Starting phenix.real_space_refine on Sat Aug 23 09:06:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j7y_36053/08_2025/8j7y_36053.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j7y_36053/08_2025/8j7y_36053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j7y_36053/08_2025/8j7y_36053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j7y_36053/08_2025/8j7y_36053.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j7y_36053/08_2025/8j7y_36053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j7y_36053/08_2025/8j7y_36053.map" } resolution = 3.4 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= 0.005 sd= 0.055 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 46 5.16 5 C 7044 2.51 5 N 1830 2.21 5 O 2086 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11008 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2193 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 9, 'TRANS': 270} Chain breaks: 3 Chain: "E" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1638 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1672 Classifications: {'peptide': 215} Link IDs: {'PCIS': 4, 'PTRANS': 7, 'TRANS': 203} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, F, D Time building chain proxies: 2.63, per 1000 atoms: 0.24 Number of scatterers: 11008 At special positions: 0 Unit cell: (76.7, 116.82, 159.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 46 16.00 O 2086 8.00 N 1830 7.00 C 7044 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 200 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 145 " - pdb=" SG CYS F 200 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 198 " distance=2.03 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: 1.08 Conformation dependent library (CDL) restraints added in 448.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 240 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 240 " 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2668 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 26 sheets defined 31.3% alpha, 36.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 23 through 32 removed outlier: 3.986A pdb=" N ARG A 27 " --> pdb=" O SER A 23 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 57 Processing helix chain 'A' and resid 61 through 88 removed outlier: 4.222A pdb=" N SER A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 132 Processing helix chain 'A' and resid 143 through 159 Processing helix chain 'A' and resid 232 through 259 Processing helix chain 'A' and resid 267 through 294 Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 303 through 314 removed outlier: 4.475A pdb=" N GLN A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 362 Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.527A pdb=" N ALA C 87 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'F' and resid 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'B' and resid 23 through 32 removed outlier: 3.986A pdb=" N ARG B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP B 32 " --> pdb=" O SER B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 57 Processing helix chain 'B' and resid 61 through 88 removed outlier: 4.222A pdb=" N SER B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 132 Processing helix chain 'B' and resid 143 through 159 Processing helix chain 'B' and resid 232 through 259 Processing helix chain 'B' and resid 267 through 294 Proline residue: B 284 - end of helix Processing helix chain 'B' and resid 303 through 314 removed outlier: 4.475A pdb=" N GLN B 307 " --> pdb=" O ASN B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 362 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.527A pdb=" N ALA D 87 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 132 Processing helix chain 'D' and resid 187 through 192 Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 328 removed outlier: 5.558A pdb=" N LEU A 321 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE A 341 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLU A 323 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS A 339 " --> pdb=" O GLU A 323 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A 366 " --> pdb=" O TYR A 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.666A pdb=" N THR E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.510A pdb=" N THR E 112 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR E 93 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER E 40 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.510A pdb=" N THR E 112 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR E 93 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR E 107 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 125 through 129 removed outlier: 3.861A pdb=" N GLY E 144 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER E 184 " --> pdb=" O CYS E 145 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR E 180 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 125 through 129 removed outlier: 3.861A pdb=" N GLY E 144 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER E 184 " --> pdb=" O CYS E 145 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR E 180 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 156 through 159 removed outlier: 3.856A pdb=" N CYS E 200 " --> pdb=" O LYS E 213 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS E 213 " --> pdb=" O CYS E 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.512A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N TYR C 53 " --> pdb=" O MET C 37 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.512A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR C 101 " --> pdb=" O GLN C 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AB3, first strand: chain 'C' and resid 118 through 122 removed outlier: 3.818A pdb=" N ASN C 141 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL C 137 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR C 177 " --> pdb=" O ASN C 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 157 through 159 removed outlier: 4.659A pdb=" N TRP C 152 " --> pdb=" O ARG C 159 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N HIS C 202 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N SER C 207 " --> pdb=" O HIS C 202 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.666A pdb=" N THR F 21 " --> pdb=" O SER F 7 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.510A pdb=" N THR F 112 " --> pdb=" O TYR F 93 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR F 93 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL F 50 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER F 40 " --> pdb=" O GLY F 44 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.510A pdb=" N THR F 112 " --> pdb=" O TYR F 93 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR F 93 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR F 107 " --> pdb=" O ARG F 97 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 125 through 129 removed outlier: 3.862A pdb=" N GLY F 144 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER F 184 " --> pdb=" O CYS F 145 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR F 180 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 125 through 129 removed outlier: 3.862A pdb=" N GLY F 144 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER F 184 " --> pdb=" O CYS F 145 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR F 180 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 156 through 159 removed outlier: 3.856A pdb=" N CYS F 200 " --> pdb=" O LYS F 213 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS F 213 " --> pdb=" O CYS F 200 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 318 through 328 removed outlier: 5.558A pdb=" N LEU B 321 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE B 341 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLU B 323 " --> pdb=" O LYS B 339 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS B 339 " --> pdb=" O GLU B 323 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN B 366 " --> pdb=" O TYR B 334 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 14 removed outlier: 6.512A pdb=" N LEU D 11 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS D 111 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL D 13 " --> pdb=" O LYS D 111 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET D 37 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N TYR D 53 " --> pdb=" O MET D 37 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TRP D 39 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 10 through 14 removed outlier: 6.512A pdb=" N LEU D 11 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS D 111 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL D 13 " --> pdb=" O LYS D 111 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR D 101 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AC7, first strand: chain 'D' and resid 118 through 122 removed outlier: 3.819A pdb=" N ASN D 141 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL D 137 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR D 177 " --> pdb=" O ASN D 142 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 157 through 159 removed outlier: 4.660A pdb=" N TRP D 152 " --> pdb=" O ARG D 159 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N HIS D 202 " --> pdb=" O SER D 207 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N SER D 207 " --> pdb=" O HIS D 202 " (cutoff:3.500A) 620 hydrogen bonds defined for protein. 1716 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: 2.42 Time building geometry restraints manager: 1.38 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: 3484 1.34 - 1.46: 2685 1.46 - 1.58: 5033 1.58 - 1.70: 0 1.70 - 1.81: 66 Bond restraints: 11268 Sorted by residual: bond pdb=" CG PRO C 145 " pdb=" CD PRO C 145 " ideal model delta sigma weight residual 1.512 1.486 0.026 2.70e-02 1.37e+03 9.13e-01 bond pdb=" C ASP A 267 " pdb=" N PRO A 268 " ideal model delta sigma weight residual 1.335 1.346 -0.012 1.28e-02 6.10e+03 8.51e-01 bond pdb=" CG PRO D 145 " pdb=" CD PRO D 145 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.42e-01 bond pdb=" C ASP B 267 " pdb=" N PRO B 268 " ideal model delta sigma weight residual 1.335 1.346 -0.012 1.28e-02 6.10e+03 8.18e-01 bond pdb=" CG PRO C 99 " pdb=" CD PRO C 99 " ideal model delta sigma weight residual 1.512 1.489 0.023 2.70e-02 1.37e+03 7.08e-01 ... (remaining 11263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 15014 1.40 - 2.80: 255 2.80 - 4.21: 53 4.21 - 5.61: 10 5.61 - 7.01: 10 Bond angle restraints: 15342 Sorted by residual: angle pdb=" C VAL E 188 " pdb=" CA VAL E 188 " pdb=" CB VAL E 188 " ideal model delta sigma weight residual 109.33 112.33 -3.00 9.80e-01 1.04e+00 9.39e+00 angle pdb=" C VAL F 188 " pdb=" CA VAL F 188 " pdb=" CB VAL F 188 " ideal model delta sigma weight residual 109.33 112.33 -3.00 9.80e-01 1.04e+00 9.37e+00 angle pdb=" CA VAL F 188 " pdb=" C VAL F 188 " pdb=" N PRO F 189 " ideal model delta sigma weight residual 116.57 119.43 -2.86 9.80e-01 1.04e+00 8.55e+00 angle pdb=" CA VAL E 188 " pdb=" C VAL E 188 " pdb=" N PRO E 189 " ideal model delta sigma weight residual 116.57 119.40 -2.83 9.80e-01 1.04e+00 8.37e+00 angle pdb=" CA LYS C 153 " pdb=" CB LYS C 153 " pdb=" CG LYS C 153 " ideal model delta sigma weight residual 114.10 119.54 -5.44 2.00e+00 2.50e-01 7.40e+00 ... (remaining 15337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6097 17.88 - 35.77: 463 35.77 - 53.65: 72 53.65 - 71.54: 20 71.54 - 89.42: 8 Dihedral angle restraints: 6660 sinusoidal: 2526 harmonic: 4134 Sorted by residual: dihedral pdb=" CB CYS F 145 " pdb=" SG CYS F 145 " pdb=" SG CYS F 200 " pdb=" CB CYS F 200 " ideal model delta sinusoidal sigma weight residual 93.00 149.76 -56.76 1 1.00e+01 1.00e-02 4.34e+01 dihedral pdb=" CB CYS E 145 " pdb=" SG CYS E 145 " pdb=" SG CYS E 200 " pdb=" CB CYS E 200 " ideal model delta sinusoidal sigma weight residual 93.00 149.73 -56.73 1 1.00e+01 1.00e-02 4.33e+01 dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 92 " pdb=" CB CYS D 92 " ideal model delta sinusoidal sigma weight residual 93.00 57.45 35.55 1 1.00e+01 1.00e-02 1.79e+01 ... (remaining 6657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1107 0.029 - 0.057: 406 0.057 - 0.086: 144 0.086 - 0.115: 94 0.115 - 0.144: 15 Chirality restraints: 1766 Sorted by residual: chirality pdb=" CA ILE E 92 " pdb=" N ILE E 92 " pdb=" C ILE E 92 " pdb=" CB ILE E 92 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA ILE F 92 " pdb=" N ILE F 92 " pdb=" C ILE F 92 " pdb=" CB ILE F 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ASN B 152 " pdb=" N ASN B 152 " pdb=" C ASN B 152 " pdb=" CB ASN B 152 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 1763 not shown) Planarity restraints: 1938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU F 153 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO F 154 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO F 154 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 154 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 153 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO E 154 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 154 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 154 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 188 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO F 189 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO F 189 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 189 " -0.023 5.00e-02 4.00e+02 ... (remaining 1935 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 62 2.51 - 3.11: 8088 3.11 - 3.71: 16902 3.71 - 4.30: 23705 4.30 - 4.90: 40316 Nonbonded interactions: 89073 Sorted by model distance: nonbonded pdb=" CG ASP A 74 " pdb="ZN ZN A 501 " model vdw 1.914 2.460 nonbonded pdb=" CG ASP B 74 " pdb="ZN ZN B 501 " model vdw 1.914 2.460 nonbonded pdb=" OD1 ASP A 74 " pdb="ZN ZN A 501 " model vdw 2.008 2.230 nonbonded pdb=" OD1 ASP B 74 " pdb="ZN ZN B 501 " model vdw 2.009 2.230 nonbonded pdb=" OD2 ASP B 244 " pdb="ZN ZN B 501 " model vdw 2.063 2.230 ... (remaining 89068 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.760 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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 0.106 11278 Z= 0.108 Angle : 0.504 7.010 15358 Z= 0.261 Chirality : 0.040 0.144 1766 Planarity : 0.003 0.050 1938 Dihedral : 13.140 89.420 3968 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.16 % Allowed : 0.33 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.23), residues: 1402 helix: 2.44 (0.25), residues: 422 sheet: 0.89 (0.25), residues: 470 loop : -0.29 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 97 TYR 0.017 0.001 TYR E 101 PHE 0.005 0.001 PHE C 102 TRP 0.009 0.001 TRP D 152 HIS 0.009 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00200 (11268) covalent geometry : angle 0.50462 (15342) SS BOND : bond 0.00214 ( 8) SS BOND : angle 0.32924 ( 16) hydrogen bonds : bond 0.17616 ( 584) hydrogen bonds : angle 6.85440 ( 1716) metal coordination : bond 0.10579 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 322 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8169 (pp20) cc_final: 0.7904 (pp20) REVERT: A 128 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7634 (mt-10) REVERT: A 319 TYR cc_start: 0.7798 (m-80) cc_final: 0.7569 (m-80) REVERT: C 4 LEU cc_start: 0.8703 (mt) cc_final: 0.8475 (mt) REVERT: C 78 THR cc_start: 0.8820 (m) cc_final: 0.8502 (p) REVERT: C 79 ILE cc_start: 0.8362 (mt) cc_final: 0.8128 (mt) REVERT: C 151 LYS cc_start: 0.8139 (mtpp) cc_final: 0.7564 (mmmt) REVERT: B 33 LYS cc_start: 0.9496 (pptt) cc_final: 0.9287 (tppt) REVERT: B 37 ASN cc_start: 0.9189 (m110) cc_final: 0.8798 (m-40) REVERT: B 50 PHE cc_start: 0.8885 (m-10) cc_final: 0.8529 (m-10) REVERT: B 73 PHE cc_start: 0.6674 (m-10) cc_final: 0.6469 (m-10) REVERT: B 120 PHE cc_start: 0.8059 (m-10) cc_final: 0.7826 (m-10) REVERT: B 154 ILE cc_start: 0.8674 (mm) cc_final: 0.8401 (mm) REVERT: B 257 MET cc_start: 0.5897 (tmm) cc_final: 0.5556 (ptm) REVERT: D 107 LYS cc_start: 0.8171 (mtpp) cc_final: 0.7971 (mmmt) REVERT: D 151 LYS cc_start: 0.8290 (mtpp) cc_final: 0.8080 (mmmt) REVERT: D 179 MET cc_start: 0.8227 (ttp) cc_final: 0.7978 (ttp) outliers start: 2 outliers final: 0 residues processed: 322 average time/residue: 0.0884 time to fit residues: 41.8066 Evaluate side-chains 197 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS A 295 GLN A 361 GLN C 165 ASN F 73 ASN B 295 GLN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.124836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.083854 restraints weight = 21157.516| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.45 r_work: 0.3008 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 11278 Z= 0.262 Angle : 0.688 10.659 15358 Z= 0.361 Chirality : 0.047 0.201 1766 Planarity : 0.005 0.058 1938 Dihedral : 4.118 16.102 1520 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.79 % Allowed : 11.40 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.22), residues: 1402 helix: 2.09 (0.24), residues: 428 sheet: 0.62 (0.24), residues: 462 loop : -0.48 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 365 TYR 0.017 0.002 TYR F 180 PHE 0.019 0.002 PHE D 143 TRP 0.013 0.001 TRP F 47 HIS 0.006 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00598 (11268) covalent geometry : angle 0.68636 (15342) SS BOND : bond 0.00831 ( 8) SS BOND : angle 1.44872 ( 16) hydrogen bonds : bond 0.04111 ( 584) hydrogen bonds : angle 4.86256 ( 1716) metal coordination : bond 0.00491 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8640 (t0) cc_final: 0.8116 (t70) REVERT: A 37 ASN cc_start: 0.9395 (m110) cc_final: 0.9093 (p0) REVERT: A 52 GLU cc_start: 0.8143 (pp20) cc_final: 0.7781 (pp20) REVERT: A 128 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7565 (mt-10) REVERT: A 288 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7743 (tm-30) REVERT: E 138 ASN cc_start: 0.9296 (p0) cc_final: 0.9082 (p0) REVERT: E 176 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7956 (tm-30) REVERT: C 37 MET cc_start: 0.8542 (tpp) cc_final: 0.8291 (tpp) REVERT: C 78 THR cc_start: 0.9353 (m) cc_final: 0.8990 (p) REVERT: C 160 GLN cc_start: 0.8536 (mp10) cc_final: 0.8134 (mp10) REVERT: F 72 ASP cc_start: 0.8336 (t0) cc_final: 0.7711 (t0) REVERT: B 50 PHE cc_start: 0.9115 (m-10) cc_final: 0.8727 (m-10) REVERT: B 154 ILE cc_start: 0.8886 (mm) cc_final: 0.8645 (mm) REVERT: B 257 MET cc_start: 0.5880 (tmm) cc_final: 0.5629 (ttt) REVERT: B 332 ASP cc_start: 0.8103 (p0) cc_final: 0.7873 (m-30) REVERT: D 194 ASN cc_start: 0.9175 (t0) cc_final: 0.8854 (t0) outliers start: 22 outliers final: 12 residues processed: 220 average time/residue: 0.0848 time to fit residues: 27.6338 Evaluate side-chains 191 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 154 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 79 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 43 optimal weight: 0.0870 chunk 98 optimal weight: 0.3980 chunk 128 optimal weight: 0.0030 chunk 75 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 99 optimal weight: 0.5980 chunk 133 optimal weight: 0.8980 overall best weight: 0.2968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 ASN B 70 HIS ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.123612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.084900 restraints weight = 20444.500| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.61 r_work: 0.3035 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11278 Z= 0.116 Angle : 0.565 11.361 15358 Z= 0.292 Chirality : 0.043 0.158 1766 Planarity : 0.004 0.050 1938 Dihedral : 3.838 15.074 1520 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.98 % Allowed : 13.60 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.22), residues: 1402 helix: 2.30 (0.25), residues: 412 sheet: 0.65 (0.24), residues: 464 loop : -0.38 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 159 TYR 0.013 0.001 TYR C 190 PHE 0.016 0.001 PHE A 149 TRP 0.008 0.001 TRP A 58 HIS 0.002 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00252 (11268) covalent geometry : angle 0.56451 (15342) SS BOND : bond 0.00370 ( 8) SS BOND : angle 0.63798 ( 16) hydrogen bonds : bond 0.03468 ( 584) hydrogen bonds : angle 4.53260 ( 1716) metal coordination : bond 0.00352 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8673 (t0) cc_final: 0.8186 (t0) REVERT: A 52 GLU cc_start: 0.8029 (pp20) cc_final: 0.7676 (pp20) REVERT: A 128 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7450 (mt-10) REVERT: A 288 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7661 (tm-30) REVERT: E 72 ASP cc_start: 0.8175 (t0) cc_final: 0.7971 (t0) REVERT: E 176 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7675 (tm-30) REVERT: C 37 MET cc_start: 0.8627 (tpp) cc_final: 0.8322 (tpp) REVERT: C 83 GLU cc_start: 0.8621 (pt0) cc_final: 0.8416 (pt0) REVERT: B 33 LYS cc_start: 0.9642 (ttpp) cc_final: 0.9327 (tptp) REVERT: B 50 PHE cc_start: 0.9072 (m-10) cc_final: 0.8712 (m-10) REVERT: B 154 ILE cc_start: 0.8861 (mm) cc_final: 0.8639 (mm) REVERT: B 257 MET cc_start: 0.5964 (tmm) cc_final: 0.5438 (ptm) REVERT: B 357 ASN cc_start: 0.8813 (m-40) cc_final: 0.8609 (t0) REVERT: D 179 MET cc_start: 0.8876 (ttp) cc_final: 0.8654 (ttp) outliers start: 12 outliers final: 5 residues processed: 198 average time/residue: 0.0759 time to fit residues: 22.8027 Evaluate side-chains 172 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 167 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 181 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 107 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 chunk 16 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 214 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.117458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.079143 restraints weight = 19818.120| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.37 r_work: 0.2984 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11278 Z= 0.216 Angle : 0.600 10.947 15358 Z= 0.314 Chirality : 0.044 0.173 1766 Planarity : 0.004 0.052 1938 Dihedral : 4.057 19.606 1520 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.79 % Allowed : 14.01 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.22), residues: 1402 helix: 2.22 (0.25), residues: 414 sheet: 0.53 (0.24), residues: 464 loop : -0.41 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 159 TYR 0.016 0.002 TYR F 180 PHE 0.013 0.001 PHE A 149 TRP 0.010 0.001 TRP F 108 HIS 0.005 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00497 (11268) covalent geometry : angle 0.59998 (15342) SS BOND : bond 0.00364 ( 8) SS BOND : angle 0.85812 ( 16) hydrogen bonds : bond 0.03510 ( 584) hydrogen bonds : angle 4.49185 ( 1716) metal coordination : bond 0.00590 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.432 Fit side-chains REVERT: A 32 ASP cc_start: 0.8571 (t0) cc_final: 0.8089 (t0) REVERT: A 52 GLU cc_start: 0.8122 (pp20) cc_final: 0.7755 (pp20) REVERT: A 128 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7496 (mt-10) REVERT: A 160 LYS cc_start: 0.7877 (mmtm) cc_final: 0.7603 (mmtm) REVERT: A 288 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7992 (tm-30) REVERT: E 1 GLU cc_start: 0.7852 (pp20) cc_final: 0.7644 (pp20) REVERT: E 88 ASP cc_start: 0.8810 (p0) cc_final: 0.8552 (p0) REVERT: E 138 ASN cc_start: 0.9290 (p0) cc_final: 0.8942 (p0) REVERT: E 176 GLN cc_start: 0.8361 (tm-30) cc_final: 0.7771 (tm-30) REVERT: C 160 GLN cc_start: 0.8521 (pm20) cc_final: 0.8134 (mp10) REVERT: B 50 PHE cc_start: 0.9120 (m-10) cc_final: 0.8764 (m-10) REVERT: B 71 MET cc_start: 0.8646 (ppp) cc_final: 0.8349 (ppp) REVERT: B 154 ILE cc_start: 0.8805 (mm) cc_final: 0.8573 (mm) REVERT: B 257 MET cc_start: 0.5779 (tmm) cc_final: 0.5285 (ptm) REVERT: B 372 ASP cc_start: 0.8496 (t0) cc_final: 0.8243 (t0) REVERT: D 127 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8246 (mp0) outliers start: 22 outliers final: 17 residues processed: 197 average time/residue: 0.0832 time to fit residues: 24.6567 Evaluate side-chains 190 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 127 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 89 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.121122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.082152 restraints weight = 20010.114| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.51 r_work: 0.2960 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11278 Z= 0.141 Angle : 0.560 7.124 15358 Z= 0.292 Chirality : 0.043 0.261 1766 Planarity : 0.004 0.051 1938 Dihedral : 3.890 14.741 1520 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.63 % Allowed : 15.23 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.22), residues: 1402 helix: 2.20 (0.25), residues: 416 sheet: 0.58 (0.23), residues: 470 loop : -0.31 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 159 TYR 0.020 0.001 TYR C 190 PHE 0.056 0.001 PHE A 149 TRP 0.008 0.001 TRP F 159 HIS 0.002 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00321 (11268) covalent geometry : angle 0.56004 (15342) SS BOND : bond 0.00332 ( 8) SS BOND : angle 0.57649 ( 16) hydrogen bonds : bond 0.03203 ( 584) hydrogen bonds : angle 4.35052 ( 1716) metal coordination : bond 0.00141 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.414 Fit side-chains REVERT: A 32 ASP cc_start: 0.8567 (t0) cc_final: 0.8103 (t0) REVERT: A 52 GLU cc_start: 0.8111 (pp20) cc_final: 0.7704 (pp20) REVERT: A 74 ASP cc_start: 0.7754 (m-30) cc_final: 0.7498 (m-30) REVERT: A 92 ASP cc_start: 0.9000 (p0) cc_final: 0.8704 (p0) REVERT: A 128 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7412 (mt-10) REVERT: A 160 LYS cc_start: 0.7971 (mmtm) cc_final: 0.7748 (mmtm) REVERT: A 288 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7967 (tm-30) REVERT: A 332 ASP cc_start: 0.8561 (m-30) cc_final: 0.8303 (p0) REVERT: E 1 GLU cc_start: 0.7953 (pp20) cc_final: 0.7668 (pp20) REVERT: E 88 ASP cc_start: 0.8846 (p0) cc_final: 0.8622 (p0) REVERT: E 176 GLN cc_start: 0.8388 (tm-30) cc_final: 0.7994 (tm-30) REVERT: C 109 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8201 (tt0) REVERT: C 160 GLN cc_start: 0.8446 (pm20) cc_final: 0.7987 (mp10) REVERT: F 59 TYR cc_start: 0.9203 (m-10) cc_final: 0.8977 (m-10) REVERT: B 50 PHE cc_start: 0.9119 (m-10) cc_final: 0.8751 (m-10) REVERT: B 74 ASP cc_start: 0.7602 (m-30) cc_final: 0.7346 (m-30) REVERT: B 154 ILE cc_start: 0.8833 (mm) cc_final: 0.8600 (mm) REVERT: B 372 ASP cc_start: 0.8481 (t0) cc_final: 0.8210 (t0) REVERT: D 127 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8359 (mp0) outliers start: 20 outliers final: 12 residues processed: 201 average time/residue: 0.0818 time to fit residues: 24.8101 Evaluate side-chains 183 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 127 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 69 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 85 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 112 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 128 GLN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.118534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.080349 restraints weight = 20346.185| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.87 r_work: 0.2952 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11278 Z= 0.153 Angle : 0.588 14.513 15358 Z= 0.303 Chirality : 0.043 0.204 1766 Planarity : 0.004 0.050 1938 Dihedral : 3.916 15.141 1520 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.55 % Allowed : 15.96 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.22), residues: 1402 helix: 2.11 (0.25), residues: 416 sheet: 0.58 (0.23), residues: 470 loop : -0.27 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 215 TYR 0.016 0.001 TYR C 190 PHE 0.019 0.001 PHE B 238 TRP 0.008 0.001 TRP F 159 HIS 0.004 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00349 (11268) covalent geometry : angle 0.58831 (15342) SS BOND : bond 0.00337 ( 8) SS BOND : angle 0.64110 ( 16) hydrogen bonds : bond 0.03209 ( 584) hydrogen bonds : angle 4.32229 ( 1716) metal coordination : bond 0.00371 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 0.270 Fit side-chains REVERT: A 32 ASP cc_start: 0.8544 (t0) cc_final: 0.8078 (t0) REVERT: A 52 GLU cc_start: 0.8131 (pp20) cc_final: 0.7728 (pp20) REVERT: A 128 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7632 (mt-10) REVERT: A 160 LYS cc_start: 0.8300 (mmtm) cc_final: 0.8100 (mmtm) REVERT: A 288 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7971 (tm-30) REVERT: A 332 ASP cc_start: 0.8623 (m-30) cc_final: 0.8369 (p0) REVERT: E 1 GLU cc_start: 0.7928 (pp20) cc_final: 0.7552 (pp20) REVERT: E 138 ASN cc_start: 0.9274 (p0) cc_final: 0.9040 (p0) REVERT: E 176 GLN cc_start: 0.8417 (tm-30) cc_final: 0.8006 (tm-30) REVERT: C 109 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8249 (tt0) REVERT: C 127 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8494 (mp0) REVERT: C 160 GLN cc_start: 0.8480 (pm20) cc_final: 0.8006 (mp10) REVERT: B 50 PHE cc_start: 0.9114 (m-10) cc_final: 0.8750 (m-10) REVERT: B 71 MET cc_start: 0.8679 (ppp) cc_final: 0.8452 (ppp) REVERT: B 154 ILE cc_start: 0.8901 (mm) cc_final: 0.8666 (mm) REVERT: B 372 ASP cc_start: 0.8484 (t0) cc_final: 0.8168 (t0) outliers start: 19 outliers final: 13 residues processed: 199 average time/residue: 0.0788 time to fit residues: 23.3789 Evaluate side-chains 187 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 174 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain D residue 32 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 87 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 110 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 GLN B 37 ASN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.115690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.078980 restraints weight = 19843.142| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.90 r_work: 0.2957 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11278 Z= 0.154 Angle : 0.589 13.019 15358 Z= 0.303 Chirality : 0.043 0.161 1766 Planarity : 0.004 0.051 1938 Dihedral : 3.904 15.250 1520 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.71 % Allowed : 15.64 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.22), residues: 1402 helix: 1.99 (0.25), residues: 428 sheet: 0.60 (0.23), residues: 468 loop : -0.31 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 38 TYR 0.017 0.001 TYR C 190 PHE 0.026 0.001 PHE B 114 TRP 0.008 0.001 TRP F 159 HIS 0.006 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00353 (11268) covalent geometry : angle 0.58864 (15342) SS BOND : bond 0.00345 ( 8) SS BOND : angle 0.59088 ( 16) hydrogen bonds : bond 0.03151 ( 584) hydrogen bonds : angle 4.26830 ( 1716) metal coordination : bond 0.00691 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 0.406 Fit side-chains REVERT: A 32 ASP cc_start: 0.8543 (t0) cc_final: 0.8075 (t0) REVERT: A 52 GLU cc_start: 0.8130 (pp20) cc_final: 0.7773 (pp20) REVERT: A 74 ASP cc_start: 0.7681 (m-30) cc_final: 0.7461 (m-30) REVERT: A 92 ASP cc_start: 0.9037 (p0) cc_final: 0.8798 (p0) REVERT: A 128 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7613 (mt-10) REVERT: A 288 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7936 (tm-30) REVERT: A 302 GLU cc_start: 0.8585 (tt0) cc_final: 0.8183 (tt0) REVERT: A 332 ASP cc_start: 0.8557 (m-30) cc_final: 0.8340 (p0) REVERT: E 1 GLU cc_start: 0.7922 (pp20) cc_final: 0.7561 (pp20) REVERT: E 6 GLU cc_start: 0.8677 (mp0) cc_final: 0.8401 (mp0) REVERT: E 138 ASN cc_start: 0.9325 (p0) cc_final: 0.9049 (p0) REVERT: E 176 GLN cc_start: 0.8387 (tm-30) cc_final: 0.7868 (tm-30) REVERT: C 109 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8255 (tt0) REVERT: C 127 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8521 (mp0) REVERT: C 160 GLN cc_start: 0.8465 (pm20) cc_final: 0.8015 (mp10) REVERT: B 50 PHE cc_start: 0.9138 (m-10) cc_final: 0.8770 (m-10) REVERT: B 71 MET cc_start: 0.8675 (ppp) cc_final: 0.8475 (ppp) REVERT: B 94 ASP cc_start: 0.8520 (t0) cc_final: 0.8246 (t0) REVERT: B 154 ILE cc_start: 0.8916 (mm) cc_final: 0.8707 (mm) REVERT: B 372 ASP cc_start: 0.8495 (t0) cc_final: 0.8182 (t0) outliers start: 21 outliers final: 16 residues processed: 199 average time/residue: 0.0739 time to fit residues: 22.0702 Evaluate side-chains 190 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain D residue 32 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 13 optimal weight: 6.9990 chunk 77 optimal weight: 0.0470 chunk 3 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 0.0070 chunk 86 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 102 optimal weight: 0.0370 overall best weight: 0.3374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.119855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.081130 restraints weight = 20569.895| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.57 r_work: 0.2988 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11278 Z= 0.121 Angle : 0.613 17.395 15358 Z= 0.311 Chirality : 0.043 0.186 1766 Planarity : 0.004 0.051 1938 Dihedral : 3.847 15.752 1520 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.30 % Allowed : 16.78 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.22), residues: 1402 helix: 1.96 (0.25), residues: 428 sheet: 0.69 (0.24), residues: 468 loop : -0.25 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 159 TYR 0.019 0.001 TYR C 190 PHE 0.022 0.001 PHE B 114 TRP 0.012 0.001 TRP D 167 HIS 0.004 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00274 (11268) covalent geometry : angle 0.61337 (15342) SS BOND : bond 0.00343 ( 8) SS BOND : angle 0.55547 ( 16) hydrogen bonds : bond 0.03116 ( 584) hydrogen bonds : angle 4.17293 ( 1716) metal coordination : bond 0.00109 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.301 Fit side-chains REVERT: A 32 ASP cc_start: 0.8481 (t0) cc_final: 0.8024 (t0) REVERT: A 52 GLU cc_start: 0.8132 (pp20) cc_final: 0.7785 (pp20) REVERT: A 74 ASP cc_start: 0.7806 (m-30) cc_final: 0.7544 (m-30) REVERT: A 92 ASP cc_start: 0.9021 (p0) cc_final: 0.8798 (p0) REVERT: A 128 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7611 (mt-10) REVERT: A 288 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7942 (tm-30) REVERT: E 1 GLU cc_start: 0.7894 (pp20) cc_final: 0.7532 (pp20) REVERT: E 32 TYR cc_start: 0.9256 (m-80) cc_final: 0.9044 (m-80) REVERT: E 138 ASN cc_start: 0.9308 (p0) cc_final: 0.8972 (p0) REVERT: E 176 GLN cc_start: 0.8358 (tm-30) cc_final: 0.7848 (tm-30) REVERT: C 109 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8232 (tt0) REVERT: C 127 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8677 (mp0) REVERT: C 149 ASN cc_start: 0.8629 (t0) cc_final: 0.8409 (t0) REVERT: C 160 GLN cc_start: 0.8473 (pm20) cc_final: 0.8023 (mp10) REVERT: F 59 TYR cc_start: 0.9190 (m-10) cc_final: 0.8953 (m-10) REVERT: B 50 PHE cc_start: 0.9093 (m-10) cc_final: 0.8697 (m-10) REVERT: B 154 ILE cc_start: 0.8862 (mm) cc_final: 0.8643 (mm) REVERT: B 257 MET cc_start: 0.7370 (tmm) cc_final: 0.6305 (ptm) REVERT: B 372 ASP cc_start: 0.8519 (t0) cc_final: 0.8294 (t0) outliers start: 16 outliers final: 15 residues processed: 197 average time/residue: 0.0771 time to fit residues: 22.9816 Evaluate side-chains 195 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain D residue 32 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 100 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 110 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 214 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.118388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.079379 restraints weight = 20340.883| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.56 r_work: 0.2962 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11278 Z= 0.160 Angle : 0.624 14.783 15358 Z= 0.318 Chirality : 0.043 0.160 1766 Planarity : 0.004 0.051 1938 Dihedral : 3.899 16.211 1520 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.47 % Allowed : 16.21 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.22), residues: 1402 helix: 1.94 (0.25), residues: 428 sheet: 0.68 (0.24), residues: 468 loop : -0.22 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 38 TYR 0.019 0.001 TYR C 190 PHE 0.022 0.001 PHE B 114 TRP 0.011 0.001 TRP D 167 HIS 0.002 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00370 (11268) covalent geometry : angle 0.62371 (15342) SS BOND : bond 0.00333 ( 8) SS BOND : angle 0.65798 ( 16) hydrogen bonds : bond 0.03182 ( 584) hydrogen bonds : angle 4.19074 ( 1716) metal coordination : bond 0.00099 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 0.388 Fit side-chains REVERT: A 32 ASP cc_start: 0.8506 (t0) cc_final: 0.8042 (t0) REVERT: A 52 GLU cc_start: 0.8143 (pp20) cc_final: 0.7813 (pp20) REVERT: A 74 ASP cc_start: 0.7683 (m-30) cc_final: 0.7449 (m-30) REVERT: A 128 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7618 (mt-10) REVERT: A 288 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7980 (tm-30) REVERT: E 1 GLU cc_start: 0.7944 (pp20) cc_final: 0.7581 (pp20) REVERT: E 32 TYR cc_start: 0.9287 (m-80) cc_final: 0.9074 (m-80) REVERT: E 138 ASN cc_start: 0.9331 (p0) cc_final: 0.9019 (p0) REVERT: E 176 GLN cc_start: 0.8405 (tm-30) cc_final: 0.7887 (tm-30) REVERT: C 109 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8272 (tt0) REVERT: B 50 PHE cc_start: 0.9093 (m-10) cc_final: 0.8740 (m-10) REVERT: B 154 ILE cc_start: 0.8860 (mm) cc_final: 0.8639 (mm) REVERT: B 257 MET cc_start: 0.7365 (tmm) cc_final: 0.6294 (ptm) REVERT: B 372 ASP cc_start: 0.8558 (t0) cc_final: 0.8343 (t0) REVERT: D 158 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7826 (tp30) REVERT: D 160 GLN cc_start: 0.8774 (mp10) cc_final: 0.8531 (mp10) outliers start: 18 outliers final: 14 residues processed: 201 average time/residue: 0.0749 time to fit residues: 22.7370 Evaluate side-chains 192 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain D residue 32 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 18 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 53 optimal weight: 0.2980 chunk 58 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 107 optimal weight: 40.0000 chunk 98 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS B 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.118769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.079881 restraints weight = 20521.472| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.58 r_work: 0.2970 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11278 Z= 0.144 Angle : 0.658 17.050 15358 Z= 0.331 Chirality : 0.044 0.317 1766 Planarity : 0.004 0.051 1938 Dihedral : 3.875 16.282 1520 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.47 % Allowed : 16.61 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.22), residues: 1402 helix: 1.93 (0.25), residues: 428 sheet: 0.68 (0.24), residues: 468 loop : -0.21 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 159 TYR 0.019 0.001 TYR C 190 PHE 0.022 0.001 PHE B 149 TRP 0.027 0.001 TRP B 58 HIS 0.009 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00331 (11268) covalent geometry : angle 0.65812 (15342) SS BOND : bond 0.00346 ( 8) SS BOND : angle 0.55386 ( 16) hydrogen bonds : bond 0.03149 ( 584) hydrogen bonds : angle 4.20060 ( 1716) metal coordination : bond 0.00048 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.385 Fit side-chains REVERT: A 32 ASP cc_start: 0.8437 (t0) cc_final: 0.7954 (t0) REVERT: A 52 GLU cc_start: 0.8143 (pp20) cc_final: 0.7825 (pp20) REVERT: A 74 ASP cc_start: 0.7678 (m-30) cc_final: 0.7437 (m-30) REVERT: A 128 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7645 (mt-10) REVERT: A 288 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8009 (tm-30) REVERT: E 1 GLU cc_start: 0.7935 (pp20) cc_final: 0.7556 (pp20) REVERT: E 6 GLU cc_start: 0.8746 (mp0) cc_final: 0.8531 (mp0) REVERT: E 32 TYR cc_start: 0.9276 (m-80) cc_final: 0.9065 (m-80) REVERT: E 138 ASN cc_start: 0.9291 (p0) cc_final: 0.9012 (p0) REVERT: E 176 GLN cc_start: 0.8417 (tm-30) cc_final: 0.7899 (tm-30) REVERT: C 83 GLU cc_start: 0.8606 (pm20) cc_final: 0.8397 (pm20) REVERT: C 109 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8285 (tt0) REVERT: C 147 ASP cc_start: 0.8714 (t0) cc_final: 0.8453 (t0) REVERT: B 50 PHE cc_start: 0.9022 (m-10) cc_final: 0.8628 (m-10) REVERT: B 154 ILE cc_start: 0.8773 (mm) cc_final: 0.8519 (mm) REVERT: B 257 MET cc_start: 0.7296 (tmm) cc_final: 0.6215 (ptm) REVERT: B 372 ASP cc_start: 0.8540 (t0) cc_final: 0.8316 (t0) REVERT: D 158 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7760 (tp30) REVERT: D 160 GLN cc_start: 0.8754 (mp10) cc_final: 0.8527 (mp10) outliers start: 18 outliers final: 15 residues processed: 199 average time/residue: 0.0765 time to fit residues: 23.0387 Evaluate side-chains 196 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain D residue 32 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 9 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 126 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 135 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 18 optimal weight: 0.1980 chunk 85 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 169 HIS D 128 GLN D 214 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.119098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.081099 restraints weight = 20471.631| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.88 r_work: 0.2962 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11278 Z= 0.138 Angle : 0.655 17.201 15358 Z= 0.328 Chirality : 0.043 0.235 1766 Planarity : 0.004 0.051 1938 Dihedral : 3.877 16.780 1520 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.30 % Allowed : 17.10 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.22), residues: 1402 helix: 1.94 (0.25), residues: 428 sheet: 0.71 (0.24), residues: 468 loop : -0.22 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 159 TYR 0.018 0.001 TYR C 190 PHE 0.023 0.001 PHE B 149 TRP 0.027 0.001 TRP B 58 HIS 0.002 0.001 HIS B 325 Details of bonding type rmsd covalent geometry : bond 0.00319 (11268) covalent geometry : angle 0.65545 (15342) SS BOND : bond 0.00340 ( 8) SS BOND : angle 0.54614 ( 16) hydrogen bonds : bond 0.03137 ( 584) hydrogen bonds : angle 4.18352 ( 1716) metal coordination : bond 0.00030 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2524.29 seconds wall clock time: 44 minutes 2.58 seconds (2642.58 seconds total)