Starting phenix.real_space_refine on Mon Jun 16 14:53:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cl4_16712/06_2025/8cl4_16712.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cl4_16712/06_2025/8cl4_16712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cl4_16712/06_2025/8cl4_16712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cl4_16712/06_2025/8cl4_16712.map" model { file = "/net/cci-nas-00/data/ceres_data/8cl4_16712/06_2025/8cl4_16712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cl4_16712/06_2025/8cl4_16712.cif" } resolution = 3.14 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-5710/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: 6.15, per 1000 atoms: 0.46 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: 3.48 Conformation dependent library (CDL) restraints added in 1.8 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: 1.44 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: 3.48 Time building geometry restraints manager: 4.07 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: 0.10 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: 4.040 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: 0.090 Set scattering table: 0.120 Process input model: 29.770 Find NCS groups from input model: 0.240 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: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 13595 Z= 0.227 Angle : 0.824 5.144 18440 Z= 0.497 Chirality : 0.048 0.164 2085 Planarity : 0.009 0.086 2390 Dihedral : 12.071 78.424 5110 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 166 ASP cc_start: 0.7780 (m-30) cc_final: 0.7438 (m-30) REVERT: C 183 ASN cc_start: 0.8263 (m-40) cc_final: 0.8010 (m-40) REVERT: C 213 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7316 (mt-10) REVERT: A 41 SER cc_start: 0.8854 (t) cc_final: 0.8203 (p) REVERT: A 117 TRP cc_start: 0.7838 (m-10) cc_final: 0.7626 (m-90) REVERT: A 183 ASN cc_start: 0.8226 (m-40) cc_final: 0.8026 (m-40) REVERT: D 159 GLU cc_start: 0.8455 (tt0) cc_final: 0.8138 (tt0) REVERT: E 166 ASP cc_start: 0.7808 (m-30) cc_final: 0.7544 (m-30) REVERT: E 168 PHE cc_start: 0.8860 (t80) cc_final: 0.8620 (t80) REVERT: E 213 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7367 (mt-10) REVERT: F 41 SER cc_start: 0.9051 (t) cc_final: 0.8514 (p) REVERT: I 25 LYS cc_start: 0.8235 (mttt) cc_final: 0.8009 (mtmt) REVERT: I 41 SER cc_start: 0.9003 (t) cc_final: 0.8500 (p) REVERT: I 68 MET cc_start: 0.8488 (mtp) cc_final: 0.7987 (mtp) REVERT: I 183 ASN cc_start: 0.8099 (m-40) cc_final: 0.7892 (m-40) REVERT: J 159 GLU cc_start: 0.8496 (tt0) cc_final: 0.8203 (tt0) REVERT: K 182 LYS cc_start: 0.8377 (mttt) cc_final: 0.8091 (mttp) REVERT: K 183 ASN cc_start: 0.8252 (m-40) cc_final: 0.7885 (m-40) REVERT: K 213 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7342 (mt-10) REVERT: L 25 LYS cc_start: 0.8204 (mttt) cc_final: 0.7974 (mtmt) REVERT: L 41 SER cc_start: 0.8927 (t) cc_final: 0.8401 (p) REVERT: L 183 ASN cc_start: 0.8055 (m-40) cc_final: 0.7679 (m-40) REVERT: L 195 ASN cc_start: 0.8189 (p0) cc_final: 0.7778 (p0) REVERT: N 213 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7350 (mt-10) REVERT: O 41 SER cc_start: 0.8938 (t) cc_final: 0.8359 (p) REVERT: O 117 TRP cc_start: 0.7806 (m-10) cc_final: 0.7417 (m-90) REVERT: O 183 ASN cc_start: 0.8214 (m-40) cc_final: 0.7989 (m-40) outliers start: 0 outliers final: 0 residues processed: 681 average time/residue: 0.2962 time to fit residues: 275.6271 Evaluate side-chains 491 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 491 time to evaluate : 1.543 ------------------------------------------------------------------------------- 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: 2.9990 chunk 84 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 0.0170 chunk 96 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN F 50 GLN I 120 HIS J 219 GLN M 179 GLN 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 = 0.3826 r_free = 0.3826 target = 0.133682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.101379 restraints weight = 22747.183| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.66 r_work: 0.3271 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13595 Z= 0.135 Angle : 0.611 9.655 18440 Z= 0.319 Chirality : 0.041 0.154 2085 Planarity : 0.005 0.039 2390 Dihedral : 5.058 25.145 1820 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Rotamer: Outliers : 2.25 % Allowed : 11.55 % Favored : 86.20 % 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: 1.41 (0.20), residues: 1685 helix: 0.96 (0.14), residues: 1175 sheet: -1.89 (0.64), residues: 45 loop : 1.62 (0.28), residues: 465 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 F 40 TYR 0.016 0.002 TYR H 164 ARG 0.005 0.000 ARG L 82 Details of bonding type rmsd hydrogen bonds : bond 0.04336 ( 840) hydrogen bonds : angle 4.31727 ( 2490) covalent geometry : bond 0.00309 (13595) covalent geometry : angle 0.61141 (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 590 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 558 time to evaluate : 1.547 Fit side-chains REVERT: B 175 GLU cc_start: 0.8517 (tp30) cc_final: 0.8207 (tp30) REVERT: B 195 ASN cc_start: 0.7505 (t0) cc_final: 0.7000 (t0) REVERT: C 166 ASP cc_start: 0.7851 (m-30) cc_final: 0.7493 (m-30) REVERT: C 168 PHE cc_start: 0.8699 (t80) cc_final: 0.8118 (t80) REVERT: C 200 THR cc_start: 0.8771 (m) cc_final: 0.8455 (p) REVERT: C 213 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7912 (mt-10) REVERT: A 192 GLN cc_start: 0.8606 (tm-30) cc_final: 0.7673 (tm-30) REVERT: E 166 ASP cc_start: 0.8081 (m-30) cc_final: 0.7808 (m-30) REVERT: E 171 THR cc_start: 0.8645 (m) cc_final: 0.8273 (p) REVERT: E 200 THR cc_start: 0.8686 (m) cc_final: 0.8458 (p) REVERT: E 213 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7966 (mt-10) REVERT: F 3 VAL cc_start: 0.8862 (t) cc_final: 0.8638 (m) REVERT: F 66 MET cc_start: 0.8946 (tpt) cc_final: 0.8740 (tpt) REVERT: H 183 ASN cc_start: 0.8119 (m-40) cc_final: 0.7914 (m-40) REVERT: H 200 THR cc_start: 0.8732 (m) cc_final: 0.8502 (p) REVERT: H 213 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7906 (mt-10) REVERT: I 183 ASN cc_start: 0.8562 (m-40) cc_final: 0.8315 (m-40) REVERT: J 167 ARG cc_start: 0.8636 (mtm-85) cc_final: 0.8421 (ttp80) REVERT: J 216 THR cc_start: 0.9289 (m) cc_final: 0.9083 (p) REVERT: K 166 ASP cc_start: 0.7882 (m-30) cc_final: 0.7641 (m-30) REVERT: K 167 ARG cc_start: 0.8273 (mtp85) cc_final: 0.8020 (mtp85) REVERT: K 171 THR cc_start: 0.8622 (m) cc_final: 0.8267 (p) REVERT: K 182 LYS cc_start: 0.8384 (mttt) cc_final: 0.8084 (mttp) REVERT: K 200 THR cc_start: 0.8793 (m) cc_final: 0.8551 (p) REVERT: K 213 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8108 (mt-10) REVERT: L 183 ASN cc_start: 0.8496 (m-40) cc_final: 0.8255 (m-40) REVERT: L 192 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8002 (tm-30) REVERT: L 195 ASN cc_start: 0.8184 (p0) cc_final: 0.7920 (p0) REVERT: L 210 THR cc_start: 0.8933 (p) cc_final: 0.8442 (p) REVERT: L 213 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8216 (mp0) REVERT: M 179 GLN cc_start: 0.7003 (mm-40) cc_final: 0.6741 (tt0) REVERT: M 198 CYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8140 (m) REVERT: N 168 PHE cc_start: 0.8843 (t80) cc_final: 0.8631 (t80) REVERT: N 170 LYS cc_start: 0.8534 (ttpp) cc_final: 0.8261 (ttmm) REVERT: N 200 THR cc_start: 0.8775 (m) cc_final: 0.8552 (p) REVERT: N 213 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7915 (mt-10) REVERT: O 195 ASN cc_start: 0.8244 (p0) cc_final: 0.7860 (p0) outliers start: 32 outliers final: 14 residues processed: 579 average time/residue: 0.2942 time to fit residues: 234.8482 Evaluate side-chains 490 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 475 time to evaluate : 1.505 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain O residue 188 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 134 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 A 50 GLN E 192 GLN I 120 HIS ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 219 GLN O 176 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.130837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.097382 restraints weight = 23153.017| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.74 r_work: 0.3205 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13595 Z= 0.174 Angle : 0.609 9.023 18440 Z= 0.317 Chirality : 0.043 0.179 2085 Planarity : 0.005 0.041 2390 Dihedral : 4.811 21.054 1820 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.82 % Allowed : 15.42 % Favored : 81.76 % 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: 1.38 (0.20), residues: 1685 helix: 0.98 (0.14), residues: 1185 sheet: -1.89 (0.64), residues: 45 loop : 1.48 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 184 HIS 0.003 0.001 HIS I 120 PHE 0.022 0.002 PHE H 168 TYR 0.008 0.001 TYR H 164 ARG 0.006 0.000 ARG F 82 Details of bonding type rmsd hydrogen bonds : bond 0.04215 ( 840) hydrogen bonds : angle 4.35339 ( 2490) covalent geometry : bond 0.00420 (13595) covalent geometry : angle 0.60867 (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 541 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 501 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8616 (tp30) cc_final: 0.8339 (tp30) REVERT: C 166 ASP cc_start: 0.7897 (m-30) cc_final: 0.7581 (m-30) REVERT: C 168 PHE cc_start: 0.8543 (t80) cc_final: 0.8276 (t80) REVERT: C 200 THR cc_start: 0.8708 (m) cc_final: 0.8432 (p) REVERT: A 178 SER cc_start: 0.8447 (OUTLIER) cc_final: 0.8232 (p) REVERT: A 192 GLN cc_start: 0.8743 (tm-30) cc_final: 0.7878 (tm-30) REVERT: A 199 LYS cc_start: 0.8962 (ttmt) cc_final: 0.8728 (ttmt) REVERT: A 215 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7945 (mtp) REVERT: E 166 ASP cc_start: 0.7843 (m-30) cc_final: 0.7640 (m-30) REVERT: E 168 PHE cc_start: 0.8888 (t80) cc_final: 0.8534 (t80) REVERT: E 171 THR cc_start: 0.8766 (m) cc_final: 0.8559 (p) REVERT: E 200 THR cc_start: 0.8705 (m) cc_final: 0.8493 (p) REVERT: E 213 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8057 (mp0) REVERT: F 3 VAL cc_start: 0.8893 (t) cc_final: 0.8671 (m) REVERT: F 66 MET cc_start: 0.9004 (tpt) cc_final: 0.8745 (tpt) REVERT: F 82 ARG cc_start: 0.8167 (ttp80) cc_final: 0.7937 (ttp80) REVERT: F 130 TYR cc_start: 0.9155 (t80) cc_final: 0.8878 (t80) REVERT: F 203 LYS cc_start: 0.8943 (mmtm) cc_final: 0.8736 (mmtt) REVERT: H 200 THR cc_start: 0.8757 (m) cc_final: 0.8557 (p) REVERT: H 213 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7916 (mt-10) REVERT: I 183 ASN cc_start: 0.8561 (m-40) cc_final: 0.8296 (m-40) REVERT: K 200 THR cc_start: 0.8797 (m) cc_final: 0.8561 (p) REVERT: K 213 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8062 (mt-10) REVERT: L 183 ASN cc_start: 0.8444 (m-40) cc_final: 0.8205 (m-40) REVERT: L 192 GLN cc_start: 0.8656 (tm-30) cc_final: 0.8149 (tm-30) REVERT: N 170 LYS cc_start: 0.8596 (ttpp) cc_final: 0.8346 (ttmm) REVERT: N 200 THR cc_start: 0.8774 (m) cc_final: 0.8560 (p) REVERT: N 213 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8065 (mp0) outliers start: 40 outliers final: 29 residues processed: 523 average time/residue: 0.2881 time to fit residues: 207.9726 Evaluate side-chains 497 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 466 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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 110 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain L residue 58 THR Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain M residue 198 CYS Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 135 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: 0.3980 chunk 15 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 GLN B 219 GLN A 195 ASN H 192 GLN I 195 ASN M 219 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.133407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.100595 restraints weight = 22674.293| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.66 r_work: 0.3285 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4207 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= 0.138 Angle : 0.582 8.724 18440 Z= 0.303 Chirality : 0.041 0.164 2085 Planarity : 0.005 0.043 2390 Dihedral : 4.612 22.711 1820 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.52 % Allowed : 15.63 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.56 (0.20), residues: 1685 helix: 1.13 (0.15), residues: 1175 sheet: -1.81 (0.65), residues: 45 loop : 1.50 (0.28), 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 0.018 0.001 PHE H 168 TYR 0.008 0.001 TYR E 164 ARG 0.005 0.000 ARG O 132 Details of bonding type rmsd hydrogen bonds : bond 0.03875 ( 840) hydrogen bonds : angle 4.22267 ( 2490) covalent geometry : bond 0.00327 (13595) covalent geometry : angle 0.58152 (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 528 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 478 time to evaluate : 1.709 Fit side-chains revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8541 (tp30) cc_final: 0.8265 (tp30) REVERT: C 166 ASP cc_start: 0.7811 (m-30) cc_final: 0.7496 (m-30) REVERT: C 168 PHE cc_start: 0.8378 (t80) cc_final: 0.8162 (t80) REVERT: C 200 THR cc_start: 0.8729 (m) cc_final: 0.8454 (p) REVERT: C 201 ILE cc_start: 0.8860 (mm) cc_final: 0.8659 (mm) REVERT: C 213 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8107 (mp0) REVERT: A 176 GLN cc_start: 0.8264 (tt0) cc_final: 0.7863 (tp40) REVERT: A 178 SER cc_start: 0.8402 (OUTLIER) cc_final: 0.8015 (p) REVERT: A 192 GLN cc_start: 0.8735 (tm-30) cc_final: 0.7928 (tm-30) REVERT: A 199 LYS cc_start: 0.8835 (ttmt) cc_final: 0.8577 (ttmt) REVERT: D 157 PRO cc_start: 0.8600 (Cg_endo) cc_final: 0.8313 (Cg_exo) REVERT: E 166 ASP cc_start: 0.7804 (m-30) cc_final: 0.7589 (m-30) REVERT: E 168 PHE cc_start: 0.8814 (t80) cc_final: 0.8430 (t80) REVERT: E 200 THR cc_start: 0.8636 (m) cc_final: 0.8427 (p) REVERT: E 213 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8069 (mp0) REVERT: F 3 VAL cc_start: 0.8833 (t) cc_final: 0.8606 (m) REVERT: F 66 MET cc_start: 0.8950 (tpt) cc_final: 0.8707 (tpt) REVERT: H 168 PHE cc_start: 0.8451 (t80) cc_final: 0.7912 (t80) REVERT: H 213 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7939 (mt-10) REVERT: I 183 ASN cc_start: 0.8558 (m-40) cc_final: 0.8301 (m-40) REVERT: K 200 THR cc_start: 0.8728 (m) cc_final: 0.8504 (p) REVERT: K 213 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8040 (mt-10) REVERT: L 96 MET cc_start: 0.4384 (pmm) cc_final: 0.4099 (ptp) REVERT: L 192 GLN cc_start: 0.8580 (tm-30) cc_final: 0.8073 (tm-30) REVERT: L 197 ASP cc_start: 0.8368 (p0) cc_final: 0.8057 (p0) REVERT: M 199 LYS cc_start: 0.8396 (ttmt) cc_final: 0.7985 (ttmt) REVERT: N 170 LYS cc_start: 0.8535 (ttpp) cc_final: 0.8300 (ttmm) REVERT: N 200 THR cc_start: 0.8785 (m) cc_final: 0.8571 (p) REVERT: N 213 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7965 (mt-10) REVERT: O 70 LYS cc_start: 0.8420 (mptt) cc_final: 0.8215 (mptt) REVERT: O 192 GLN cc_start: 0.8542 (tm-30) cc_final: 0.7721 (tm-30) outliers start: 50 outliers final: 24 residues processed: 498 average time/residue: 0.2778 time to fit residues: 191.7650 Evaluate side-chains 470 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 445 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain 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 71 GLU 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 N residue 191 VAL Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain O residue 178 SER Chi-restraints excluded: chain O residue 210 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 102 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN G 193 ASN I 195 ASN J 155 GLN L 179 GLN L 183 ASN L 195 ASN M 219 GLN O 50 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.131499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.098305 restraints weight = 22754.905| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.67 r_work: 0.3257 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13595 Z= 0.161 Angle : 0.581 8.582 18440 Z= 0.305 Chirality : 0.042 0.163 2085 Planarity : 0.005 0.041 2390 Dihedral : 4.548 23.289 1820 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.24 % Allowed : 16.20 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.60 (0.20), residues: 1685 helix: 1.20 (0.15), residues: 1165 sheet: -1.68 (0.66), residues: 45 loop : 1.35 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 184 HIS 0.001 0.000 HIS A 12 PHE 0.021 0.001 PHE H 168 TYR 0.008 0.001 TYR E 164 ARG 0.009 0.000 ARG I 82 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 840) hydrogen bonds : angle 4.29532 ( 2490) covalent geometry : bond 0.00387 (13595) covalent geometry : angle 0.58103 (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 506 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 460 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 166 ASP cc_start: 0.7823 (m-30) cc_final: 0.7525 (m-30) REVERT: A 192 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8231 (tm-30) REVERT: A 215 MET cc_start: 0.8303 (mtp) cc_final: 0.7934 (mtp) REVERT: E 166 ASP cc_start: 0.7791 (m-30) cc_final: 0.7590 (m-30) REVERT: E 213 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8081 (mp0) REVERT: F 3 VAL cc_start: 0.8851 (t) cc_final: 0.8599 (m) REVERT: F 66 MET cc_start: 0.8956 (tpt) cc_final: 0.8683 (tpt) REVERT: F 192 GLN cc_start: 0.8752 (tm-30) cc_final: 0.7875 (tm-30) REVERT: H 213 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8062 (mp0) REVERT: I 152 ASP cc_start: 0.8965 (m-30) cc_final: 0.8751 (m-30) REVERT: I 183 ASN cc_start: 0.8506 (m-40) cc_final: 0.8257 (m-40) REVERT: J 158 LYS cc_start: 0.8509 (mmtm) cc_final: 0.8249 (tppt) REVERT: K 213 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8004 (mt-10) REVERT: L 182 LYS cc_start: 0.8701 (mttt) cc_final: 0.8488 (mmmm) REVERT: L 197 ASP cc_start: 0.8126 (p0) cc_final: 0.7918 (p0) REVERT: M 167 ARG cc_start: 0.8720 (ttp80) cc_final: 0.8463 (ttp-170) REVERT: N 200 THR cc_start: 0.8840 (m) cc_final: 0.8639 (p) REVERT: N 213 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7883 (mt-10) REVERT: O 192 GLN cc_start: 0.8661 (tm-30) cc_final: 0.7808 (tm-30) outliers start: 46 outliers final: 30 residues processed: 478 average time/residue: 0.2734 time to fit residues: 183.4374 Evaluate side-chains 462 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 432 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain G residue 195 ASN 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 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 71 GLU 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 N residue 191 VAL Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain O residue 189 LEU Chi-restraints excluded: chain O residue 210 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 101 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 120 optimal weight: 7.9990 chunk 87 optimal weight: 0.3980 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN L 179 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 = 0.3831 r_free = 0.3831 target = 0.134027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.101004 restraints weight = 22901.633| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.70 r_work: 0.3243 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4600 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= 0.128 Angle : 0.566 10.301 18440 Z= 0.296 Chirality : 0.041 0.165 2085 Planarity : 0.005 0.041 2390 Dihedral : 4.414 23.064 1820 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.54 % Allowed : 18.52 % Favored : 78.94 % 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: 1.63 (0.20), residues: 1685 helix: 1.22 (0.15), residues: 1170 sheet: -1.45 (0.67), residues: 45 loop : 1.36 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 184 HIS 0.001 0.000 HIS F 12 PHE 0.022 0.001 PHE H 168 TYR 0.009 0.001 TYR E 164 ARG 0.008 0.000 ARG I 82 Details of bonding type rmsd hydrogen bonds : bond 0.03703 ( 840) hydrogen bonds : angle 4.20586 ( 2490) covalent geometry : bond 0.00296 (13595) covalent geometry : angle 0.56609 (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 489 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 453 time to evaluate : 1.475 Fit side-chains revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8637 (tp30) cc_final: 0.8332 (tp30) REVERT: C 166 ASP cc_start: 0.7815 (m-30) cc_final: 0.7501 (m-30) REVERT: C 213 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8099 (mp0) REVERT: A 167 ARG cc_start: 0.8600 (mtm-85) cc_final: 0.8391 (mtm-85) REVERT: A 182 LYS cc_start: 0.8793 (mmtt) cc_final: 0.8584 (mmmm) REVERT: A 215 MET cc_start: 0.8259 (mtp) cc_final: 0.7833 (mtp) REVERT: E 166 ASP cc_start: 0.7808 (m-30) cc_final: 0.7601 (m-30) REVERT: E 213 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8075 (mp0) REVERT: F 3 VAL cc_start: 0.8911 (t) cc_final: 0.8688 (m) REVERT: F 66 MET cc_start: 0.8891 (tpt) cc_final: 0.8676 (tpt) REVERT: H 213 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7860 (mt-10) REVERT: I 183 ASN cc_start: 0.8490 (m-40) cc_final: 0.8264 (m-40) REVERT: J 158 LYS cc_start: 0.8404 (mmtm) cc_final: 0.8160 (tppt) REVERT: K 213 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8010 (mt-10) REVERT: L 192 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8128 (tm-30) REVERT: L 197 ASP cc_start: 0.7929 (p0) cc_final: 0.7609 (p0) REVERT: N 168 PHE cc_start: 0.7963 (t80) cc_final: 0.7528 (t80) REVERT: N 213 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7939 (mt-10) REVERT: O 70 LYS cc_start: 0.8510 (mptt) cc_final: 0.8239 (mptt) REVERT: O 192 GLN cc_start: 0.8640 (tm-30) cc_final: 0.7815 (tm-30) outliers start: 36 outliers final: 24 residues processed: 468 average time/residue: 0.2660 time to fit residues: 174.2052 Evaluate side-chains 440 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 416 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain H residue 215 MET Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 124 ILE Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 218 CYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain M residue 198 CYS Chi-restraints excluded: chain M residue 218 CYS Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain O residue 210 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 19 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 153 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.132471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.099283 restraints weight = 22682.201| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.69 r_work: 0.3239 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13595 Z= 0.148 Angle : 0.582 9.597 18440 Z= 0.304 Chirality : 0.042 0.180 2085 Planarity : 0.005 0.042 2390 Dihedral : 4.400 22.712 1820 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.68 % Allowed : 20.00 % Favored : 77.32 % 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: 1.55 (0.20), residues: 1685 helix: 1.13 (0.15), residues: 1170 sheet: -1.27 (0.68), residues: 45 loop : 1.41 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 184 HIS 0.001 0.000 HIS F 12 PHE 0.014 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 0.03860 ( 840) hydrogen bonds : angle 4.34292 ( 2490) covalent geometry : bond 0.00355 (13595) covalent geometry : angle 0.58194 (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 478 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 440 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8609 (tp30) cc_final: 0.8296 (tp30) REVERT: C 166 ASP cc_start: 0.7843 (m-30) cc_final: 0.7554 (m-30) REVERT: E 213 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8065 (mp0) REVERT: F 66 MET cc_start: 0.8938 (tpt) cc_final: 0.8674 (tpt) REVERT: F 111 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8461 (tt) REVERT: F 192 GLN cc_start: 0.8751 (tm-30) cc_final: 0.7792 (tm-30) REVERT: F 197 ASP cc_start: 0.8178 (p0) cc_final: 0.7950 (p0) REVERT: H 199 LYS cc_start: 0.8806 (ttpt) cc_final: 0.8549 (ttmt) REVERT: H 213 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7979 (mp0) REVERT: I 183 ASN cc_start: 0.8499 (m-40) cc_final: 0.8251 (m-40) REVERT: J 158 LYS cc_start: 0.8496 (mmtm) cc_final: 0.8175 (tppt) REVERT: K 213 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8005 (mt-10) REVERT: L 192 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8104 (tm-30) REVERT: L 197 ASP cc_start: 0.8018 (p0) cc_final: 0.7756 (p0) REVERT: N 213 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8039 (mp0) REVERT: O 192 GLN cc_start: 0.8576 (tm-30) cc_final: 0.7748 (tm-30) outliers start: 38 outliers final: 32 residues processed: 456 average time/residue: 0.2717 time to fit residues: 173.4764 Evaluate side-chains 448 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 415 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain G residue 221 VAL 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 63 GLN Chi-restraints excluded: chain O residue 210 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 122 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 152 optimal weight: 9.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.130463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.097098 restraints weight = 23141.772| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.72 r_work: 0.3189 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13595 Z= 0.217 Angle : 0.640 10.794 18440 Z= 0.335 Chirality : 0.045 0.172 2085 Planarity : 0.005 0.043 2390 Dihedral : 4.574 24.614 1820 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.10 % Allowed : 20.42 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.25 (0.20), residues: 1685 helix: 0.88 (0.15), residues: 1175 sheet: -1.17 (0.68), residues: 45 loop : 1.31 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 184 HIS 0.002 0.000 HIS F 12 PHE 0.013 0.001 PHE C 168 TYR 0.015 0.001 TYR F 130 ARG 0.008 0.001 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 840) hydrogen bonds : angle 4.58809 ( 2490) covalent geometry : bond 0.00527 (13595) covalent geometry : angle 0.64040 (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 459 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 415 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.8684 (tp30) cc_final: 0.8308 (tp30) REVERT: C 166 ASP cc_start: 0.7891 (m-30) cc_final: 0.7607 (m-30) REVERT: C 211 LEU cc_start: 0.8421 (tt) cc_final: 0.8191 (tt) REVERT: C 213 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8122 (mp0) REVERT: E 213 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8058 (mp0) REVERT: F 66 MET cc_start: 0.8969 (tpt) cc_final: 0.8655 (tpt) REVERT: F 111 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8470 (tt) REVERT: F 197 ASP cc_start: 0.8151 (p0) cc_final: 0.7909 (p0) REVERT: H 213 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8007 (mp0) REVERT: I 68 MET cc_start: 0.8486 (mtp) cc_final: 0.8231 (mtp) REVERT: I 183 ASN cc_start: 0.8510 (m-40) cc_final: 0.8275 (m-40) REVERT: L 192 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8194 (tm-30) REVERT: L 197 ASP cc_start: 0.7958 (p0) cc_final: 0.7568 (p0) REVERT: M 203 LYS cc_start: 0.8450 (mtpp) cc_final: 0.8193 (mtmt) REVERT: N 213 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8026 (mp0) REVERT: O 192 GLN cc_start: 0.8737 (tm-30) cc_final: 0.7897 (tm-30) outliers start: 44 outliers final: 32 residues processed: 440 average time/residue: 0.2751 time to fit residues: 168.9731 Evaluate side-chains 433 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 400 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 LEU 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 178 SER Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 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 63 GLN Chi-restraints excluded: chain O residue 178 SER Chi-restraints excluded: chain O residue 210 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 75 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 99 optimal weight: 8.9990 chunk 154 optimal weight: 5.9990 chunk 126 optimal weight: 0.5980 chunk 78 optimal weight: 0.0170 chunk 60 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 50 GLN O 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.134874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.100735 restraints weight = 22318.436| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.80 r_work: 0.3275 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4889 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= 0.132 Angle : 0.582 10.512 18440 Z= 0.307 Chirality : 0.042 0.169 2085 Planarity : 0.005 0.043 2390 Dihedral : 4.401 23.369 1820 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.18 % Allowed : 21.20 % Favored : 76.62 % 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: 1.44 (0.20), residues: 1685 helix: 1.05 (0.15), residues: 1170 sheet: -1.08 (0.70), residues: 45 loop : 1.32 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 184 HIS 0.001 0.000 HIS F 12 PHE 0.008 0.001 PHE F 40 TYR 0.009 0.001 TYR F 130 ARG 0.007 0.000 ARG I 82 Details of bonding type rmsd hydrogen bonds : bond 0.03724 ( 840) hydrogen bonds : angle 4.38802 ( 2490) covalent geometry : bond 0.00306 (13595) covalent geometry : angle 0.58186 (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 474 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 443 time to evaluate : 1.582 Fit side-chains revert: symmetry clash REVERT: B 172 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8390 (tp) REVERT: C 166 ASP cc_start: 0.7849 (m-30) cc_final: 0.7531 (m-30) REVERT: C 213 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8064 (mp0) REVERT: A 70 LYS cc_start: 0.8512 (mptt) cc_final: 0.8205 (mptt) REVERT: A 192 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8117 (tm-30) REVERT: E 213 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8025 (mp0) REVERT: F 45 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7471 (mm-30) REVERT: F 66 MET cc_start: 0.8943 (tpt) cc_final: 0.8677 (tpt) REVERT: F 111 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8253 (tt) REVERT: F 112 GLN cc_start: 0.8871 (tp40) cc_final: 0.8435 (mp10) REVERT: F 192 GLN cc_start: 0.8799 (tm-30) cc_final: 0.7742 (tm-30) REVERT: F 197 ASP cc_start: 0.8069 (p0) cc_final: 0.7798 (p0) REVERT: I 152 ASP cc_start: 0.8929 (m-30) cc_final: 0.8572 (m-30) REVERT: I 183 ASN cc_start: 0.8599 (m-40) cc_final: 0.8359 (m-40) REVERT: K 213 GLU cc_start: 0.8445 (mt-10) cc_final: 0.7946 (mt-10) REVERT: L 192 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8142 (tm-30) REVERT: L 197 ASP cc_start: 0.7936 (p0) cc_final: 0.7684 (p0) REVERT: M 203 LYS cc_start: 0.8427 (mtpp) cc_final: 0.8215 (mtmt) REVERT: N 213 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7991 (mp0) REVERT: O 192 GLN cc_start: 0.8596 (tm-30) cc_final: 0.7830 (tm-30) outliers start: 31 outliers final: 23 residues processed: 458 average time/residue: 0.2685 time to fit residues: 173.3462 Evaluate side-chains 436 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 411 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 71 GLU Chi-restraints excluded: chain I residue 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 195 ASN 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: 4.9990 chunk 119 optimal weight: 9.9990 chunk 15 optimal weight: 0.5980 chunk 112 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 104 optimal weight: 0.0980 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.134514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.099703 restraints weight = 22616.858| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.85 r_work: 0.3244 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13595 Z= 0.137 Angle : 0.593 10.545 18440 Z= 0.314 Chirality : 0.042 0.171 2085 Planarity : 0.005 0.042 2390 Dihedral : 4.323 21.345 1820 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.18 % Allowed : 21.41 % Favored : 76.41 % 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: 1.57 (0.20), residues: 1685 helix: 1.08 (0.15), residues: 1170 sheet: -0.94 (0.69), residues: 45 loop : 1.57 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 184 HIS 0.006 0.001 HIS I 120 PHE 0.007 0.001 PHE F 40 TYR 0.009 0.001 TYR F 130 ARG 0.007 0.000 ARG L 82 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 840) hydrogen bonds : angle 4.45187 ( 2490) covalent geometry : bond 0.00322 (13595) covalent geometry : angle 0.59275 (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 449 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 418 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 166 ASP cc_start: 0.7849 (m-30) cc_final: 0.7533 (m-30) REVERT: C 213 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8043 (mp0) REVERT: A 70 LYS cc_start: 0.8578 (mptt) cc_final: 0.8285 (mptt) REVERT: E 213 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8030 (mp0) REVERT: F 45 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7440 (mm-30) REVERT: F 66 MET cc_start: 0.8900 (tpt) cc_final: 0.8655 (tpt) REVERT: F 111 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8411 (tt) REVERT: F 152 ASP cc_start: 0.8851 (m-30) cc_final: 0.8543 (m-30) REVERT: F 197 ASP cc_start: 0.7938 (p0) cc_final: 0.7673 (p0) REVERT: I 152 ASP cc_start: 0.8913 (m-30) cc_final: 0.8632 (m-30) REVERT: I 183 ASN cc_start: 0.8585 (m-40) cc_final: 0.8330 (m-40) REVERT: L 185 MET cc_start: 0.8707 (ttm) cc_final: 0.8366 (mtp) REVERT: L 197 ASP cc_start: 0.7846 (p0) cc_final: 0.7455 (p0) REVERT: N 199 LYS cc_start: 0.8712 (ttpt) cc_final: 0.8312 (ttmt) REVERT: N 213 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7972 (mp0) REVERT: O 192 GLN cc_start: 0.8605 (tm-30) cc_final: 0.7864 (tm-30) outliers start: 31 outliers final: 25 residues processed: 434 average time/residue: 0.2708 time to fit residues: 167.5266 Evaluate side-chains 430 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 404 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 178 SER 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 210 THR Chi-restraints excluded: chain J residue 218 CYS Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 71 GLU Chi-restraints excluded: chain 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 45 optimal weight: 3.9990 chunk 160 optimal weight: 0.5980 chunk 22 optimal weight: 0.0870 chunk 145 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.135096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.101554 restraints weight = 22482.655| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.77 r_work: 0.3268 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13595 Z= 0.131 Angle : 0.601 10.366 18440 Z= 0.319 Chirality : 0.042 0.169 2085 Planarity : 0.005 0.042 2390 Dihedral : 4.285 23.008 1820 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.04 % Allowed : 22.32 % Favored : 75.63 % 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: 1.59 (0.20), residues: 1685 helix: 1.09 (0.15), residues: 1170 sheet: -0.83 (0.69), residues: 45 loop : 1.58 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 184 HIS 0.006 0.001 HIS I 120 PHE 0.007 0.001 PHE F 40 TYR 0.008 0.001 TYR F 130 ARG 0.007 0.000 ARG I 82 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 840) hydrogen bonds : angle 4.47008 ( 2490) covalent geometry : bond 0.00306 (13595) covalent geometry : angle 0.60075 (18440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8290.39 seconds wall clock time: 143 minutes 12.34 seconds (8592.34 seconds total)