cc_start: 0.8702 (m) cc_final: 0.8458 (p) REVERT: I 183 ASN cc_start: 0.8515 (m-40) cc_final: 0.8275 (m-40) REVERT: J 172 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8407 (tp) REVERT: K 167 ARG cc_start: 0.8291 (mtp85) cc_final: 0.8061 (ttp-110) REVERT: K 175 GLU cc_start: 0.4311 (mt-10) cc_final: 0.4062 (mt-10) REVERT: L 185 MET cc_start: 0.8720 (mtm) cc_final: 0.8487 (mtp) REVERT: L 195 ASN cc_start: 0.8192 (p0) cc_final: 0.7428 (p0) REVERT: M 179 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7262 (tt0) REVERT: M 183 ASN cc_start: 0.8377 (m-40) cc_final: 0.8132 (m-40) REVERT: M 203 LYS cc_start: 0.8534 (mtpp) cc_final: 0.8304 (mtmt) REVERT: N 166 ASP cc_start: 0.7685 (m-30) cc_final: 0.7424 (m-30) REVERT: N 213 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7917 (mt-10) REVERT: O 192 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8248 (tm-30) REVERT: O 199 LYS cc_start: 0.8904 (tttt) cc_final: 0.8680 (ttmt) outliers start: 47 outliers final: 38 residues processed: 448 average time/residue: 0.1215 time to fit residues: 77.1260 Evaluate side-chains 458 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 418 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 197 ASP 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 18 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 189 LEU 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 G residue 195 ASN 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 210 THR Chi-restraints excluded: chain J residue 172 LEU 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 198 CYS Chi-restraints excluded: chain M residue 218 CYS Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 18 ARG Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain O residue 178 SER Chi-restraints excluded: chain O residue 210 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 13 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 146 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 chunk 12 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.132815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.099172 restraints weight = 22678.508| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.76 r_work: 0.3203 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.4799 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= 0.157 Angle : 0.606 10.477 18440 Z= 0.320 Chirality : 0.043 0.168 2085 Planarity : 0.005 0.042 2390 Dihedral : 4.355 22.036 1820 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.38 % Allowed : 21.48 % Favored : 75.14 % 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: 1.42 (0.20), residues: 1685 helix: 1.02 (0.15), residues: 1175 sheet: -0.98 (0.68), residues: 45 loop : 1.36 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 143 TYR 0.008 0.001 TYR H 164 PHE 0.021 0.001 PHE H 168 TRP 0.012 0.001 TRP H 184 HIS 0.001 0.000 HIS F 12 Details of bonding type rmsd covalent geometry : bond 0.00379 (13595) covalent geometry : angle 0.60581 (18440) hydrogen bonds : bond 0.03918 ( 840) hydrogen bonds : angle 4.50784 ( 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 471 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 423 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8627 (tp30) cc_final: 0.8396 (tp30) REVERT: C 166 ASP cc_start: 0.7586 (m-30) cc_final: 0.7310 (m-30) REVERT: C 213 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7998 (mp0) REVERT: A 192 GLN cc_start: 0.8806 (tm-30) cc_final: 0.8217 (tm-30) REVERT: E 213 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8051 (mp0) REVERT: F 66 MET cc_start: 0.8917 (tpt) cc_final: 0.8658 (tpt) REVERT: F 152 ASP cc_start: 0.8909 (m-30) cc_final: 0.8667 (m-30) REVERT: H 168 PHE cc_start: 0.8641 (t80) cc_final: 0.8190 (t80) REVERT: H 171 THR cc_start: 0.8755 (m) cc_final: 0.8509 (p) REVERT: H 213 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8127 (mp0) REVERT: I 183 ASN cc_start: 0.8533 (m-40) cc_final: 0.8291 (m-40) REVERT: J 172 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8432 (tp) REVERT: L 185 MET cc_start: 0.8731 (mtm) cc_final: 0.8518 (mtp) REVERT: L 195 ASN cc_start: 0.8150 (p0) cc_final: 0.7396 (p0) REVERT: M 179 GLN cc_start: 0.7786 (mm-40) cc_final: 0.7324 (tt0) REVERT: M 183 ASN cc_start: 0.8434 (m-40) cc_final: 0.8164 (m-40) REVERT: N 213 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7855 (mt-10) REVERT: O 130 TYR cc_start: 0.9142 (t80) cc_final: 0.8857 (t80) REVERT: O 192 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8318 (tm-30) REVERT: O 199 LYS cc_start: 0.8914 (tttt) cc_final: 0.8698 (ttmt) outliers start: 48 outliers final: 40 residues processed: 446 average time/residue: 0.1252 time to fit residues: 78.8701 Evaluate side-chains 449 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 408 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 197 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain C residue 189 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 D residue 172 LEU Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 189 LEU 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 115 ILE 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 195 ASN 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 210 THR Chi-restraints excluded: chain J residue 172 LEU 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 L residue 178 SER Chi-restraints excluded: chain M residue 198 CYS Chi-restraints excluded: chain M residue 218 CYS Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain N residue 190 LEU Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 18 ARG Chi-restraints excluded: chain O residue 63 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 41 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 155 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 22 optimal weight: 0.0030 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN I 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.135805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.102502 restraints weight = 22468.953| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.76 r_work: 0.3284 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5032 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= 0.127 Angle : 0.594 10.296 18440 Z= 0.315 Chirality : 0.042 0.171 2085 Planarity : 0.005 0.042 2390 Dihedral : 4.235 21.142 1820 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.75 % Allowed : 21.90 % Favored : 75.35 % 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: 1.64 (0.20), residues: 1685 helix: 1.14 (0.15), residues: 1170 sheet: -0.81 (0.69), residues: 45 loop : 1.54 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 82 TYR 0.009 0.001 TYR N 164 PHE 0.027 0.001 PHE N 168 TRP 0.011 0.001 TRP F 184 HIS 0.001 0.000 HIS F 12 Details of bonding type rmsd covalent geometry : bond 0.00296 (13595) covalent geometry : angle 0.59360 (18440) hydrogen bonds : bond 0.03770 ( 840) hydrogen bonds : angle 4.43359 ( 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 472 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 433 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8490 (tp) REVERT: B 175 GLU cc_start: 0.8555 (tp30) cc_final: 0.8332 (tp30) REVERT: C 166 ASP cc_start: 0.7827 (m-30) cc_final: 0.7515 (m-30) REVERT: C 213 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7978 (mp0) REVERT: A 192 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8173 (tm-30) REVERT: E 213 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8043 (mp0) REVERT: F 66 MET cc_start: 0.8894 (tpt) cc_final: 0.8663 (tpt) REVERT: F 152 ASP cc_start: 0.8832 (m-30) cc_final: 0.8560 (m-30) REVERT: F 195 ASN cc_start: 0.8079 (p0) cc_final: 0.7723 (p0) REVERT: H 168 PHE cc_start: 0.8498 (t80) cc_final: 0.8033 (t80) REVERT: H 171 THR cc_start: 0.8750 (m) cc_final: 0.8474 (p) REVERT: H 213 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8002 (mp0) REVERT: I 152 ASP cc_start: 0.8891 (m-30) cc_final: 0.8593 (m-30) REVERT: I 183 ASN cc_start: 0.8604 (m-40) cc_final: 0.8362 (m-40) REVERT: K 175 GLU cc_start: 0.4523 (mt-10) cc_final: 0.4308 (mt-10) REVERT: L 185 MET cc_start: 0.8654 (mtm) cc_final: 0.8387 (mtp) REVERT: L 195 ASN cc_start: 0.8076 (p0) cc_final: 0.7376 (p0) REVERT: M 179 GLN cc_start: 0.7653 (mm-40) cc_final: 0.7199 (tt0) REVERT: M 183 ASN cc_start: 0.8394 (m-40) cc_final: 0.8156 (m-40) REVERT: N 199 LYS cc_start: 0.8685 (ttpt) cc_final: 0.8468 (tttt) REVERT: N 213 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7806 (mt-10) REVERT: O 112 GLN cc_start: 0.8711 (tp40) cc_final: 0.8360 (mp10) REVERT: O 192 GLN cc_start: 0.8758 (tm-30) cc_final: 0.8256 (tm-30) outliers start: 39 outliers final: 32 residues processed: 452 average time/residue: 0.1183 time to fit residues: 76.1120 Evaluate side-chains 442 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 409 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 197 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 189 LEU 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 124 ILE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain G residue 195 ASN 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 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 198 CYS Chi-restraints excluded: chain M residue 218 CYS Chi-restraints excluded: chain O residue 2 ILE 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: 0.9990 chunk 133 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 154 optimal weight: 0.9980 chunk 147 optimal weight: 0.0770 chunk 71 optimal weight: 0.0070 chunk 70 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.136333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.103497 restraints weight = 22510.033| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.72 r_work: 0.3323 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13595 Z= 0.126 Angle : 0.590 9.939 18440 Z= 0.314 Chirality : 0.042 0.168 2085 Planarity : 0.005 0.042 2390 Dihedral : 4.190 21.118 1820 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.18 % Allowed : 22.54 % Favored : 75.28 % 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: 1.15 (0.15), residues: 1170 sheet: -0.63 (0.69), residues: 45 loop : 1.52 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 82 TYR 0.010 0.001 TYR N 164 PHE 0.013 0.001 PHE H 168 TRP 0.011 0.001 TRP F 184 HIS 0.001 0.000 HIS L 62 Details of bonding type rmsd covalent geometry : bond 0.00293 (13595) covalent geometry : angle 0.59020 (18440) hydrogen bonds : bond 0.03734 ( 840) hydrogen bonds : angle 4.46679 ( 2490) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3913.76 seconds wall clock time: 67 minutes 52.11 seconds (4072.11 seconds total)