Starting phenix.real_space_refine on Mon May 19 16:26:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cl2_16710/05_2025/8cl2_16710.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cl2_16710/05_2025/8cl2_16710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cl2_16710/05_2025/8cl2_16710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cl2_16710/05_2025/8cl2_16710.map" model { file = "/net/cci-nas-00/data/ceres_data/8cl2_16710/05_2025/8cl2_16710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cl2_16710/05_2025/8cl2_16710.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 38 Restraints were copied for chains: F, I, L, O, E, H, K, N, D, G, J, M Time building chain proxies: 5.44, per 1000 atoms: 0.41 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: 3.49 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.38 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: 3.57 Time building geometry restraints manager: 4.04 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' } 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: 2.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 27.990 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 13595 Z= 0.227 Angle : 0.824 5.144 18440 Z= 0.497 Chirality : 0.048 0.164 2085 Planarity : 0.009 0.086 2390 Dihedral : 12.071 78.424 5110 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (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 TRP 0.017 0.004 TRP O 117 HIS 0.007 0.003 HIS A 12 PHE 0.024 0.003 PHE A 40 TYR 0.014 0.004 TYR O 169 ARG 0.011 0.002 ARG L 18 Details of bonding type rmsd hydrogen bonds : bond 0.12089 ( 840) hydrogen bonds : angle 6.27745 ( 2490) covalent geometry : bond 0.00447 (13595) covalent geometry : angle 0.82357 (18440) *********************** 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 : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 LYS cc_start: 0.8710 (tttm) cc_final: 0.8427 (tppt) REVERT: C 166 ASP cc_start: 0.7844 (m-30) cc_final: 0.7479 (m-30) REVERT: C 183 ASN cc_start: 0.8349 (m-40) cc_final: 0.8040 (m-40) REVERT: C 213 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7483 (mt-10) REVERT: A 41 SER cc_start: 0.9001 (t) cc_final: 0.8262 (p) REVERT: A 117 TRP cc_start: 0.8103 (m-10) cc_final: 0.7749 (m-90) REVERT: A 167 ARG cc_start: 0.7978 (mtp180) cc_final: 0.7727 (mtm-85) REVERT: A 183 ASN cc_start: 0.8615 (m-40) cc_final: 0.8405 (m-40) REVERT: A 192 GLN cc_start: 0.8591 (tp40) cc_final: 0.8216 (tm-30) REVERT: D 159 GLU cc_start: 0.8502 (tt0) cc_final: 0.8102 (tt0) REVERT: D 170 LYS cc_start: 0.8690 (tttm) cc_final: 0.8471 (tppt) REVERT: E 166 ASP cc_start: 0.7870 (m-30) cc_final: 0.7594 (m-30) REVERT: E 168 PHE cc_start: 0.8949 (t80) cc_final: 0.8661 (t80) REVERT: E 213 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7498 (mt-10) REVERT: F 39 MET cc_start: 0.8466 (mtt) cc_final: 0.8230 (mtm) REVERT: F 41 SER cc_start: 0.9200 (t) cc_final: 0.8547 (p) REVERT: F 70 LYS cc_start: 0.8720 (mmmm) cc_final: 0.8518 (mptt) REVERT: F 192 GLN cc_start: 0.8575 (tp40) cc_final: 0.8171 (tm-30) REVERT: G 170 LYS cc_start: 0.8634 (tttm) cc_final: 0.8417 (tppt) REVERT: I 41 SER cc_start: 0.9176 (t) cc_final: 0.8552 (p) REVERT: I 68 MET cc_start: 0.8790 (mtp) cc_final: 0.8313 (mtp) REVERT: I 183 ASN cc_start: 0.8494 (m-40) cc_final: 0.8254 (m-40) REVERT: I 192 GLN cc_start: 0.8506 (tp40) cc_final: 0.8209 (tm-30) REVERT: J 159 GLU cc_start: 0.8524 (tt0) cc_final: 0.8207 (tt0) REVERT: J 170 LYS cc_start: 0.8632 (tttm) cc_final: 0.8365 (tppt) REVERT: K 182 LYS cc_start: 0.8494 (mttt) cc_final: 0.8166 (mttp) REVERT: K 183 ASN cc_start: 0.8337 (m-40) cc_final: 0.7921 (m-40) REVERT: K 192 GLN cc_start: 0.8343 (mt0) cc_final: 0.8085 (tt0) REVERT: K 213 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7486 (mt-10) REVERT: L 25 LYS cc_start: 0.8326 (mttt) cc_final: 0.8102 (mtmt) REVERT: L 41 SER cc_start: 0.9112 (t) cc_final: 0.8401 (p) REVERT: L 183 ASN cc_start: 0.8512 (m-40) cc_final: 0.8091 (m-40) REVERT: L 192 GLN cc_start: 0.8518 (tp40) cc_final: 0.8110 (tm-30) REVERT: L 195 ASN cc_start: 0.8522 (p0) cc_final: 0.8064 (p0) REVERT: L 215 MET cc_start: 0.8794 (mtp) cc_final: 0.8589 (mtm) REVERT: M 170 LYS cc_start: 0.8660 (tttm) cc_final: 0.8402 (tppt) REVERT: N 213 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7530 (mt-10) REVERT: O 39 MET cc_start: 0.8458 (mtt) cc_final: 0.8178 (mtp) REVERT: O 41 SER cc_start: 0.9124 (t) cc_final: 0.8407 (p) REVERT: O 117 TRP cc_start: 0.8111 (m-10) cc_final: 0.7518 (m-90) REVERT: O 183 ASN cc_start: 0.8599 (m-40) cc_final: 0.8372 (m-40) REVERT: O 192 GLN cc_start: 0.8636 (tp40) cc_final: 0.8299 (tm-30) REVERT: O 214 MET cc_start: 0.9045 (mtp) cc_final: 0.8842 (mtm) outliers start: 0 outliers final: 0 residues processed: 681 average time/residue: 0.2899 time to fit residues: 269.8070 Evaluate side-chains 495 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 495 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.3980 chunk 125 optimal weight: 0.4980 chunk 69 optimal weight: 0.6980 chunk 42 optimal weight: 0.1980 chunk 84 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 129 optimal weight: 0.8980 chunk 50 optimal weight: 0.3980 chunk 78 optimal weight: 0.0170 chunk 96 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.3018 ------------------------------------------------------------------------------- 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** 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 = 0.3755 r_free = 0.3755 target = 0.134799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.102713 restraints weight = 22850.551| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.54 r_work: 0.3177 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13595 Z= 0.132 Angle : 0.607 9.531 18440 Z= 0.317 Chirality : 0.041 0.154 2085 Planarity : 0.005 0.038 2390 Dihedral : 5.061 25.112 1820 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 2.04 % Allowed : 11.55 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.19), residues: 1685 helix: 1.03 (0.14), residues: 1160 sheet: -1.92 (0.64), residues: 45 loop : 1.52 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 184 HIS 0.003 0.000 HIS I 120 PHE 0.013 0.001 PHE L 40 TYR 0.017 0.001 TYR H 164 ARG 0.005 0.000 ARG L 82 Details of bonding type rmsd hydrogen bonds : bond 0.04341 ( 840) hydrogen bonds : angle 4.31328 ( 2490) covalent geometry : bond 0.00292 (13595) covalent geometry : angle 0.60705 (18440) *********************** 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 594 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 565 time to evaluate : 1.407 Fit side-chains REVERT: B 175 GLU cc_start: 0.8623 (tp30) cc_final: 0.8309 (tp30) REVERT: B 195 ASN cc_start: 0.7754 (t0) cc_final: 0.7247 (t0) REVERT: C 166 ASP cc_start: 0.7924 (m-30) cc_final: 0.7543 (m-30) REVERT: C 168 PHE cc_start: 0.8767 (t80) cc_final: 0.8515 (t80) REVERT: C 200 THR cc_start: 0.8796 (m) cc_final: 0.8487 (p) REVERT: C 213 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7936 (mt-10) REVERT: D 170 LYS cc_start: 0.8843 (tttm) cc_final: 0.8540 (tppt) REVERT: E 166 ASP cc_start: 0.8180 (m-30) cc_final: 0.7888 (m-30) REVERT: E 171 THR cc_start: 0.8756 (m) cc_final: 0.8403 (p) REVERT: E 200 THR cc_start: 0.8729 (m) cc_final: 0.8492 (p) REVERT: E 213 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7992 (mt-10) REVERT: F 3 VAL cc_start: 0.9076 (t) cc_final: 0.8869 (m) REVERT: F 70 LYS cc_start: 0.8874 (mmmm) cc_final: 0.8510 (mmtm) REVERT: F 199 LYS cc_start: 0.8930 (tttt) cc_final: 0.8699 (ttmt) REVERT: H 200 THR cc_start: 0.8785 (m) cc_final: 0.8555 (p) REVERT: H 213 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7973 (mt-10) REVERT: J 167 ARG cc_start: 0.8650 (mtm-85) cc_final: 0.8406 (ttp80) REVERT: J 170 LYS cc_start: 0.8878 (tttm) cc_final: 0.8658 (tppt) REVERT: K 166 ASP cc_start: 0.7962 (m-30) cc_final: 0.7686 (m-30) REVERT: K 167 ARG cc_start: 0.8303 (mtp85) cc_final: 0.8032 (mtp85) REVERT: K 171 THR cc_start: 0.8750 (m) cc_final: 0.8410 (p) REVERT: K 182 LYS cc_start: 0.8564 (mttt) cc_final: 0.8215 (mttp) REVERT: K 192 GLN cc_start: 0.8329 (mt0) cc_final: 0.8052 (tt0) REVERT: K 200 THR cc_start: 0.8849 (m) cc_final: 0.8615 (p) REVERT: K 213 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8139 (mt-10) REVERT: L 179 GLN cc_start: 0.9135 (tp40) cc_final: 0.8843 (tp40) REVERT: L 192 GLN cc_start: 0.8726 (tp40) cc_final: 0.8278 (tm-30) REVERT: L 195 ASN cc_start: 0.8633 (p0) cc_final: 0.8365 (p0) REVERT: L 213 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8356 (mp0) REVERT: M 170 LYS cc_start: 0.8858 (tttm) cc_final: 0.8599 (tppt) REVERT: M 198 CYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8240 (m) REVERT: N 168 PHE cc_start: 0.8931 (t80) cc_final: 0.8728 (t80) REVERT: N 170 LYS cc_start: 0.8685 (ttpp) cc_final: 0.8410 (ttmm) REVERT: N 200 THR cc_start: 0.8806 (m) cc_final: 0.8574 (p) REVERT: N 213 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7987 (mt-10) REVERT: O 3 VAL cc_start: 0.9057 (t) cc_final: 0.8854 (m) REVERT: O 195 ASN cc_start: 0.8631 (p0) cc_final: 0.8257 (p0) outliers start: 29 outliers final: 13 residues processed: 585 average time/residue: 0.2931 time to fit residues: 235.4964 Evaluate side-chains 486 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 472 time to evaluate : 1.507 ------------------------------------------------------------------------------- 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 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 149 SER Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain M residue 198 CYS Chi-restraints excluded: chain N residue 189 LEU Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 110 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 GLN D 183 ASN E 192 GLN I 120 HIS ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 193 ASN M 219 GLN O 193 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.129135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.096048 restraints weight = 22766.931| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.44 r_work: 0.3039 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3742 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 : 0.608 9.078 18440 Z= 0.317 Chirality : 0.043 0.172 2085 Planarity : 0.005 0.041 2390 Dihedral : 4.797 21.212 1820 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.10 % Allowed : 15.42 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.20), residues: 1685 helix: 1.00 (0.15), residues: 1180 sheet: -1.79 (0.66), residues: 45 loop : 1.55 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 184 HIS 0.003 0.000 HIS I 120 PHE 0.016 0.002 PHE H 168 TYR 0.008 0.001 TYR I 130 ARG 0.005 0.000 ARG F 82 Details of bonding type rmsd hydrogen bonds : bond 0.04224 ( 840) hydrogen bonds : angle 4.38310 ( 2490) covalent geometry : bond 0.00414 (13595) covalent geometry : angle 0.60832 (18440) *********************** 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 537 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 493 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8747 (tp30) cc_final: 0.8465 (tp30) REVERT: C 166 ASP cc_start: 0.7876 (m-30) cc_final: 0.7509 (m-30) REVERT: C 168 PHE cc_start: 0.8794 (t80) cc_final: 0.8272 (t80) REVERT: C 200 THR cc_start: 0.8736 (m) cc_final: 0.8440 (p) REVERT: A 199 LYS cc_start: 0.9086 (ttmt) cc_final: 0.8834 (ttmt) REVERT: D 170 LYS cc_start: 0.8873 (tttm) cc_final: 0.8592 (tppt) REVERT: E 166 ASP cc_start: 0.7926 (m-30) cc_final: 0.7714 (m-30) REVERT: E 200 THR cc_start: 0.8745 (m) cc_final: 0.8525 (p) REVERT: E 213 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8079 (mp0) REVERT: F 3 VAL cc_start: 0.9051 (t) cc_final: 0.8832 (m) REVERT: F 70 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8548 (mmtm) REVERT: F 199 LYS cc_start: 0.9002 (tttt) cc_final: 0.8788 (ttmt) REVERT: H 213 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7955 (mt-10) REVERT: K 200 THR cc_start: 0.8883 (m) cc_final: 0.8667 (p) REVERT: K 203 LYS cc_start: 0.8723 (mmtt) cc_final: 0.8493 (mmtp) REVERT: K 213 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8075 (mt-10) REVERT: K 215 MET cc_start: 0.8419 (mtp) cc_final: 0.8147 (mtp) REVERT: L 192 GLN cc_start: 0.8892 (tp40) cc_final: 0.8448 (tm-30) REVERT: M 170 LYS cc_start: 0.8897 (tttm) cc_final: 0.8652 (tppt) REVERT: N 170 LYS cc_start: 0.8748 (ttpp) cc_final: 0.8502 (ttmm) REVERT: N 200 THR cc_start: 0.8789 (m) cc_final: 0.8588 (p) REVERT: N 213 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7968 (mt-10) REVERT: O 192 GLN cc_start: 0.8798 (tp40) cc_final: 0.8397 (tm-30) outliers start: 44 outliers final: 28 residues processed: 514 average time/residue: 0.2953 time to fit residues: 209.6419 Evaluate side-chains 484 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 456 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 191 VAL 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 124 ILE Chi-restraints excluded: chain E residue 181 VAL 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 I residue 2 ILE Chi-restraints excluded: chain I residue 58 THR 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 M residue 197 ASP Chi-restraints excluded: chain M residue 198 CYS Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain O residue 178 SER Chi-restraints excluded: chain O residue 189 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 22 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 2 optimal weight: 0.0570 chunk 134 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 139 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 overall best weight: 0.7502 ------------------------------------------------------------------------------- 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 A 195 ASN H 192 GLN I 195 ASN M 219 GLN O 50 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.134174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.101103 restraints weight = 22397.474| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.54 r_work: 0.3157 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13595 Z= 0.129 Angle : 0.569 9.158 18440 Z= 0.297 Chirality : 0.041 0.177 2085 Planarity : 0.005 0.042 2390 Dihedral : 4.539 20.941 1820 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.68 % Allowed : 16.90 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.20), residues: 1685 helix: 1.16 (0.15), residues: 1175 sheet: -1.69 (0.69), residues: 45 loop : 1.56 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 184 HIS 0.001 0.000 HIS F 12 PHE 0.016 0.001 PHE H 168 TYR 0.019 0.001 TYR E 164 ARG 0.006 0.000 ARG L 82 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 840) hydrogen bonds : angle 4.15959 ( 2490) covalent geometry : bond 0.00299 (13595) covalent geometry : angle 0.56904 (18440) *********************** 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 523 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 485 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8675 (tp30) cc_final: 0.8456 (tp30) REVERT: C 164 TYR cc_start: 0.7656 (t80) cc_final: 0.7359 (t80) REVERT: C 166 ASP cc_start: 0.7576 (m-30) cc_final: 0.7222 (m-30) REVERT: C 200 THR cc_start: 0.8764 (m) cc_final: 0.8510 (p) REVERT: C 201 ILE cc_start: 0.9046 (mm) cc_final: 0.8835 (mm) REVERT: C 213 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8016 (mt-10) REVERT: A 68 MET cc_start: 0.8583 (mtp) cc_final: 0.8381 (mtm) REVERT: A 199 LYS cc_start: 0.9123 (ttmt) cc_final: 0.8850 (ttmt) REVERT: D 170 LYS cc_start: 0.8804 (tttm) cc_final: 0.8604 (tppt) REVERT: D 199 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8723 (ttmm) REVERT: E 166 ASP cc_start: 0.7909 (m-30) cc_final: 0.7669 (m-30) REVERT: E 168 PHE cc_start: 0.8900 (t80) cc_final: 0.8670 (t80) REVERT: E 200 THR cc_start: 0.8631 (m) cc_final: 0.8419 (p) REVERT: E 213 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8067 (mp0) REVERT: F 3 VAL cc_start: 0.9036 (t) cc_final: 0.8812 (m) REVERT: F 70 LYS cc_start: 0.8932 (mmmm) cc_final: 0.8563 (mmtm) REVERT: F 199 LYS cc_start: 0.8981 (tttt) cc_final: 0.8747 (ttmt) REVERT: H 168 PHE cc_start: 0.8200 (t80) cc_final: 0.7785 (t80) REVERT: H 213 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8002 (mt-10) REVERT: I 145 TYR cc_start: 0.9236 (m-80) cc_final: 0.8996 (m-80) REVERT: K 200 THR cc_start: 0.8779 (m) cc_final: 0.8565 (p) REVERT: K 203 LYS cc_start: 0.8675 (mmtt) cc_final: 0.8393 (mmtp) REVERT: K 213 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8080 (mt-10) REVERT: L 192 GLN cc_start: 0.8906 (tp40) cc_final: 0.8346 (tm-30) REVERT: M 199 LYS cc_start: 0.8836 (ttmt) cc_final: 0.8557 (ttmt) REVERT: N 170 LYS cc_start: 0.8725 (ttpp) cc_final: 0.8484 (ttmm) REVERT: N 213 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8120 (mm-30) REVERT: O 192 GLN cc_start: 0.8687 (tp40) cc_final: 0.8446 (tm-30) outliers start: 38 outliers final: 21 residues processed: 500 average time/residue: 0.2758 time to fit residues: 190.8624 Evaluate side-chains 459 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 438 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 181 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain M residue 198 CYS Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 124 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 102 optimal weight: 0.9980 chunk 74 optimal weight: 0.3980 chunk 76 optimal weight: 0.0370 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 2 optimal weight: 0.0870 chunk 141 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 193 ASN H 192 GLN M 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.136077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.103295 restraints weight = 22551.548| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.57 r_work: 0.3186 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4537 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= 0.117 Angle : 0.553 9.815 18440 Z= 0.289 Chirality : 0.040 0.159 2085 Planarity : 0.005 0.041 2390 Dihedral : 4.363 19.977 1820 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.46 % Allowed : 17.25 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.20), residues: 1685 helix: 1.28 (0.15), residues: 1180 sheet: -1.57 (0.69), residues: 45 loop : 1.67 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 184 HIS 0.000 0.000 HIS A 120 PHE 0.009 0.001 PHE L 40 TYR 0.008 0.001 TYR E 164 ARG 0.009 0.000 ARG I 82 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 840) hydrogen bonds : angle 4.08770 ( 2490) covalent geometry : bond 0.00260 (13595) covalent geometry : angle 0.55347 (18440) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3370 Ramachandran restraints generated. 1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 461 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 159 GLU cc_start: 0.8859 (tt0) cc_final: 0.8350 (tt0) REVERT: B 175 GLU cc_start: 0.8617 (tp30) cc_final: 0.8416 (tp30) REVERT: C 166 ASP cc_start: 0.7353 (m-30) cc_final: 0.7012 (m-30) REVERT: C 200 THR cc_start: 0.8780 (m) cc_final: 0.8576 (p) REVERT: C 201 ILE cc_start: 0.9013 (mm) cc_final: 0.8785 (pt) REVERT: C 213 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8094 (mm-30) REVERT: A 68 MET cc_start: 0.8498 (mtp) cc_final: 0.8285 (mtm) REVERT: A 176 GLN cc_start: 0.8359 (tt0) cc_final: 0.8120 (tp40) REVERT: A 199 LYS cc_start: 0.9062 (ttmt) cc_final: 0.8836 (ttmt) REVERT: D 158 LYS cc_start: 0.8538 (mmtm) cc_final: 0.8338 (tppt) REVERT: E 166 ASP cc_start: 0.7858 (m-30) cc_final: 0.7581 (m-30) REVERT: E 213 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8099 (mp0) REVERT: F 70 LYS cc_start: 0.8919 (mmmm) cc_final: 0.8577 (mmtm) REVERT: H 213 GLU cc_start: 0.8368 (mt-10) cc_final: 0.7911 (mt-10) REVERT: J 167 ARG cc_start: 0.8734 (ttp80) cc_final: 0.8533 (ttp-110) REVERT: K 213 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8086 (mt-10) REVERT: L 182 LYS cc_start: 0.8969 (mttt) cc_final: 0.8766 (mmmt) REVERT: N 166 ASP cc_start: 0.7619 (m-30) cc_final: 0.7253 (m-30) REVERT: N 168 PHE cc_start: 0.7982 (t80) cc_final: 0.7727 (t80) REVERT: N 197 ASP cc_start: 0.8097 (p0) cc_final: 0.7356 (t0) REVERT: N 213 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8120 (mm-30) REVERT: O 39 MET cc_start: 0.8735 (mtt) cc_final: 0.8475 (mtp) REVERT: O 192 GLN cc_start: 0.8635 (tp40) cc_final: 0.8300 (tm-30) outliers start: 35 outliers final: 21 residues processed: 476 average time/residue: 0.2737 time to fit residues: 181.1813 Evaluate side-chains 459 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 438 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 218 CYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain M residue 198 CYS Chi-restraints excluded: chain M residue 213 GLU Chi-restraints excluded: chain M residue 218 CYS Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain N residue 191 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 101 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 120 optimal weight: 0.0870 chunk 87 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 82 optimal weight: 0.0470 chunk 115 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN I 195 ASN M 219 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.136416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.103428 restraints weight = 22846.718| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.58 r_work: 0.3207 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4746 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= 0.120 Angle : 0.565 9.879 18440 Z= 0.294 Chirality : 0.041 0.159 2085 Planarity : 0.005 0.041 2390 Dihedral : 4.280 18.742 1820 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.54 % Allowed : 18.38 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.20), residues: 1685 helix: 1.27 (0.15), residues: 1185 sheet: -1.38 (0.69), residues: 45 loop : 1.53 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 184 HIS 0.001 0.000 HIS I 62 PHE 0.007 0.001 PHE N 168 TYR 0.008 0.001 TYR H 164 ARG 0.008 0.000 ARG I 82 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 840) hydrogen bonds : angle 4.11458 ( 2490) covalent geometry : bond 0.00268 (13595) covalent geometry : angle 0.56491 (18440) *********************** 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 490 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 454 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8570 (tp30) cc_final: 0.8364 (tp30) REVERT: C 213 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8213 (mp0) REVERT: A 68 MET cc_start: 0.8528 (mtp) cc_final: 0.8303 (mtm) REVERT: E 166 ASP cc_start: 0.7873 (m-30) cc_final: 0.7613 (m-30) REVERT: F 70 LYS cc_start: 0.8968 (mmmm) cc_final: 0.8615 (mmtm) REVERT: F 111 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8374 (tt) REVERT: F 152 ASP cc_start: 0.8919 (m-30) cc_final: 0.8639 (m-30) REVERT: H 213 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7886 (mt-10) REVERT: K 213 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8071 (mt-10) REVERT: L 70 LYS cc_start: 0.8590 (mptt) cc_final: 0.8316 (mmtm) REVERT: L 152 ASP cc_start: 0.8846 (m-30) cc_final: 0.8617 (m-30) REVERT: N 166 ASP cc_start: 0.7602 (m-30) cc_final: 0.7212 (m-30) REVERT: N 214 MET cc_start: 0.8699 (mtp) cc_final: 0.8494 (ptp) REVERT: O 39 MET cc_start: 0.8735 (mtt) cc_final: 0.8487 (mtp) REVERT: O 192 GLN cc_start: 0.8664 (tp40) cc_final: 0.8309 (tm-30) REVERT: O 199 LYS cc_start: 0.9006 (tttt) cc_final: 0.8793 (ttmt) outliers start: 36 outliers final: 21 residues processed: 467 average time/residue: 0.2714 time to fit residues: 177.1756 Evaluate side-chains 446 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 424 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain F residue 2 ILE 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 H residue 215 MET Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 218 CYS Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain M residue 198 CYS Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain O residue 63 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 63 GLN M 219 GLN ** O 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.128769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.095441 restraints weight = 22667.096| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.52 r_work: 0.3077 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13595 Z= 0.227 Angle : 0.653 10.917 18440 Z= 0.340 Chirality : 0.045 0.166 2085 Planarity : 0.005 0.042 2390 Dihedral : 4.564 22.635 1820 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.96 % Allowed : 20.21 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.20), residues: 1685 helix: 0.96 (0.15), residues: 1175 sheet: -1.28 (0.69), residues: 45 loop : 1.39 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 184 HIS 0.007 0.001 HIS I 120 PHE 0.015 0.001 PHE C 168 TYR 0.012 0.001 TYR C 164 ARG 0.007 0.001 ARG I 82 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 840) hydrogen bonds : angle 4.55730 ( 2490) covalent geometry : bond 0.00553 (13595) covalent geometry : angle 0.65304 (18440) *********************** 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 470 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 428 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8779 (tp30) cc_final: 0.8473 (tp30) REVERT: C 166 ASP cc_start: 0.7685 (m-30) cc_final: 0.7364 (m-30) REVERT: C 203 LYS cc_start: 0.8613 (tppt) cc_final: 0.8307 (mmtm) REVERT: E 213 GLU cc_start: 0.8438 (mp0) cc_final: 0.7976 (mp0) REVERT: F 45 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7726 (mm-30) REVERT: F 70 LYS cc_start: 0.9018 (mmmm) cc_final: 0.8695 (mmtm) REVERT: F 192 GLN cc_start: 0.8927 (tp40) cc_final: 0.8301 (tm-30) REVERT: H 213 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8188 (mp0) REVERT: K 213 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8085 (mt-10) REVERT: L 182 LYS cc_start: 0.8983 (mttt) cc_final: 0.8750 (mmmt) REVERT: L 192 GLN cc_start: 0.8966 (tp40) cc_final: 0.8332 (tm-30) REVERT: N 170 LYS cc_start: 0.8704 (ttpp) cc_final: 0.8439 (ttmm) REVERT: O 130 TYR cc_start: 0.9385 (t80) cc_final: 0.9050 (t80) REVERT: O 192 GLN cc_start: 0.8886 (tp40) cc_final: 0.8634 (tm-30) outliers start: 42 outliers final: 26 residues processed: 449 average time/residue: 0.2768 time to fit residues: 176.3314 Evaluate side-chains 432 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 406 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 178 SER Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain I residue 2 ILE 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 K residue 191 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 191 VAL Chi-restraints excluded: chain M residue 195 ASN 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 178 SER Chi-restraints excluded: chain O residue 191 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 122 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 152 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 219 GLN ** O 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.134287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.101005 restraints weight = 22642.183| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.55 r_work: 0.3148 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4807 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 : 0.590 10.322 18440 Z= 0.308 Chirality : 0.042 0.168 2085 Planarity : 0.005 0.043 2390 Dihedral : 4.368 21.665 1820 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.39 % Allowed : 21.27 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.20), residues: 1685 helix: 1.05 (0.15), residues: 1175 sheet: -1.15 (0.70), residues: 45 loop : 1.41 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 184 HIS 0.008 0.001 HIS I 120 PHE 0.012 0.001 PHE O 40 TYR 0.007 0.001 TYR H 164 ARG 0.008 0.000 ARG I 82 Details of bonding type rmsd hydrogen bonds : bond 0.03751 ( 840) hydrogen bonds : angle 4.35360 ( 2490) covalent geometry : bond 0.00305 (13595) covalent geometry : angle 0.59026 (18440) *********************** 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 464 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 430 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8706 (tp30) cc_final: 0.8389 (tp30) REVERT: C 166 ASP cc_start: 0.7687 (m-30) cc_final: 0.7395 (m-30) REVERT: C 213 GLU cc_start: 0.8304 (mp0) cc_final: 0.7843 (mp0) REVERT: A 70 LYS cc_start: 0.8706 (mptt) cc_final: 0.8462 (mptt) REVERT: E 213 GLU cc_start: 0.8328 (mp0) cc_final: 0.8019 (mp0) REVERT: F 45 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7585 (mm-30) REVERT: F 70 LYS cc_start: 0.8986 (mmmm) cc_final: 0.8522 (mmtt) REVERT: F 111 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8443 (tt) REVERT: F 192 GLN cc_start: 0.8948 (tp40) cc_final: 0.8308 (tm-30) REVERT: K 175 GLU cc_start: 0.4927 (mt-10) cc_final: 0.4668 (mt-10) REVERT: K 213 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8055 (mt-10) REVERT: L 195 ASN cc_start: 0.8357 (p0) cc_final: 0.7499 (p0) REVERT: O 192 GLN cc_start: 0.8916 (tp40) cc_final: 0.8593 (tm-30) outliers start: 34 outliers final: 28 residues processed: 443 average time/residue: 0.2760 time to fit residues: 171.2202 Evaluate side-chains 438 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 409 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 195 ASN 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 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 221 VAL Chi-restraints excluded: chain O residue 18 ARG Chi-restraints excluded: chain O residue 178 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 75 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 193 ASN M 219 GLN O 50 GLN ** O 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.134301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.100652 restraints weight = 22432.682| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.59 r_work: 0.3148 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13595 Z= 0.140 Angle : 0.605 10.751 18440 Z= 0.316 Chirality : 0.042 0.170 2085 Planarity : 0.005 0.043 2390 Dihedral : 4.380 21.667 1820 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.11 % Allowed : 21.55 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.20), residues: 1685 helix: 1.03 (0.15), residues: 1175 sheet: -1.09 (0.70), residues: 45 loop : 1.42 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 184 HIS 0.008 0.001 HIS I 120 PHE 0.024 0.001 PHE N 168 TYR 0.008 0.001 TYR H 164 ARG 0.008 0.000 ARG I 82 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 840) hydrogen bonds : angle 4.40480 ( 2490) covalent geometry : bond 0.00333 (13595) covalent geometry : angle 0.60456 (18440) *********************** 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 457 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 427 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 166 ASP cc_start: 0.7639 (m-30) cc_final: 0.7305 (m-30) REVERT: C 213 GLU cc_start: 0.8314 (mp0) cc_final: 0.7822 (mp0) REVERT: A 70 LYS cc_start: 0.8754 (mptt) cc_final: 0.8529 (mptt) REVERT: A 192 GLN cc_start: 0.8897 (tp40) cc_final: 0.8465 (tm-30) REVERT: E 213 GLU cc_start: 0.8373 (mp0) cc_final: 0.7909 (mp0) REVERT: F 45 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7556 (mm-30) REVERT: F 70 LYS cc_start: 0.9020 (mmmm) cc_final: 0.8602 (mmtt) REVERT: F 111 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8416 (tt) REVERT: F 197 ASP cc_start: 0.7926 (p0) cc_final: 0.7697 (p0) REVERT: K 175 GLU cc_start: 0.4954 (mt-10) cc_final: 0.4721 (mt-10) REVERT: K 213 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7999 (mt-10) REVERT: L 185 MET cc_start: 0.8939 (ttm) cc_final: 0.8736 (mtp) REVERT: L 195 ASN cc_start: 0.8346 (p0) cc_final: 0.7423 (p0) REVERT: N 166 ASP cc_start: 0.7784 (m-30) cc_final: 0.7520 (m-30) REVERT: O 192 GLN cc_start: 0.8931 (tp40) cc_final: 0.8663 (tm-30) outliers start: 30 outliers final: 27 residues processed: 441 average time/residue: 0.2619 time to fit residues: 163.2531 Evaluate side-chains 434 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 406 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 195 ASN Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 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 18 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 144 optimal weight: 0.2980 chunk 119 optimal weight: 8.9990 chunk 15 optimal weight: 0.0170 chunk 112 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** I 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.136751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.103136 restraints weight = 22509.521| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.61 r_work: 0.3190 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.5046 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= 0.126 Angle : 0.600 11.619 18440 Z= 0.313 Chirality : 0.041 0.171 2085 Planarity : 0.005 0.043 2390 Dihedral : 4.296 20.655 1820 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.76 % Allowed : 22.18 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.20), residues: 1685 helix: 1.11 (0.15), residues: 1170 sheet: -0.94 (0.71), residues: 45 loop : 1.51 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 184 HIS 0.009 0.001 HIS I 120 PHE 0.021 0.001 PHE N 168 TYR 0.007 0.001 TYR N 164 ARG 0.007 0.000 ARG I 82 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 840) hydrogen bonds : angle 4.33812 ( 2490) covalent geometry : bond 0.00290 (13595) covalent geometry : angle 0.60028 (18440) ********************** 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 451 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 426 time to evaluate : 1.545 Fit side-chains revert: symmetry clash REVERT: C 166 ASP cc_start: 0.7644 (m-30) cc_final: 0.7319 (m-30) REVERT: C 199 LYS cc_start: 0.8593 (mttt) cc_final: 0.8380 (mttt) REVERT: C 213 GLU cc_start: 0.8298 (mp0) cc_final: 0.7807 (mp0) REVERT: E 203 LYS cc_start: 0.8510 (tppt) cc_final: 0.8165 (mmtp) REVERT: E 213 GLU cc_start: 0.8403 (mp0) cc_final: 0.7919 (mp0) REVERT: F 70 LYS cc_start: 0.9021 (mmmm) cc_final: 0.8705 (mptt) REVERT: F 197 ASP cc_start: 0.7842 (p0) cc_final: 0.7609 (p0) REVERT: H 164 TYR cc_start: 0.7860 (t80) cc_final: 0.7643 (t80) REVERT: I 70 LYS cc_start: 0.8582 (mptt) cc_final: 0.8251 (mmtt) REVERT: I 112 GLN cc_start: 0.8624 (tp40) cc_final: 0.8335 (mp10) REVERT: I 152 ASP cc_start: 0.8963 (m-30) cc_final: 0.8689 (m-30) REVERT: I 192 GLN cc_start: 0.8892 (tp40) cc_final: 0.8196 (tm-30) REVERT: J 192 GLN cc_start: 0.8797 (tp40) cc_final: 0.8288 (tm-30) REVERT: K 199 LYS cc_start: 0.8676 (ttpt) cc_final: 0.8469 (mttt) REVERT: K 213 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8026 (mt-10) REVERT: L 112 GLN cc_start: 0.8682 (tp40) cc_final: 0.8421 (mp10) REVERT: L 185 MET cc_start: 0.8946 (ttm) cc_final: 0.8740 (mtp) REVERT: L 195 ASN cc_start: 0.8357 (p0) cc_final: 0.7444 (p0) REVERT: N 166 ASP cc_start: 0.7557 (m-30) cc_final: 0.7279 (m-30) REVERT: N 201 ILE cc_start: 0.8637 (mt) cc_final: 0.8431 (pt) REVERT: N 212 GLU cc_start: 0.8788 (tt0) cc_final: 0.8207 (tm-30) REVERT: N 213 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7894 (mt-10) REVERT: O 192 GLN cc_start: 0.8944 (tp40) cc_final: 0.8668 (tm-30) outliers start: 25 outliers final: 25 residues processed: 438 average time/residue: 0.2642 time to fit residues: 163.9746 Evaluate side-chains 430 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 405 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 191 VAL Chi-restraints excluded: chain D residue 195 ASN 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 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 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 221 VAL Chi-restraints excluded: chain O residue 18 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 45 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 22 optimal weight: 0.0980 chunk 145 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 0.0870 chunk 19 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN ** I 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 179 GLN L 183 ASN ** O 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.136314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.102574 restraints weight = 22656.260| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.63 r_work: 0.3176 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.5116 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 : 0.611 11.925 18440 Z= 0.319 Chirality : 0.042 0.170 2085 Planarity : 0.005 0.042 2390 Dihedral : 4.284 19.301 1820 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.90 % Allowed : 22.61 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.20), residues: 1685 helix: 1.09 (0.15), residues: 1170 sheet: -0.84 (0.72), residues: 45 loop : 1.53 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 184 HIS 0.008 0.001 HIS I 120 PHE 0.020 0.001 PHE N 168 TYR 0.007 0.001 TYR E 164 ARG 0.007 0.000 ARG I 82 Details of bonding type rmsd hydrogen bonds : bond 0.03726 ( 840) hydrogen bonds : angle 4.44757 ( 2490) covalent geometry : bond 0.00317 (13595) covalent geometry : angle 0.61104 (18440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7322.08 seconds wall clock time: 127 minutes 22.81 seconds (7642.81 seconds total)