Starting phenix.real_space_refine on Thu Feb 5 13:30:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jps_61713/02_2026/9jps_61713.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jps_61713/02_2026/9jps_61713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jps_61713/02_2026/9jps_61713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jps_61713/02_2026/9jps_61713.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jps_61713/02_2026/9jps_61713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jps_61713/02_2026/9jps_61713.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 11040 2.51 5 N 2976 2.21 5 O 3320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17416 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2177 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain breaks: 1 Chain: "B" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2177 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain breaks: 1 Chain: "C" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2177 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain breaks: 1 Chain: "D" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2177 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain breaks: 1 Chain: "E" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2177 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain breaks: 1 Chain: "F" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2177 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain breaks: 1 Chain: "G" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2177 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain breaks: 1 Chain: "H" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2177 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain breaks: 1 Time building chain proxies: 3.56, per 1000 atoms: 0.20 Number of scatterers: 17416 At special positions: 0 Unit cell: (155.8, 98.8, 196.65, 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 80 16.00 O 3320 8.00 N 2976 7.00 C 11040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 537.3 milliseconds 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4128 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 26 sheets defined 38.1% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 removed outlier: 4.123A pdb=" N THR A 40 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 41 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 87 through 90 Processing helix chain 'A' and resid 99 through 105 Processing helix chain 'A' and resid 110 through 121 Processing helix chain 'A' and resid 123 through 135 Processing helix chain 'A' and resid 136 through 140 Processing helix chain 'A' and resid 145 through 157 Processing helix chain 'A' and resid 179 through 188 removed outlier: 3.734A pdb=" N ASP A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 201 Processing helix chain 'A' and resid 262 through 267 Processing helix chain 'A' and resid 268 through 273 removed outlier: 4.032A pdb=" N ARG A 272 " --> pdb=" O LYS A 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 removed outlier: 4.124A pdb=" N THR B 40 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 41 " --> pdb=" O ASP B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 56 Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 99 through 105 Processing helix chain 'B' and resid 110 through 121 Processing helix chain 'B' and resid 123 through 135 Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'B' and resid 145 through 157 Processing helix chain 'B' and resid 179 through 188 removed outlier: 3.733A pdb=" N ASP B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 201 Processing helix chain 'B' and resid 262 through 267 Processing helix chain 'B' and resid 268 through 273 removed outlier: 4.032A pdb=" N ARG B 272 " --> pdb=" O LYS B 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 41 removed outlier: 4.123A pdb=" N THR C 40 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 41 " --> pdb=" O ASP C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 56 Processing helix chain 'C' and resid 87 through 90 Processing helix chain 'C' and resid 99 through 105 Processing helix chain 'C' and resid 110 through 121 Processing helix chain 'C' and resid 123 through 135 Processing helix chain 'C' and resid 136 through 140 Processing helix chain 'C' and resid 145 through 157 Processing helix chain 'C' and resid 179 through 188 removed outlier: 3.734A pdb=" N ASP C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 201 Processing helix chain 'C' and resid 262 through 267 Processing helix chain 'C' and resid 268 through 273 removed outlier: 4.032A pdb=" N ARG C 272 " --> pdb=" O LYS C 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 41 removed outlier: 4.124A pdb=" N THR D 40 " --> pdb=" O SER D 37 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL D 41 " --> pdb=" O ASP D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 56 Processing helix chain 'D' and resid 87 through 90 Processing helix chain 'D' and resid 99 through 105 Processing helix chain 'D' and resid 110 through 121 Processing helix chain 'D' and resid 123 through 135 Processing helix chain 'D' and resid 136 through 140 Processing helix chain 'D' and resid 145 through 157 Processing helix chain 'D' and resid 179 through 188 removed outlier: 3.733A pdb=" N ASP D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 201 Processing helix chain 'D' and resid 262 through 267 Processing helix chain 'D' and resid 268 through 273 removed outlier: 4.032A pdb=" N ARG D 272 " --> pdb=" O LYS D 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 41 removed outlier: 4.124A pdb=" N THR E 40 " --> pdb=" O SER E 37 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL E 41 " --> pdb=" O ASP E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 56 Processing helix chain 'E' and resid 87 through 90 Processing helix chain 'E' and resid 99 through 105 Processing helix chain 'E' and resid 110 through 121 Processing helix chain 'E' and resid 123 through 135 Processing helix chain 'E' and resid 136 through 140 Processing helix chain 'E' and resid 145 through 157 Processing helix chain 'E' and resid 179 through 188 removed outlier: 3.734A pdb=" N ASP E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 201 Processing helix chain 'E' and resid 262 through 267 Processing helix chain 'E' and resid 268 through 273 removed outlier: 4.032A pdb=" N ARG E 272 " --> pdb=" O LYS E 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 41 removed outlier: 4.124A pdb=" N THR F 40 " --> pdb=" O SER F 37 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL F 41 " --> pdb=" O ASP F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 56 Processing helix chain 'F' and resid 87 through 90 Processing helix chain 'F' and resid 99 through 105 Processing helix chain 'F' and resid 110 through 121 Processing helix chain 'F' and resid 123 through 135 Processing helix chain 'F' and resid 136 through 140 Processing helix chain 'F' and resid 145 through 157 Processing helix chain 'F' and resid 179 through 188 removed outlier: 3.734A pdb=" N ASP F 183 " --> pdb=" O SER F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 201 Processing helix chain 'F' and resid 262 through 267 Processing helix chain 'F' and resid 268 through 273 removed outlier: 4.032A pdb=" N ARG F 272 " --> pdb=" O LYS F 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 41 removed outlier: 4.124A pdb=" N THR G 40 " --> pdb=" O SER G 37 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL G 41 " --> pdb=" O ASP G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 56 Processing helix chain 'G' and resid 87 through 90 Processing helix chain 'G' and resid 99 through 105 Processing helix chain 'G' and resid 110 through 121 Processing helix chain 'G' and resid 123 through 135 Processing helix chain 'G' and resid 136 through 140 Processing helix chain 'G' and resid 145 through 157 Processing helix chain 'G' and resid 179 through 188 removed outlier: 3.733A pdb=" N ASP G 183 " --> pdb=" O SER G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 201 Processing helix chain 'G' and resid 262 through 267 Processing helix chain 'G' and resid 268 through 273 removed outlier: 4.031A pdb=" N ARG G 272 " --> pdb=" O LYS G 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 41 removed outlier: 4.123A pdb=" N THR H 40 " --> pdb=" O SER H 37 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL H 41 " --> pdb=" O ASP H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 56 Processing helix chain 'H' and resid 87 through 90 Processing helix chain 'H' and resid 99 through 105 Processing helix chain 'H' and resid 110 through 121 Processing helix chain 'H' and resid 123 through 135 Processing helix chain 'H' and resid 136 through 140 Processing helix chain 'H' and resid 145 through 157 Processing helix chain 'H' and resid 179 through 188 removed outlier: 3.734A pdb=" N ASP H 183 " --> pdb=" O SER H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 201 Processing helix chain 'H' and resid 262 through 267 Processing helix chain 'H' and resid 268 through 273 removed outlier: 4.033A pdb=" N ARG H 272 " --> pdb=" O LYS H 269 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 66 Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 95 Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 175 removed outlier: 6.565A pdb=" N SER A 205 " --> pdb=" O GLN A 287 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ILE A 289 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR A 207 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 66 Processing sheet with id=AA5, first strand: chain 'B' and resid 92 through 95 Processing sheet with id=AA6, first strand: chain 'B' and resid 172 through 175 removed outlier: 6.564A pdb=" N SER B 205 " --> pdb=" O GLN B 287 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ILE B 289 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR B 207 " --> pdb=" O ILE B 289 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 254 through 255 removed outlier: 4.185A pdb=" N ARG B 254 " --> pdb=" O GLN E 258 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 58 through 66 Processing sheet with id=AA9, first strand: chain 'C' and resid 92 through 95 Processing sheet with id=AB1, first strand: chain 'C' and resid 172 through 175 removed outlier: 6.565A pdb=" N SER C 205 " --> pdb=" O GLN C 287 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ILE C 289 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N THR C 207 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 58 through 66 Processing sheet with id=AB3, first strand: chain 'D' and resid 92 through 95 Processing sheet with id=AB4, first strand: chain 'D' and resid 172 through 175 removed outlier: 6.565A pdb=" N SER D 205 " --> pdb=" O GLN D 287 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ILE D 289 " --> pdb=" O SER D 205 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N THR D 207 " --> pdb=" O ILE D 289 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 254 through 255 removed outlier: 4.233A pdb=" N ARG D 254 " --> pdb=" O GLN G 258 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN G 258 " --> pdb=" O ARG D 254 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 58 through 66 Processing sheet with id=AB7, first strand: chain 'E' and resid 92 through 95 Processing sheet with id=AB8, first strand: chain 'E' and resid 172 through 175 removed outlier: 6.565A pdb=" N SER E 205 " --> pdb=" O GLN E 287 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ILE E 289 " --> pdb=" O SER E 205 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N THR E 207 " --> pdb=" O ILE E 289 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 58 through 66 Processing sheet with id=AC1, first strand: chain 'F' and resid 92 through 95 Processing sheet with id=AC2, first strand: chain 'F' and resid 172 through 175 removed outlier: 6.564A pdb=" N SER F 205 " --> pdb=" O GLN F 287 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ILE F 289 " --> pdb=" O SER F 205 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N THR F 207 " --> pdb=" O ILE F 289 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 58 through 66 Processing sheet with id=AC4, first strand: chain 'G' and resid 92 through 95 Processing sheet with id=AC5, first strand: chain 'G' and resid 172 through 175 removed outlier: 6.565A pdb=" N SER G 205 " --> pdb=" O GLN G 287 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ILE G 289 " --> pdb=" O SER G 205 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR G 207 " --> pdb=" O ILE G 289 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 58 through 66 Processing sheet with id=AC7, first strand: chain 'H' and resid 92 through 95 Processing sheet with id=AC8, first strand: chain 'H' and resid 172 through 175 removed outlier: 6.564A pdb=" N SER H 205 " --> pdb=" O GLN H 287 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ILE H 289 " --> pdb=" O SER H 205 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR H 207 " --> pdb=" O ILE H 289 " (cutoff:3.500A) 617 hydrogen bonds defined for protein. 1611 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.12 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5816 1.35 - 1.46: 3836 1.46 - 1.58: 7972 1.58 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 17728 Sorted by residual: bond pdb=" CB PRO F 66 " pdb=" CG PRO F 66 " ideal model delta sigma weight residual 1.492 1.524 -0.032 5.00e-02 4.00e+02 4.06e-01 bond pdb=" CB PRO E 66 " pdb=" CG PRO E 66 " ideal model delta sigma weight residual 1.492 1.524 -0.032 5.00e-02 4.00e+02 4.06e-01 bond pdb=" CB PRO G 66 " pdb=" CG PRO G 66 " ideal model delta sigma weight residual 1.492 1.524 -0.032 5.00e-02 4.00e+02 4.02e-01 bond pdb=" CB PRO D 66 " pdb=" CG PRO D 66 " ideal model delta sigma weight residual 1.492 1.523 -0.031 5.00e-02 4.00e+02 3.93e-01 bond pdb=" CB PRO H 66 " pdb=" CG PRO H 66 " ideal model delta sigma weight residual 1.492 1.523 -0.031 5.00e-02 4.00e+02 3.92e-01 ... (remaining 17723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 23569 1.46 - 2.92: 323 2.92 - 4.38: 92 4.38 - 5.84: 10 5.84 - 7.29: 14 Bond angle restraints: 24008 Sorted by residual: angle pdb=" N GLY F 177 " pdb=" CA GLY F 177 " pdb=" C GLY F 177 " ideal model delta sigma weight residual 110.63 114.24 -3.61 1.45e+00 4.76e-01 6.19e+00 angle pdb=" N GLY D 177 " pdb=" CA GLY D 177 " pdb=" C GLY D 177 " ideal model delta sigma weight residual 110.63 114.22 -3.59 1.45e+00 4.76e-01 6.11e+00 angle pdb=" N GLY A 177 " pdb=" CA GLY A 177 " pdb=" C GLY A 177 " ideal model delta sigma weight residual 110.63 114.21 -3.58 1.45e+00 4.76e-01 6.11e+00 angle pdb=" N GLY B 177 " pdb=" CA GLY B 177 " pdb=" C GLY B 177 " ideal model delta sigma weight residual 110.63 114.21 -3.58 1.45e+00 4.76e-01 6.09e+00 angle pdb=" N GLY G 177 " pdb=" CA GLY G 177 " pdb=" C GLY G 177 " ideal model delta sigma weight residual 110.63 114.20 -3.57 1.45e+00 4.76e-01 6.06e+00 ... (remaining 24003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.21: 9456 16.21 - 32.41: 958 32.41 - 48.62: 314 48.62 - 64.83: 16 64.83 - 81.03: 72 Dihedral angle restraints: 10816 sinusoidal: 4432 harmonic: 6384 Sorted by residual: dihedral pdb=" CB GLU B 90 " pdb=" CG GLU B 90 " pdb=" CD GLU B 90 " pdb=" OE1 GLU B 90 " ideal model delta sinusoidal sigma weight residual 0.00 81.03 -81.03 1 3.00e+01 1.11e-03 9.00e+00 dihedral pdb=" CB GLU C 90 " pdb=" CG GLU C 90 " pdb=" CD GLU C 90 " pdb=" OE1 GLU C 90 " ideal model delta sinusoidal sigma weight residual 0.00 81.02 -81.02 1 3.00e+01 1.11e-03 9.00e+00 dihedral pdb=" CB GLU A 90 " pdb=" CG GLU A 90 " pdb=" CD GLU A 90 " pdb=" OE1 GLU A 90 " ideal model delta sinusoidal sigma weight residual 0.00 80.97 -80.97 1 3.00e+01 1.11e-03 8.99e+00 ... (remaining 10813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1380 0.025 - 0.050: 767 0.050 - 0.075: 378 0.075 - 0.100: 90 0.100 - 0.124: 81 Chirality restraints: 2696 Sorted by residual: chirality pdb=" CA ILE B 65 " pdb=" N ILE B 65 " pdb=" C ILE B 65 " pdb=" CB ILE B 65 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ILE D 65 " pdb=" N ILE D 65 " pdb=" C ILE D 65 " pdb=" CB ILE D 65 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CA ILE G 65 " pdb=" N ILE G 65 " pdb=" C ILE G 65 " pdb=" CB ILE G 65 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.69e-01 ... (remaining 2693 not shown) Planarity restraints: 3144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 135 " 0.080 9.50e-02 1.11e+02 3.59e-02 8.67e-01 pdb=" NE ARG F 135 " -0.003 2.00e-02 2.50e+03 pdb=" CZ ARG F 135 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG F 135 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG F 135 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 135 " 0.080 9.50e-02 1.11e+02 3.59e-02 8.60e-01 pdb=" NE ARG G 135 " -0.003 2.00e-02 2.50e+03 pdb=" CZ ARG G 135 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG G 135 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG G 135 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 135 " 0.079 9.50e-02 1.11e+02 3.57e-02 8.51e-01 pdb=" NE ARG E 135 " -0.003 2.00e-02 2.50e+03 pdb=" CZ ARG E 135 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG E 135 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 135 " 0.004 2.00e-02 2.50e+03 ... (remaining 3141 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 203 2.68 - 3.24: 16839 3.24 - 3.79: 26006 3.79 - 4.35: 36308 4.35 - 4.90: 61557 Nonbonded interactions: 140913 Sorted by model distance: nonbonded pdb=" OE1 GLN D 260 " pdb=" N GLN G 252 " model vdw 2.127 3.120 nonbonded pdb=" OG SER B 32 " pdb=" OD1 ASP G 29 " model vdw 2.194 3.040 nonbonded pdb=" OD1 ASP B 29 " pdb=" OG SER G 32 " model vdw 2.199 3.040 nonbonded pdb=" OE1 GLN B 260 " pdb=" N GLN E 252 " model vdw 2.238 3.120 nonbonded pdb=" ND2 ASN D 262 " pdb=" O GLU G 248 " model vdw 2.310 3.120 ... (remaining 140908 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 13.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.180 Find NCS groups from input model: 0.100 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 : 0.002 0.032 17728 Z= 0.080 Angle : 0.498 7.294 24008 Z= 0.252 Chirality : 0.040 0.124 2696 Planarity : 0.003 0.036 3144 Dihedral : 15.588 81.032 6688 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.18), residues: 2128 helix: 0.14 (0.20), residues: 688 sheet: -0.94 (0.31), residues: 248 loop : -0.16 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 135 TYR 0.005 0.001 TYR A 100 PHE 0.004 0.001 PHE B 19 TRP 0.003 0.001 TRP A 45 HIS 0.001 0.000 HIS D 51 Details of bonding type rmsd covalent geometry : bond 0.00169 (17728) covalent geometry : angle 0.49817 (24008) hydrogen bonds : bond 0.11625 ( 617) hydrogen bonds : angle 6.20375 ( 1611) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 446 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8544 (mmtp) cc_final: 0.8201 (mmmt) REVERT: A 128 ASN cc_start: 0.8045 (m-40) cc_final: 0.7536 (m110) REVERT: D 126 LYS cc_start: 0.8528 (mmmt) cc_final: 0.8206 (mmtt) REVERT: D 143 GLU cc_start: 0.7149 (pm20) cc_final: 0.6941 (pm20) REVERT: E 182 ASP cc_start: 0.6714 (m-30) cc_final: 0.6504 (m-30) REVERT: F 153 LEU cc_start: 0.8392 (tp) cc_final: 0.8140 (tt) REVERT: F 249 ASN cc_start: 0.8059 (m-40) cc_final: 0.7715 (t0) REVERT: F 267 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7942 (mt0) REVERT: G 42 ASP cc_start: 0.7581 (t0) cc_final: 0.7264 (t70) REVERT: G 133 GLN cc_start: 0.8162 (mt0) cc_final: 0.7554 (mt0) outliers start: 0 outliers final: 0 residues processed: 446 average time/residue: 0.1727 time to fit residues: 105.9679 Evaluate side-chains 234 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.0370 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 0.0870 chunk 77 optimal weight: 6.9990 overall best weight: 1.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN C 247 ASN C 252 GLN D 105 ASN D 247 ASN E 150 ASN E 247 ASN G 105 ASN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.132663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.098329 restraints weight = 24456.401| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.75 r_work: 0.2989 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17728 Z= 0.213 Angle : 0.582 9.665 24008 Z= 0.290 Chirality : 0.044 0.153 2696 Planarity : 0.004 0.029 3144 Dihedral : 4.016 16.373 2392 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.02 % Allowed : 10.10 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.17), residues: 2128 helix: -0.23 (0.19), residues: 688 sheet: -1.23 (0.29), residues: 248 loop : -0.21 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 222 TYR 0.017 0.001 TYR F 100 PHE 0.015 0.001 PHE B 140 TRP 0.011 0.002 TRP G 45 HIS 0.002 0.001 HIS E 51 Details of bonding type rmsd covalent geometry : bond 0.00513 (17728) covalent geometry : angle 0.58174 (24008) hydrogen bonds : bond 0.02833 ( 617) hydrogen bonds : angle 5.78575 ( 1611) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 246 time to evaluate : 0.682 Fit side-chains REVERT: A 124 LYS cc_start: 0.8601 (mmtp) cc_final: 0.8043 (mmmt) REVERT: A 128 ASN cc_start: 0.8228 (m-40) cc_final: 0.7730 (m110) REVERT: A 135 ARG cc_start: 0.8007 (mmp80) cc_final: 0.7375 (mtp180) REVERT: A 154 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7790 (ppt-90) REVERT: B 42 ASP cc_start: 0.7866 (t0) cc_final: 0.7659 (t0) REVERT: C 222 ARG cc_start: 0.8014 (mtp85) cc_final: 0.7797 (mtp85) REVERT: D 126 LYS cc_start: 0.8570 (mmmt) cc_final: 0.8332 (mmtt) REVERT: D 250 ARG cc_start: 0.8476 (ptp-170) cc_final: 0.8202 (ptp90) REVERT: E 83 ASP cc_start: 0.8021 (t0) cc_final: 0.7757 (t0) REVERT: E 85 LYS cc_start: 0.8640 (mmmt) cc_final: 0.8141 (mmtm) REVERT: E 250 ARG cc_start: 0.8275 (ptt-90) cc_final: 0.8043 (ttp80) REVERT: F 153 LEU cc_start: 0.8691 (tp) cc_final: 0.8362 (tt) REVERT: F 183 ASP cc_start: 0.7626 (m-30) cc_final: 0.7389 (m-30) REVERT: F 249 ASN cc_start: 0.7987 (m-40) cc_final: 0.7574 (m110) REVERT: F 267 GLN cc_start: 0.8408 (mm-40) cc_final: 0.8089 (mt0) REVERT: F 271 SER cc_start: 0.9244 (t) cc_final: 0.8982 (m) REVERT: G 42 ASP cc_start: 0.8146 (t0) cc_final: 0.7916 (t0) REVERT: G 147 GLU cc_start: 0.8209 (pp20) cc_final: 0.7923 (pp20) REVERT: G 182 ASP cc_start: 0.7692 (m-30) cc_final: 0.7304 (t0) REVERT: G 250 ARG cc_start: 0.7210 (ptp-110) cc_final: 0.6773 (ptt90) REVERT: H 268 GLN cc_start: 0.8192 (tp40) cc_final: 0.7690 (tm-30) REVERT: H 286 LYS cc_start: 0.8594 (mttt) cc_final: 0.8292 (mtpp) outliers start: 20 outliers final: 15 residues processed: 259 average time/residue: 0.1924 time to fit residues: 68.1326 Evaluate side-chains 224 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 208 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 154 ARG Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain H residue 154 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 113 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.0670 chunk 172 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 202 optimal weight: 8.9990 chunk 203 optimal weight: 4.9990 chunk 160 optimal weight: 0.0040 overall best weight: 0.4730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN C 252 GLN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 ASN H 214 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.135240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.101159 restraints weight = 24552.741| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.60 r_work: 0.3051 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17728 Z= 0.091 Angle : 0.472 11.219 24008 Z= 0.233 Chirality : 0.041 0.164 2696 Planarity : 0.003 0.024 3144 Dihedral : 3.599 13.374 2392 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.82 % Allowed : 11.43 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.17), residues: 2128 helix: 0.09 (0.20), residues: 688 sheet: -1.02 (0.30), residues: 248 loop : -0.16 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 154 TYR 0.013 0.001 TYR C 137 PHE 0.008 0.001 PHE B 140 TRP 0.006 0.001 TRP G 45 HIS 0.001 0.000 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00211 (17728) covalent geometry : angle 0.47228 (24008) hydrogen bonds : bond 0.02295 ( 617) hydrogen bonds : angle 5.30794 ( 1611) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 236 time to evaluate : 0.668 Fit side-chains REVERT: A 128 ASN cc_start: 0.8247 (m-40) cc_final: 0.7822 (m110) REVERT: A 135 ARG cc_start: 0.8086 (mmp80) cc_final: 0.7404 (mtp180) REVERT: B 42 ASP cc_start: 0.7734 (t0) cc_final: 0.7516 (t0) REVERT: D 126 LYS cc_start: 0.8586 (mmmt) cc_final: 0.8376 (mmtt) REVERT: D 268 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7695 (tm-30) REVERT: E 83 ASP cc_start: 0.7966 (t0) cc_final: 0.7763 (t0) REVERT: E 154 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7981 (ptp-170) REVERT: E 229 LEU cc_start: 0.8850 (mp) cc_final: 0.8634 (pp) REVERT: E 286 LYS cc_start: 0.8458 (mtpp) cc_final: 0.8053 (mtpp) REVERT: F 183 ASP cc_start: 0.7524 (m-30) cc_final: 0.7308 (m-30) REVERT: F 249 ASN cc_start: 0.8034 (m-40) cc_final: 0.7621 (m110) REVERT: F 267 GLN cc_start: 0.8276 (mm-40) cc_final: 0.8012 (mt0) REVERT: G 42 ASP cc_start: 0.8069 (t0) cc_final: 0.7652 (t70) REVERT: G 97 GLN cc_start: 0.8030 (pt0) cc_final: 0.7723 (mt0) REVERT: G 147 GLU cc_start: 0.8190 (pp20) cc_final: 0.7882 (pp20) REVERT: G 250 ARG cc_start: 0.7275 (ptp-110) cc_final: 0.6795 (ptt90) REVERT: H 135 ARG cc_start: 0.7933 (mmm160) cc_final: 0.7733 (mmm160) REVERT: H 268 GLN cc_start: 0.8149 (tp40) cc_final: 0.7707 (tm-30) outliers start: 16 outliers final: 10 residues processed: 246 average time/residue: 0.1728 time to fit residues: 58.7296 Evaluate side-chains 207 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 196 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 154 ARG Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain H residue 154 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 71 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 206 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN B 247 ASN D 105 ASN D 150 ASN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.131330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.097120 restraints weight = 24606.947| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.59 r_work: 0.3010 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17728 Z= 0.159 Angle : 0.518 12.016 24008 Z= 0.254 Chirality : 0.042 0.156 2696 Planarity : 0.003 0.026 3144 Dihedral : 3.806 14.948 2392 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.28 % Allowed : 13.27 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.17), residues: 2128 helix: -0.08 (0.20), residues: 696 sheet: -1.08 (0.30), residues: 248 loop : -0.04 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 222 TYR 0.011 0.001 TYR A 149 PHE 0.013 0.001 PHE B 140 TRP 0.009 0.002 TRP F 45 HIS 0.002 0.001 HIS G 51 Details of bonding type rmsd covalent geometry : bond 0.00381 (17728) covalent geometry : angle 0.51845 (24008) hydrogen bonds : bond 0.02530 ( 617) hydrogen bonds : angle 5.40298 ( 1611) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 221 time to evaluate : 0.703 Fit side-chains REVERT: A 135 ARG cc_start: 0.8170 (mmp80) cc_final: 0.7246 (mtp85) REVERT: B 42 ASP cc_start: 0.7749 (t0) cc_final: 0.7549 (t0) REVERT: D 126 LYS cc_start: 0.8636 (mmmt) cc_final: 0.8153 (mmtt) REVERT: D 268 GLN cc_start: 0.8020 (tm-30) cc_final: 0.7728 (tm-30) REVERT: E 229 LEU cc_start: 0.8902 (mp) cc_final: 0.8702 (pp) REVERT: F 100 TYR cc_start: 0.8976 (p90) cc_final: 0.8718 (p90) REVERT: F 267 GLN cc_start: 0.8312 (mm-40) cc_final: 0.8095 (mt0) REVERT: F 271 SER cc_start: 0.9209 (t) cc_final: 0.8980 (m) REVERT: G 42 ASP cc_start: 0.8146 (t0) cc_final: 0.7831 (t0) REVERT: G 147 GLU cc_start: 0.8190 (pp20) cc_final: 0.7923 (pp20) REVERT: G 250 ARG cc_start: 0.7303 (ptp-110) cc_final: 0.6958 (ptt90) REVERT: H 135 ARG cc_start: 0.7975 (mmm160) cc_final: 0.7752 (mmm160) REVERT: H 268 GLN cc_start: 0.8137 (tp40) cc_final: 0.7672 (tm-30) REVERT: H 286 LYS cc_start: 0.8595 (mttt) cc_final: 0.8302 (mtpp) outliers start: 25 outliers final: 17 residues processed: 234 average time/residue: 0.1824 time to fit residues: 58.9529 Evaluate side-chains 215 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain E residue 154 ARG Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 154 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 105 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 1 optimal weight: 0.4980 chunk 208 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN B 247 ASN C 214 GLN ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.131694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.097675 restraints weight = 24371.298| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.57 r_work: 0.3014 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17728 Z= 0.149 Angle : 0.514 11.732 24008 Z= 0.252 Chirality : 0.042 0.167 2696 Planarity : 0.003 0.025 3144 Dihedral : 3.779 14.394 2392 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.33 % Allowed : 14.13 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.17), residues: 2128 helix: -0.10 (0.20), residues: 696 sheet: -1.02 (0.30), residues: 248 loop : 0.01 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 154 TYR 0.011 0.001 TYR A 149 PHE 0.012 0.001 PHE B 140 TRP 0.009 0.002 TRP G 45 HIS 0.002 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00358 (17728) covalent geometry : angle 0.51383 (24008) hydrogen bonds : bond 0.02429 ( 617) hydrogen bonds : angle 5.34711 ( 1611) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 0.633 Fit side-chains REVERT: A 135 ARG cc_start: 0.8155 (mmp80) cc_final: 0.7239 (mtp85) REVERT: C 154 ARG cc_start: 0.8395 (tmm-80) cc_final: 0.7820 (mtm110) REVERT: F 260 GLN cc_start: 0.5178 (mp10) cc_final: 0.4868 (mp10) REVERT: G 42 ASP cc_start: 0.8147 (t0) cc_final: 0.7840 (t0) REVERT: G 97 GLN cc_start: 0.8083 (pt0) cc_final: 0.7874 (mt0) REVERT: G 250 ARG cc_start: 0.7354 (ptp-110) cc_final: 0.6958 (ptt90) REVERT: H 135 ARG cc_start: 0.8031 (mmm160) cc_final: 0.7780 (mmm160) REVERT: H 250 ARG cc_start: 0.8278 (ptm160) cc_final: 0.8068 (ptp-170) REVERT: H 268 GLN cc_start: 0.8120 (tp40) cc_final: 0.7694 (tm-30) REVERT: H 286 LYS cc_start: 0.8600 (mttt) cc_final: 0.8292 (mtpp) outliers start: 26 outliers final: 14 residues processed: 227 average time/residue: 0.1715 time to fit residues: 54.0468 Evaluate side-chains 204 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 190 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain B residue 135 ARG Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 154 ARG Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 154 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 33 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 36 optimal weight: 0.0270 chunk 111 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 192 optimal weight: 0.5980 chunk 215 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 overall best weight: 1.5244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN B 160 ASN B 247 ASN ** E 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN H 150 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.129777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.095645 restraints weight = 24518.180| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.57 r_work: 0.2992 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17728 Z= 0.176 Angle : 0.548 12.081 24008 Z= 0.265 Chirality : 0.043 0.174 2696 Planarity : 0.003 0.026 3144 Dihedral : 3.888 15.531 2392 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.89 % Allowed : 15.10 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.17), residues: 2128 helix: -0.16 (0.20), residues: 696 sheet: -1.05 (0.29), residues: 248 loop : 0.01 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 154 TYR 0.011 0.001 TYR F 100 PHE 0.013 0.001 PHE B 140 TRP 0.009 0.002 TRP F 45 HIS 0.003 0.001 HIS G 51 Details of bonding type rmsd covalent geometry : bond 0.00423 (17728) covalent geometry : angle 0.54838 (24008) hydrogen bonds : bond 0.02527 ( 617) hydrogen bonds : angle 5.43029 ( 1611) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 0.581 Fit side-chains REVERT: A 135 ARG cc_start: 0.8210 (mmp80) cc_final: 0.7309 (mtp85) REVERT: A 172 GLU cc_start: 0.6661 (mp0) cc_final: 0.6329 (mp0) REVERT: B 143 GLU cc_start: 0.7973 (mp0) cc_final: 0.7742 (pm20) REVERT: C 124 LYS cc_start: 0.8774 (mmtp) cc_final: 0.8522 (mmtm) REVERT: C 154 ARG cc_start: 0.8389 (tmm-80) cc_final: 0.7857 (mtm110) REVERT: G 42 ASP cc_start: 0.8226 (t0) cc_final: 0.7901 (t0) REVERT: G 134 LEU cc_start: 0.8878 (mt) cc_final: 0.8675 (mp) REVERT: G 250 ARG cc_start: 0.7351 (ptp-110) cc_final: 0.6972 (ptt90) REVERT: H 135 ARG cc_start: 0.8114 (mmm160) cc_final: 0.7862 (mmm160) REVERT: H 250 ARG cc_start: 0.8263 (ptm160) cc_final: 0.8048 (ptp-170) REVERT: H 268 GLN cc_start: 0.8114 (tp40) cc_final: 0.7654 (tm-30) REVERT: H 286 LYS cc_start: 0.8616 (mttt) cc_final: 0.8301 (mtpp) outliers start: 37 outliers final: 23 residues processed: 226 average time/residue: 0.1788 time to fit residues: 55.8617 Evaluate side-chains 202 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 154 ARG Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain H residue 154 ARG Chi-restraints excluded: chain H residue 156 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 5 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 9 optimal weight: 0.0270 chunk 41 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 129 optimal weight: 6.9990 chunk 154 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 177 optimal weight: 7.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN B 160 ASN B 247 ASN D 105 ASN D 247 ASN D 277 GLN F 160 ASN F 249 ASN F 277 GLN G 97 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.132316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.098650 restraints weight = 24320.741| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.55 r_work: 0.3039 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17728 Z= 0.099 Angle : 0.497 12.204 24008 Z= 0.240 Chirality : 0.041 0.158 2696 Planarity : 0.003 0.041 3144 Dihedral : 3.639 13.644 2392 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.07 % Allowed : 16.28 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.17), residues: 2128 helix: -0.33 (0.19), residues: 744 sheet: -0.82 (0.31), residues: 240 loop : -0.43 (0.16), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 154 TYR 0.012 0.001 TYR F 100 PHE 0.009 0.001 PHE B 140 TRP 0.007 0.001 TRP G 45 HIS 0.001 0.000 HIS G 51 Details of bonding type rmsd covalent geometry : bond 0.00236 (17728) covalent geometry : angle 0.49712 (24008) hydrogen bonds : bond 0.02205 ( 617) hydrogen bonds : angle 5.17650 ( 1611) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.720 Fit side-chains REVERT: A 135 ARG cc_start: 0.8159 (mmp80) cc_final: 0.7487 (mtp180) REVERT: A 172 GLU cc_start: 0.6453 (mp0) cc_final: 0.6146 (mp0) REVERT: B 143 GLU cc_start: 0.7948 (mp0) cc_final: 0.7700 (pm20) REVERT: C 124 LYS cc_start: 0.8717 (mmtp) cc_final: 0.8481 (mmtm) REVERT: C 136 MET cc_start: 0.6892 (ptt) cc_final: 0.6664 (ptt) REVERT: C 143 GLU cc_start: 0.7858 (pm20) cc_final: 0.7653 (pm20) REVERT: C 154 ARG cc_start: 0.8344 (tmm-80) cc_final: 0.7754 (mtm110) REVERT: D 156 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7747 (mp) REVERT: D 211 GLU cc_start: 0.8265 (pm20) cc_final: 0.8028 (pm20) REVERT: F 212 ASP cc_start: 0.8129 (m-30) cc_final: 0.7727 (t0) REVERT: F 253 ILE cc_start: 0.9065 (mm) cc_final: 0.8540 (tt) REVERT: G 42 ASP cc_start: 0.8145 (t0) cc_final: 0.7848 (t0) REVERT: G 134 LEU cc_start: 0.8794 (mt) cc_final: 0.8575 (mp) REVERT: G 250 ARG cc_start: 0.7426 (ptp-110) cc_final: 0.7079 (ptt90) REVERT: H 135 ARG cc_start: 0.8116 (mmm160) cc_final: 0.7855 (mmm160) REVERT: H 204 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7851 (mt-10) REVERT: H 268 GLN cc_start: 0.8095 (tp40) cc_final: 0.7704 (tm-30) outliers start: 21 outliers final: 13 residues processed: 207 average time/residue: 0.1692 time to fit residues: 48.9038 Evaluate side-chains 199 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain H residue 154 ARG Chi-restraints excluded: chain H residue 229 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 118 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 110 optimal weight: 0.0050 chunk 194 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN B 160 ASN D 105 ASN F 150 ASN F 160 ASN F 249 ASN G 97 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.133278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.099565 restraints weight = 24275.089| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.55 r_work: 0.3044 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17728 Z= 0.101 Angle : 0.500 12.186 24008 Z= 0.240 Chirality : 0.041 0.204 2696 Planarity : 0.003 0.028 3144 Dihedral : 3.596 13.838 2392 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.97 % Allowed : 16.68 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.17), residues: 2128 helix: -0.29 (0.19), residues: 744 sheet: -0.76 (0.31), residues: 240 loop : -0.39 (0.16), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 154 TYR 0.012 0.001 TYR F 100 PHE 0.009 0.001 PHE B 140 TRP 0.006 0.002 TRP A 45 HIS 0.001 0.001 HIS G 51 Details of bonding type rmsd covalent geometry : bond 0.00241 (17728) covalent geometry : angle 0.49975 (24008) hydrogen bonds : bond 0.02182 ( 617) hydrogen bonds : angle 5.10907 ( 1611) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 0.702 Fit side-chains REVERT: A 135 ARG cc_start: 0.8156 (mmp80) cc_final: 0.7489 (mtp180) REVERT: A 172 GLU cc_start: 0.6452 (mp0) cc_final: 0.6137 (mp0) REVERT: B 143 GLU cc_start: 0.7926 (mp0) cc_final: 0.7690 (pm20) REVERT: C 124 LYS cc_start: 0.8702 (mmtp) cc_final: 0.8480 (mmtm) REVERT: C 143 GLU cc_start: 0.7879 (pm20) cc_final: 0.7672 (pm20) REVERT: C 154 ARG cc_start: 0.8350 (tmm-80) cc_final: 0.7752 (mtm110) REVERT: C 211 GLU cc_start: 0.8014 (pm20) cc_final: 0.7512 (pm20) REVERT: D 156 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7736 (mp) REVERT: D 211 GLU cc_start: 0.8231 (pm20) cc_final: 0.7994 (pm20) REVERT: F 67 ASP cc_start: 0.8411 (p0) cc_final: 0.8019 (p0) REVERT: F 212 ASP cc_start: 0.8118 (m-30) cc_final: 0.7734 (t0) REVERT: F 253 ILE cc_start: 0.9066 (mm) cc_final: 0.8557 (tt) REVERT: G 42 ASP cc_start: 0.8153 (t0) cc_final: 0.7862 (t0) REVERT: G 134 LEU cc_start: 0.8815 (mt) cc_final: 0.8609 (mp) REVERT: G 250 ARG cc_start: 0.7395 (ptp-110) cc_final: 0.7170 (ptp-110) REVERT: H 132 GLN cc_start: 0.8185 (pt0) cc_final: 0.7844 (mp10) REVERT: H 204 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7854 (mt-10) REVERT: H 268 GLN cc_start: 0.8090 (tp40) cc_final: 0.7703 (tm-30) outliers start: 19 outliers final: 15 residues processed: 206 average time/residue: 0.1674 time to fit residues: 48.4254 Evaluate side-chains 200 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 ARG Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain H residue 154 ARG Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain H residue 229 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 141 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 105 optimal weight: 0.3980 chunk 153 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 118 optimal weight: 0.4980 chunk 175 optimal weight: 0.5980 chunk 198 optimal weight: 0.0060 chunk 37 optimal weight: 0.5980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN B 160 ASN F 160 ASN F 249 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.134947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.101277 restraints weight = 24366.273| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.57 r_work: 0.3067 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17728 Z= 0.087 Angle : 0.494 12.239 24008 Z= 0.236 Chirality : 0.040 0.187 2696 Planarity : 0.003 0.031 3144 Dihedral : 3.495 14.117 2392 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.12 % Allowed : 16.84 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.17), residues: 2128 helix: -0.21 (0.19), residues: 744 sheet: -0.64 (0.32), residues: 240 loop : -0.38 (0.16), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 154 TYR 0.011 0.001 TYR F 100 PHE 0.007 0.001 PHE B 140 TRP 0.006 0.001 TRP G 45 HIS 0.001 0.000 HIS G 51 Details of bonding type rmsd covalent geometry : bond 0.00205 (17728) covalent geometry : angle 0.49388 (24008) hydrogen bonds : bond 0.02093 ( 617) hydrogen bonds : angle 4.99809 ( 1611) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 135 ARG cc_start: 0.8063 (mmp80) cc_final: 0.7198 (mtp85) REVERT: A 172 GLU cc_start: 0.6439 (mp0) cc_final: 0.6081 (mp0) REVERT: B 143 GLU cc_start: 0.7855 (mp0) cc_final: 0.7617 (pm20) REVERT: C 124 LYS cc_start: 0.8690 (mmtp) cc_final: 0.8470 (mmtm) REVERT: C 154 ARG cc_start: 0.8332 (tmm-80) cc_final: 0.7724 (mtm110) REVERT: C 211 GLU cc_start: 0.8019 (pm20) cc_final: 0.7522 (pm20) REVERT: D 156 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7775 (mp) REVERT: D 211 GLU cc_start: 0.8203 (pm20) cc_final: 0.7986 (pm20) REVERT: F 67 ASP cc_start: 0.8394 (p0) cc_final: 0.8030 (p0) REVERT: F 143 GLU cc_start: 0.7254 (pm20) cc_final: 0.7004 (pm20) REVERT: F 212 ASP cc_start: 0.8133 (m-30) cc_final: 0.7737 (t0) REVERT: F 253 ILE cc_start: 0.9064 (mm) cc_final: 0.8547 (tt) REVERT: G 42 ASP cc_start: 0.8113 (t0) cc_final: 0.7832 (t0) REVERT: G 250 ARG cc_start: 0.7478 (ptp-110) cc_final: 0.7253 (ptp-110) REVERT: H 132 GLN cc_start: 0.8245 (pt0) cc_final: 0.7939 (mp10) REVERT: H 204 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7819 (mt-10) REVERT: H 268 GLN cc_start: 0.8094 (tp40) cc_final: 0.7711 (tm-30) outliers start: 22 outliers final: 14 residues processed: 212 average time/residue: 0.1618 time to fit residues: 48.4321 Evaluate side-chains 204 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 189 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain H residue 154 ARG Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain H residue 229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 193 optimal weight: 0.9990 chunk 114 optimal weight: 0.3980 chunk 15 optimal weight: 7.9990 chunk 140 optimal weight: 0.9980 chunk 211 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 214 optimal weight: 1.9990 chunk 79 optimal weight: 0.0370 chunk 204 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN B 160 ASN B 247 ASN F 249 ASN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.134820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.100831 restraints weight = 24274.977| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.60 r_work: 0.3034 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17728 Z= 0.102 Angle : 0.509 12.191 24008 Z= 0.243 Chirality : 0.041 0.175 2696 Planarity : 0.003 0.035 3144 Dihedral : 3.520 14.261 2392 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.97 % Allowed : 17.45 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.17), residues: 2128 helix: -0.25 (0.19), residues: 744 sheet: -0.64 (0.32), residues: 240 loop : -0.32 (0.16), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 154 TYR 0.012 0.001 TYR F 100 PHE 0.008 0.001 PHE B 140 TRP 0.009 0.002 TRP H 45 HIS 0.002 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00246 (17728) covalent geometry : angle 0.50949 (24008) hydrogen bonds : bond 0.02213 ( 617) hydrogen bonds : angle 5.05623 ( 1611) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 200 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 135 ARG cc_start: 0.8173 (mmp80) cc_final: 0.7301 (mtp85) REVERT: A 141 ARG cc_start: 0.7399 (mtm-85) cc_final: 0.7109 (mtm-85) REVERT: A 172 GLU cc_start: 0.6464 (mp0) cc_final: 0.6118 (mp0) REVERT: B 143 GLU cc_start: 0.7865 (mp0) cc_final: 0.7628 (pm20) REVERT: C 124 LYS cc_start: 0.8664 (mmtp) cc_final: 0.8453 (mmtm) REVERT: C 154 ARG cc_start: 0.8348 (tmm-80) cc_final: 0.7725 (mtm110) REVERT: D 132 GLN cc_start: 0.8161 (mm-40) cc_final: 0.7887 (mp10) REVERT: D 156 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7706 (mp) REVERT: F 67 ASP cc_start: 0.8409 (p0) cc_final: 0.8031 (p0) REVERT: F 143 GLU cc_start: 0.7293 (pm20) cc_final: 0.7036 (pm20) REVERT: F 212 ASP cc_start: 0.8151 (m-30) cc_final: 0.7730 (t0) REVERT: F 253 ILE cc_start: 0.9080 (mm) cc_final: 0.8573 (tt) REVERT: G 42 ASP cc_start: 0.8153 (t0) cc_final: 0.7833 (t0) REVERT: H 204 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7830 (mt-10) REVERT: H 268 GLN cc_start: 0.8132 (tp40) cc_final: 0.7698 (tm-30) outliers start: 19 outliers final: 17 residues processed: 211 average time/residue: 0.1639 time to fit residues: 48.4289 Evaluate side-chains 212 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 136 MET Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain F residue 122 ASP Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain H residue 154 ARG Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain H residue 229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 175 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 193 optimal weight: 0.0470 chunk 152 optimal weight: 0.7980 chunk 176 optimal weight: 0.5980 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN B 160 ASN F 249 ASN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.133170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.099468 restraints weight = 24389.559| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.56 r_work: 0.3045 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17728 Z= 0.120 Angle : 0.518 12.056 24008 Z= 0.249 Chirality : 0.042 0.172 2696 Planarity : 0.003 0.032 3144 Dihedral : 3.604 18.069 2392 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.07 % Allowed : 17.35 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.17), residues: 2128 helix: -0.33 (0.19), residues: 752 sheet: -0.66 (0.32), residues: 240 loop : -0.30 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 154 TYR 0.010 0.001 TYR A 149 PHE 0.009 0.001 PHE B 140 TRP 0.013 0.002 TRP G 45 HIS 0.002 0.001 HIS H 51 Details of bonding type rmsd covalent geometry : bond 0.00289 (17728) covalent geometry : angle 0.51836 (24008) hydrogen bonds : bond 0.02260 ( 617) hydrogen bonds : angle 5.09021 ( 1611) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3787.65 seconds wall clock time: 66 minutes 3.02 seconds (3963.02 seconds total)