Starting phenix.real_space_refine on Tue Jul 29 06:00:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j7y_36053/07_2025/8j7y_36053.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j7y_36053/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j7y_36053/07_2025/8j7y_36053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j7y_36053/07_2025/8j7y_36053.map" model { file = "/net/cci-nas-00/data/ceres_data/8j7y_36053/07_2025/8j7y_36053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j7y_36053/07_2025/8j7y_36053.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: D, B, F Time building chain proxies: 7.32, per 1000 atoms: 0.66 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: 3.10 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.42 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: 3.83 Time building geometry restraints manager: 3.59 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: 0.06 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 1.240 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.390 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.770 ------------------------------------------------------------------------------- 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 : 7.04 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (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 TRP 0.009 0.001 TRP D 152 HIS 0.009 0.001 HIS A 240 PHE 0.005 0.001 PHE C 102 TYR 0.017 0.001 TYR E 101 ARG 0.001 0.000 ARG E 97 Details of bonding type rmsd hydrogen bonds : bond 0.17616 ( 584) hydrogen bonds : angle 6.85440 ( 1716) metal coordination : bond 0.10579 ( 2) SS BOND : bond 0.00214 ( 8) SS BOND : angle 0.32924 ( 16) covalent geometry : bond 0.00200 (11268) covalent geometry : angle 0.50462 (15342) *********************** 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 : 1.368 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: 0.2132 time to fit residues: 99.1816 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 : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.0370 chunk 106 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- 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 57 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.119107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.081229 restraints weight = 19826.597| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.41 r_work: 0.3061 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11278 Z= 0.169 Angle : 0.625 11.629 15358 Z= 0.326 Chirality : 0.045 0.182 1766 Planarity : 0.004 0.054 1938 Dihedral : 3.887 16.080 1520 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.47 % Allowed : 11.32 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.22), residues: 1402 helix: 2.19 (0.25), residues: 424 sheet: 0.82 (0.24), residues: 460 loop : -0.43 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 152 HIS 0.005 0.001 HIS A 240 PHE 0.019 0.002 PHE B 359 TYR 0.015 0.002 TYR E 150 ARG 0.004 0.000 ARG F 66 Details of bonding type rmsd hydrogen bonds : bond 0.03689 ( 584) hydrogen bonds : angle 4.76622 ( 1716) metal coordination : bond 0.00601 ( 2) SS BOND : bond 0.00585 ( 8) SS BOND : angle 1.12092 ( 16) covalent geometry : bond 0.00367 (11268) covalent geometry : angle 0.62381 (15342) *********************** 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 232 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 214 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8685 (t0) cc_final: 0.8209 (t0) REVERT: A 37 ASN cc_start: 0.9370 (m110) cc_final: 0.9090 (p0) REVERT: A 52 GLU cc_start: 0.8128 (pp20) cc_final: 0.7777 (pp20) REVERT: A 74 ASP cc_start: 0.7607 (m-30) cc_final: 0.7343 (m-30) REVERT: A 128 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7533 (mt-10) REVERT: A 240 HIS cc_start: 0.8105 (t-90) cc_final: 0.7767 (t-90) REVERT: E 72 ASP cc_start: 0.8046 (t0) cc_final: 0.7831 (t0) REVERT: E 176 GLN cc_start: 0.8054 (tm-30) cc_final: 0.7606 (tm-30) REVERT: E 212 ASP cc_start: 0.8513 (m-30) cc_final: 0.8306 (m-30) REVERT: C 37 MET cc_start: 0.8304 (tpp) cc_final: 0.8073 (tpp) REVERT: C 160 GLN cc_start: 0.8507 (mp10) cc_final: 0.8005 (mp10) REVERT: C 189 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7921 (mp0) REVERT: F 32 TYR cc_start: 0.8758 (m-80) cc_final: 0.8422 (m-80) REVERT: F 59 TYR cc_start: 0.8782 (m-10) cc_final: 0.8360 (m-10) REVERT: F 72 ASP cc_start: 0.8266 (t0) cc_final: 0.7643 (t0) REVERT: B 50 PHE cc_start: 0.9044 (m-10) cc_final: 0.8644 (m-10) REVERT: B 154 ILE cc_start: 0.8837 (mm) cc_final: 0.8589 (mm) REVERT: B 257 MET cc_start: 0.5979 (tmm) cc_final: 0.5779 (ttt) REVERT: D 194 ASN cc_start: 0.9082 (t0) cc_final: 0.8817 (t0) outliers start: 18 outliers final: 11 residues processed: 226 average time/residue: 0.1994 time to fit residues: 66.7219 Evaluate side-chains 190 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 179 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 178 ASP Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain F residue 113 SER 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 88 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain D residue 32 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 102 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 116 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 GLN F 201 ASN B 70 HIS ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.118364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.082008 restraints weight = 20132.323| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.81 r_work: 0.3074 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11278 Z= 0.152 Angle : 0.568 12.038 15358 Z= 0.294 Chirality : 0.043 0.155 1766 Planarity : 0.004 0.053 1938 Dihedral : 3.802 14.696 1520 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.71 % Allowed : 12.54 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.22), residues: 1402 helix: 2.19 (0.24), residues: 424 sheet: 0.88 (0.24), residues: 454 loop : -0.42 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 47 HIS 0.004 0.001 HIS B 240 PHE 0.031 0.001 PHE A 149 TYR 0.012 0.001 TYR C 190 ARG 0.003 0.000 ARG C 159 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 584) hydrogen bonds : angle 4.47935 ( 1716) metal coordination : bond 0.00347 ( 2) SS BOND : bond 0.00403 ( 8) SS BOND : angle 0.74851 ( 16) covalent geometry : bond 0.00343 (11268) covalent geometry : angle 0.56812 (15342) *********************** 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 216 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8714 (t0) cc_final: 0.8244 (t0) REVERT: A 52 GLU cc_start: 0.7993 (pp20) cc_final: 0.7663 (pp20) REVERT: A 74 ASP cc_start: 0.7764 (m-30) cc_final: 0.7468 (m-30) REVERT: A 128 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7462 (mt-10) REVERT: A 240 HIS cc_start: 0.8397 (t-90) cc_final: 0.7908 (t-90) REVERT: A 288 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7597 (tm-30) REVERT: E 72 ASP cc_start: 0.8085 (t0) cc_final: 0.7758 (t0) REVERT: E 120 LYS cc_start: 0.8930 (mmmm) cc_final: 0.8678 (mmmm) REVERT: E 176 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7639 (tm-30) REVERT: C 83 GLU cc_start: 0.8537 (pt0) cc_final: 0.8236 (pt0) REVERT: F 43 LYS cc_start: 0.8914 (ptpt) cc_final: 0.8627 (ptpt) REVERT: F 72 ASP cc_start: 0.8289 (t0) cc_final: 0.8057 (t0) REVERT: B 50 PHE cc_start: 0.9031 (m-10) cc_final: 0.8677 (m-10) REVERT: B 74 ASP cc_start: 0.7391 (m-30) cc_final: 0.7052 (m-30) REVERT: B 128 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8495 (tm-30) REVERT: B 154 ILE cc_start: 0.8795 (mm) cc_final: 0.8567 (mm) REVERT: B 257 MET cc_start: 0.5940 (tmm) cc_final: 0.5631 (ttt) REVERT: B 347 ASP cc_start: 0.8848 (t0) cc_final: 0.8636 (t0) REVERT: D 169 ASP cc_start: 0.8745 (m-30) cc_final: 0.8537 (m-30) REVERT: D 194 ASN cc_start: 0.9093 (t0) cc_final: 0.8889 (t0) outliers start: 21 outliers final: 15 residues processed: 209 average time/residue: 0.2091 time to fit residues: 64.9244 Evaluate side-chains 194 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR 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 178 ASP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain D residue 32 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 18 optimal weight: 0.0010 chunk 44 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 104 optimal weight: 0.3980 chunk 32 optimal weight: 0.0980 chunk 110 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 201 ASN D 160 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.119027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.081346 restraints weight = 19853.584| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.43 r_work: 0.3095 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11278 Z= 0.120 Angle : 0.557 8.515 15358 Z= 0.289 Chirality : 0.043 0.204 1766 Planarity : 0.004 0.051 1938 Dihedral : 3.724 14.754 1520 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.30 % Allowed : 14.25 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.22), residues: 1402 helix: 2.19 (0.25), residues: 424 sheet: 0.94 (0.24), residues: 452 loop : -0.40 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 58 HIS 0.002 0.000 HIS F 35 PHE 0.023 0.001 PHE A 149 TYR 0.014 0.001 TYR C 190 ARG 0.003 0.000 ARG C 159 Details of bonding type rmsd hydrogen bonds : bond 0.03187 ( 584) hydrogen bonds : angle 4.32361 ( 1716) metal coordination : bond 0.00158 ( 2) SS BOND : bond 0.00421 ( 8) SS BOND : angle 0.58002 ( 16) covalent geometry : bond 0.00266 (11268) covalent geometry : angle 0.55710 (15342) *********************** 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 207 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8574 (t0) cc_final: 0.8081 (t0) REVERT: A 52 GLU cc_start: 0.8032 (pp20) cc_final: 0.7710 (pp20) REVERT: A 128 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7485 (mt-10) REVERT: A 288 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7662 (tm-30) REVERT: E 72 ASP cc_start: 0.8135 (t0) cc_final: 0.7792 (t0) REVERT: E 176 GLN cc_start: 0.8178 (tm-30) cc_final: 0.7803 (tm-30) REVERT: C 160 GLN cc_start: 0.8495 (pm20) cc_final: 0.8214 (mp10) REVERT: F 59 TYR cc_start: 0.8957 (m-10) cc_final: 0.8747 (m-10) REVERT: B 50 PHE cc_start: 0.9032 (m-10) cc_final: 0.8678 (m-10) REVERT: B 74 ASP cc_start: 0.7396 (m-30) cc_final: 0.7074 (m-30) REVERT: B 92 ASP cc_start: 0.9027 (p0) cc_final: 0.8755 (p0) REVERT: B 128 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8450 (tm-30) REVERT: B 154 ILE cc_start: 0.8759 (mm) cc_final: 0.8518 (mm) REVERT: D 194 ASN cc_start: 0.9124 (t0) cc_final: 0.8916 (t0) outliers start: 16 outliers final: 12 residues processed: 201 average time/residue: 0.1945 time to fit residues: 58.0997 Evaluate side-chains 187 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 C residue 140 LEU 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 181 THR Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 323 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 62 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 102 optimal weight: 0.0970 chunk 89 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.115685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.078059 restraints weight = 19370.598| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.34 r_work: 0.3024 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11278 Z= 0.176 Angle : 0.577 7.374 15358 Z= 0.301 Chirality : 0.043 0.160 1766 Planarity : 0.004 0.050 1938 Dihedral : 3.830 14.663 1520 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.47 % Allowed : 15.07 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.22), residues: 1402 helix: 2.17 (0.24), residues: 428 sheet: 0.73 (0.24), residues: 462 loop : -0.38 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 159 HIS 0.004 0.001 HIS A 240 PHE 0.026 0.001 PHE B 238 TYR 0.016 0.001 TYR C 190 ARG 0.003 0.000 ARG C 159 Details of bonding type rmsd hydrogen bonds : bond 0.03326 ( 584) hydrogen bonds : angle 4.25079 ( 1716) metal coordination : bond 0.01157 ( 2) SS BOND : bond 0.00356 ( 8) SS BOND : angle 0.75027 ( 16) covalent geometry : bond 0.00400 (11268) covalent geometry : angle 0.57702 (15342) *********************** 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 200 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 1.209 Fit side-chains revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8561 (t0) cc_final: 0.8066 (t0) REVERT: A 52 GLU cc_start: 0.8093 (pp20) cc_final: 0.7735 (pp20) REVERT: A 128 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7498 (mt-10) REVERT: A 288 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7882 (tm-30) REVERT: E 72 ASP cc_start: 0.8237 (t0) cc_final: 0.7853 (t0) REVERT: E 138 ASN cc_start: 0.9240 (p0) cc_final: 0.8961 (p0) REVERT: E 176 GLN cc_start: 0.8298 (tm-30) cc_final: 0.7791 (tm-30) REVERT: C 83 GLU cc_start: 0.8544 (pt0) cc_final: 0.8309 (pt0) REVERT: C 160 GLN cc_start: 0.8518 (pm20) cc_final: 0.8179 (mp10) REVERT: F 72 ASP cc_start: 0.8330 (t0) cc_final: 0.8057 (t0) REVERT: F 181 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8933 (m) REVERT: B 50 PHE cc_start: 0.9035 (m-10) cc_final: 0.8680 (m-10) REVERT: B 74 ASP cc_start: 0.7475 (m-30) cc_final: 0.7149 (m-30) REVERT: B 92 ASP cc_start: 0.9025 (p0) cc_final: 0.8740 (p0) REVERT: B 118 THR cc_start: 0.9315 (m) cc_final: 0.9056 (t) REVERT: B 128 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8417 (tm-30) REVERT: B 154 ILE cc_start: 0.8750 (mm) cc_final: 0.8516 (mm) REVERT: D 194 ASN cc_start: 0.9126 (t0) cc_final: 0.8923 (t0) outliers start: 18 outliers final: 15 residues processed: 192 average time/residue: 0.2094 time to fit residues: 59.4587 Evaluate side-chains 195 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR 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 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 181 THR Chi-restraints excluded: chain F residue 201 ASN Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain D residue 32 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 97 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 133 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 201 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.116994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.079893 restraints weight = 19863.034| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.76 r_work: 0.2948 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11278 Z= 0.188 Angle : 0.598 14.787 15358 Z= 0.310 Chirality : 0.044 0.209 1766 Planarity : 0.004 0.051 1938 Dihedral : 3.894 16.025 1520 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.55 % Allowed : 15.72 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.22), residues: 1402 helix: 2.06 (0.25), residues: 428 sheet: 0.68 (0.24), residues: 464 loop : -0.30 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 108 HIS 0.005 0.001 HIS A 240 PHE 0.016 0.001 PHE A 149 TYR 0.015 0.001 TYR C 190 ARG 0.003 0.000 ARG F 38 Details of bonding type rmsd hydrogen bonds : bond 0.03249 ( 584) hydrogen bonds : angle 4.28349 ( 1716) metal coordination : bond 0.01237 ( 2) SS BOND : bond 0.00344 ( 8) SS BOND : angle 0.72662 ( 16) covalent geometry : bond 0.00428 (11268) covalent geometry : angle 0.59794 (15342) *********************** 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 : 1.229 Fit side-chains revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8558 (t0) cc_final: 0.8098 (t0) REVERT: A 52 GLU cc_start: 0.8122 (pp20) cc_final: 0.7773 (pp20) REVERT: A 128 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7423 (mt-10) REVERT: A 288 GLU cc_start: 0.8342 (tm-30) cc_final: 0.8027 (tm-30) REVERT: A 347 ASP cc_start: 0.8686 (t0) cc_final: 0.8424 (t0) REVERT: E 1 GLU cc_start: 0.7917 (pp20) cc_final: 0.7711 (pp20) REVERT: E 72 ASP cc_start: 0.8231 (t0) cc_final: 0.7800 (t0) REVERT: E 88 ASP cc_start: 0.8847 (p0) cc_final: 0.8630 (p0) REVERT: E 176 GLN cc_start: 0.8397 (tm-30) cc_final: 0.7882 (tm-30) REVERT: C 127 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8474 (mp0) REVERT: C 160 GLN cc_start: 0.8579 (pm20) cc_final: 0.8148 (mp10) REVERT: F 59 TYR cc_start: 0.9238 (m-10) cc_final: 0.9032 (m-10) REVERT: B 50 PHE cc_start: 0.9120 (m-10) cc_final: 0.8774 (m-10) REVERT: B 92 ASP cc_start: 0.9044 (p0) cc_final: 0.8735 (p0) REVERT: B 128 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8328 (tm-30) REVERT: B 153 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9072 (pp) REVERT: B 154 ILE cc_start: 0.8775 (mm) cc_final: 0.8505 (mm) outliers start: 19 outliers final: 13 residues processed: 198 average time/residue: 0.1993 time to fit residues: 58.3965 Evaluate side-chains 187 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE 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 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 F residue 211 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 328 THR 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 24 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 53 optimal weight: 0.0020 chunk 88 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 11 optimal weight: 0.0570 chunk 40 optimal weight: 0.0870 chunk 121 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 63 optimal weight: 0.0570 overall best weight: 0.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 GLN B 316 GLN D 128 GLN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.120179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.081512 restraints weight = 20570.704| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.60 r_work: 0.3007 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11278 Z= 0.110 Angle : 0.577 14.216 15358 Z= 0.294 Chirality : 0.042 0.159 1766 Planarity : 0.004 0.050 1938 Dihedral : 3.773 15.780 1520 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.47 % Allowed : 15.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.22), residues: 1402 helix: 2.01 (0.25), residues: 428 sheet: 0.80 (0.24), residues: 464 loop : -0.20 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 159 HIS 0.007 0.001 HIS B 240 PHE 0.023 0.001 PHE A 157 TYR 0.020 0.001 TYR C 190 ARG 0.003 0.000 ARG D 159 Details of bonding type rmsd hydrogen bonds : bond 0.03012 ( 584) hydrogen bonds : angle 4.13163 ( 1716) metal coordination : bond 0.00329 ( 2) SS BOND : bond 0.00316 ( 8) SS BOND : angle 0.53235 ( 16) covalent geometry : bond 0.00240 (11268) covalent geometry : angle 0.57695 (15342) *********************** 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 206 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 1.197 Fit side-chains REVERT: A 32 ASP cc_start: 0.8499 (t0) cc_final: 0.8032 (t0) REVERT: A 52 GLU cc_start: 0.8105 (pp20) cc_final: 0.7738 (pp20) REVERT: A 74 ASP cc_start: 0.7834 (m-30) cc_final: 0.7560 (m-30) REVERT: A 92 ASP cc_start: 0.9019 (p0) cc_final: 0.8687 (p0) REVERT: A 128 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7582 (mt-10) REVERT: A 288 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7929 (tm-30) REVERT: A 332 ASP cc_start: 0.8382 (p0) cc_final: 0.8032 (t70) REVERT: A 347 ASP cc_start: 0.8640 (t0) cc_final: 0.8425 (t0) REVERT: E 72 ASP cc_start: 0.8205 (t0) cc_final: 0.7721 (t0) REVERT: E 138 ASN cc_start: 0.9225 (p0) cc_final: 0.9005 (p0) REVERT: E 176 GLN cc_start: 0.8359 (tm-30) cc_final: 0.7836 (tm-30) REVERT: C 127 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8490 (mp0) REVERT: C 160 GLN cc_start: 0.8585 (pm20) cc_final: 0.8159 (mp10) REVERT: F 72 ASP cc_start: 0.8363 (t0) cc_final: 0.8044 (t0) REVERT: B 37 ASN cc_start: 0.9350 (m110) cc_final: 0.9077 (m110) REVERT: B 50 PHE cc_start: 0.9118 (m-10) cc_final: 0.8737 (m-10) REVERT: B 92 ASP cc_start: 0.9016 (p0) cc_final: 0.8697 (p0) REVERT: B 128 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8321 (tm-30) REVERT: B 153 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9069 (pp) REVERT: B 154 ILE cc_start: 0.8758 (mm) cc_final: 0.8458 (mm) outliers start: 18 outliers final: 14 residues processed: 202 average time/residue: 0.1925 time to fit residues: 57.6900 Evaluate side-chains 193 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 178 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 7 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 43 LYS 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 F residue 211 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain D residue 136 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 87 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 48 optimal weight: 0.0980 chunk 4 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 28 optimal weight: 0.0060 chunk 126 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.116456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.077977 restraints weight = 20256.519| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.47 r_work: 0.3005 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.4781 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= 0.131 Angle : 0.607 12.165 15358 Z= 0.310 Chirality : 0.042 0.160 1766 Planarity : 0.004 0.051 1938 Dihedral : 3.784 18.502 1520 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.30 % Allowed : 16.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.22), residues: 1402 helix: 1.98 (0.25), residues: 428 sheet: 0.80 (0.24), residues: 464 loop : -0.18 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 159 HIS 0.005 0.001 HIS B 240 PHE 0.019 0.001 PHE B 114 TYR 0.018 0.001 TYR C 190 ARG 0.002 0.000 ARG D 159 Details of bonding type rmsd hydrogen bonds : bond 0.03018 ( 584) hydrogen bonds : angle 4.10715 ( 1716) metal coordination : bond 0.00059 ( 2) SS BOND : bond 0.00323 ( 8) SS BOND : angle 0.59955 ( 16) covalent geometry : bond 0.00297 (11268) covalent geometry : angle 0.60739 (15342) *********************** 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 195 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 1.414 Fit side-chains REVERT: A 32 ASP cc_start: 0.8470 (t0) cc_final: 0.7993 (t0) REVERT: A 52 GLU cc_start: 0.8093 (pp20) cc_final: 0.7765 (pp20) REVERT: A 74 ASP cc_start: 0.7813 (m-30) cc_final: 0.7538 (m-30) REVERT: A 92 ASP cc_start: 0.9010 (p0) cc_final: 0.8695 (p0) REVERT: A 128 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7610 (mt-10) REVERT: A 288 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7905 (tm-30) REVERT: A 332 ASP cc_start: 0.8379 (p0) cc_final: 0.8010 (t70) REVERT: E 72 ASP cc_start: 0.8192 (t0) cc_final: 0.7693 (t0) REVERT: E 138 ASN cc_start: 0.9234 (p0) cc_final: 0.8991 (p0) REVERT: E 176 GLN cc_start: 0.8356 (tm-30) cc_final: 0.7833 (tm-30) REVERT: C 127 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8619 (mp0) REVERT: C 149 ASN cc_start: 0.8572 (t0) cc_final: 0.8357 (t0) REVERT: F 72 ASP cc_start: 0.8332 (t0) cc_final: 0.8002 (t0) REVERT: B 50 PHE cc_start: 0.9052 (m-10) cc_final: 0.8649 (m-10) REVERT: B 92 ASP cc_start: 0.9024 (p0) cc_final: 0.8696 (p0) REVERT: B 128 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8327 (tm-30) REVERT: B 153 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9050 (pp) REVERT: B 154 ILE cc_start: 0.8811 (mm) cc_final: 0.8511 (mm) REVERT: B 242 LEU cc_start: 0.9168 (mp) cc_final: 0.8964 (mp) REVERT: B 257 MET cc_start: 0.7501 (tmm) cc_final: 0.6431 (ptm) outliers start: 16 outliers final: 12 residues processed: 193 average time/residue: 0.1948 time to fit residues: 55.7386 Evaluate side-chains 193 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 1.271 ------------------------------------------------------------------------------- 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 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 F residue 211 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 323 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 20 optimal weight: 0.0470 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 0.0370 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 71 optimal weight: 0.0070 chunk 135 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.3174 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.120479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.081846 restraints weight = 20628.060| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.60 r_work: 0.3013 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11278 Z= 0.121 Angle : 0.612 11.981 15358 Z= 0.309 Chirality : 0.043 0.288 1766 Planarity : 0.004 0.051 1938 Dihedral : 3.743 16.211 1520 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.06 % Allowed : 17.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.22), residues: 1402 helix: 1.96 (0.25), residues: 428 sheet: 0.84 (0.24), residues: 464 loop : -0.13 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 159 HIS 0.004 0.001 HIS B 240 PHE 0.015 0.001 PHE A 149 TYR 0.017 0.001 TYR C 190 ARG 0.004 0.000 ARG C 159 Details of bonding type rmsd hydrogen bonds : bond 0.02988 ( 584) hydrogen bonds : angle 4.07966 ( 1716) metal coordination : bond 0.00019 ( 2) SS BOND : bond 0.00322 ( 8) SS BOND : angle 0.53435 ( 16) covalent geometry : bond 0.00274 (11268) covalent geometry : angle 0.61233 (15342) *********************** 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 200 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 187 time to evaluate : 1.280 Fit side-chains REVERT: A 32 ASP cc_start: 0.8471 (t0) cc_final: 0.8005 (t0) REVERT: A 52 GLU cc_start: 0.8080 (pp20) cc_final: 0.7768 (pp20) REVERT: A 74 ASP cc_start: 0.7871 (m-30) cc_final: 0.7597 (m-30) REVERT: A 92 ASP cc_start: 0.9018 (p0) cc_final: 0.8728 (p0) REVERT: A 128 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7627 (mt-10) REVERT: A 288 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7938 (tm-30) REVERT: A 332 ASP cc_start: 0.8383 (p0) cc_final: 0.7872 (t0) REVERT: E 72 ASP cc_start: 0.8170 (t0) cc_final: 0.7692 (t0) REVERT: E 138 ASN cc_start: 0.9248 (p0) cc_final: 0.9000 (p0) REVERT: E 176 GLN cc_start: 0.8367 (tm-30) cc_final: 0.7844 (tm-30) REVERT: C 127 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8619 (mp0) REVERT: F 59 TYR cc_start: 0.9140 (m-10) cc_final: 0.8875 (m-10) REVERT: F 72 ASP cc_start: 0.8298 (t0) cc_final: 0.7971 (t0) REVERT: B 50 PHE cc_start: 0.9040 (m-10) cc_final: 0.8633 (m-10) REVERT: B 92 ASP cc_start: 0.9037 (p0) cc_final: 0.8715 (p0) REVERT: B 128 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8460 (tm-30) REVERT: B 153 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9017 (pp) REVERT: B 154 ILE cc_start: 0.8776 (mm) cc_final: 0.8468 (mm) REVERT: B 257 MET cc_start: 0.7410 (tmm) cc_final: 0.6369 (ptm) REVERT: B 332 ASP cc_start: 0.8498 (p0) cc_final: 0.8018 (p0) outliers start: 13 outliers final: 11 residues processed: 196 average time/residue: 0.2380 time to fit residues: 68.2634 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 : 1.402 ------------------------------------------------------------------------------- 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 7 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 153 LEU 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 4 optimal weight: 4.9990 chunk 120 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.1980 chunk 125 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 63 optimal weight: 0.0030 chunk 42 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.120656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.081741 restraints weight = 20707.461| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.62 r_work: 0.2964 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.4972 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= 0.125 Angle : 0.635 18.549 15358 Z= 0.319 Chirality : 0.043 0.234 1766 Planarity : 0.004 0.051 1938 Dihedral : 3.764 16.728 1520 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.14 % Allowed : 17.51 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.23), residues: 1402 helix: 1.94 (0.25), residues: 428 sheet: 0.86 (0.24), residues: 464 loop : -0.11 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 159 HIS 0.007 0.001 HIS B 240 PHE 0.016 0.001 PHE B 149 TYR 0.018 0.001 TYR C 190 ARG 0.002 0.000 ARG C 159 Details of bonding type rmsd hydrogen bonds : bond 0.03019 ( 584) hydrogen bonds : angle 4.10029 ( 1716) metal coordination : bond 0.00021 ( 2) SS BOND : bond 0.00335 ( 8) SS BOND : angle 0.60710 ( 16) covalent geometry : bond 0.00285 (11268) covalent geometry : angle 0.63497 (15342) ********************** 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 198 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 184 time to evaluate : 1.330 Fit side-chains REVERT: A 32 ASP cc_start: 0.8457 (t0) cc_final: 0.7983 (t0) REVERT: A 52 GLU cc_start: 0.8158 (pp20) cc_final: 0.7868 (pp20) REVERT: A 74 ASP cc_start: 0.7877 (m-30) cc_final: 0.7587 (m-30) REVERT: A 92 ASP cc_start: 0.9035 (p0) cc_final: 0.8723 (p0) REVERT: A 128 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7636 (mt-10) REVERT: A 160 LYS cc_start: 0.8006 (mmtm) cc_final: 0.7771 (mmtm) REVERT: A 288 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7991 (tm-30) REVERT: A 332 ASP cc_start: 0.8483 (p0) cc_final: 0.7948 (t0) REVERT: E 72 ASP cc_start: 0.8175 (t0) cc_final: 0.7682 (t0) REVERT: E 138 ASN cc_start: 0.9202 (p0) cc_final: 0.8980 (p0) REVERT: E 176 GLN cc_start: 0.8368 (tm-30) cc_final: 0.7840 (tm-30) REVERT: C 109 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8010 (tt0) REVERT: C 147 ASP cc_start: 0.8533 (t0) cc_final: 0.8277 (t0) REVERT: F 72 ASP cc_start: 0.8257 (t0) cc_final: 0.7925 (t0) REVERT: B 50 PHE cc_start: 0.8998 (m-10) cc_final: 0.8573 (m-10) REVERT: B 92 ASP cc_start: 0.9044 (p0) cc_final: 0.8724 (p0) REVERT: B 128 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8347 (tm-30) REVERT: B 153 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9025 (pp) REVERT: B 154 ILE cc_start: 0.8777 (mm) cc_final: 0.8476 (mm) REVERT: B 257 MET cc_start: 0.7386 (tmm) cc_final: 0.6314 (ptm) REVERT: B 332 ASP cc_start: 0.8511 (p0) cc_final: 0.8024 (p0) outliers start: 14 outliers final: 13 residues processed: 194 average time/residue: 0.2076 time to fit residues: 59.6603 Evaluate side-chains 193 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 179 time to evaluate : 1.343 ------------------------------------------------------------------------------- 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 F residue 2 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 153 LEU 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 107 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 16 optimal weight: 20.0000 chunk 124 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.114160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.075752 restraints weight = 20047.401| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.40 r_work: 0.2890 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 11278 Z= 0.245 Angle : 0.679 15.497 15358 Z= 0.347 Chirality : 0.045 0.284 1766 Planarity : 0.004 0.052 1938 Dihedral : 4.039 16.133 1520 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.22 % Allowed : 17.83 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.23), residues: 1402 helix: 1.95 (0.25), residues: 428 sheet: 0.63 (0.24), residues: 484 loop : -0.10 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 58 HIS 0.003 0.001 HIS B 240 PHE 0.018 0.001 PHE B 114 TYR 0.024 0.002 TYR C 190 ARG 0.004 0.000 ARG F 38 Details of bonding type rmsd hydrogen bonds : bond 0.03298 ( 584) hydrogen bonds : angle 4.29582 ( 1716) metal coordination : bond 0.00074 ( 2) SS BOND : bond 0.00328 ( 8) SS BOND : angle 0.68332 ( 16) covalent geometry : bond 0.00567 (11268) covalent geometry : angle 0.67894 (15342) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6724.63 seconds wall clock time: 115 minutes 47.55 seconds (6947.55 seconds total)