Starting phenix.real_space_refine on Thu Jun 4 01:11:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w3k_65603/06_2026/9w3k_65603.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w3k_65603/06_2026/9w3k_65603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w3k_65603/06_2026/9w3k_65603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w3k_65603/06_2026/9w3k_65603.map" model { file = "/net/cci-nas-00/data/ceres_data/9w3k_65603/06_2026/9w3k_65603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w3k_65603/06_2026/9w3k_65603.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 6001 2.51 5 N 1545 2.21 5 O 1746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9329 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 3187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3187 Classifications: {'peptide': 415} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 24, 'TRANS': 390} Chain breaks: 7 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1537 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 188} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1584 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain breaks: 2 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: "A" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2054 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 12, 'TRANS': 262} Chain breaks: 3 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 2, 'TRP:plan': 3, 'PHE:plan': 3, 'ARG:plan': 2, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 103 Chain: "B" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 967 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 123} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 2.11, per 1000 atoms: 0.23 Number of scatterers: 9329 At special positions: 0 Unit cell: (132.48, 172.8, 102.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1746 8.00 N 1545 7.00 C 6001 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.03 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 96 " distance=2.04 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: 0.82 Conformation dependent library (CDL) restraints added in 334.2 milliseconds 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2274 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 18 sheets defined 37.6% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'C' and resid 18 through 27 removed outlier: 4.460A pdb=" N VAL C 24 " --> pdb=" O GLY C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 Processing helix chain 'C' and resid 66 through 74 removed outlier: 3.607A pdb=" N GLY C 70 " --> pdb=" O ASP C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 88 removed outlier: 4.147A pdb=" N ASP C 88 " --> pdb=" O LYS C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 99 removed outlier: 3.701A pdb=" N TRP C 95 " --> pdb=" O TYR C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'C' and resid 132 through 141 Processing helix chain 'C' and resid 154 through 163 removed outlier: 4.150A pdb=" N THR C 158 " --> pdb=" O GLU C 154 " (cutoff:3.500A) Proline residue: C 160 - end of helix Processing helix chain 'C' and resid 186 through 202 removed outlier: 3.940A pdb=" N ASN C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 221 Processing helix chain 'C' and resid 229 through 233 removed outlier: 3.795A pdb=" N ALA C 232 " --> pdb=" O GLY C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 288 through 298 Processing helix chain 'C' and resid 315 through 327 Processing helix chain 'C' and resid 337 through 354 Processing helix chain 'C' and resid 357 through 370 removed outlier: 3.703A pdb=" N ALA C 361 " --> pdb=" O THR C 357 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET C 370 " --> pdb=" O GLN C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 388 Processing helix chain 'C' and resid 391 through 406 Processing helix chain 'C' and resid 504 through 518 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.990A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'L' and resid 126 through 132 Processing helix chain 'L' and resid 187 through 193 removed outlier: 3.537A pdb=" N LYS L 193 " --> pdb=" O ALA L 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 37 Processing helix chain 'A' and resid 38 through 64 removed outlier: 3.708A pdb=" N VAL A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 91 Processing helix chain 'A' and resid 91 through 101 removed outlier: 3.574A pdb=" N LYS A 101 " --> pdb=" O THR A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 139 removed outlier: 5.559A pdb=" N ASP A 115 " --> pdb=" O CYS A 111 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N TRP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 130 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 131 " --> pdb=" O TRP A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 168 Processing helix chain 'A' and resid 170 through 175 removed outlier: 4.222A pdb=" N PHE A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N PHE A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 170 through 175' Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 195 through 212 Proline residue: A 207 - end of helix Processing helix chain 'A' and resid 212 through 229 removed outlier: 3.894A pdb=" N PHE A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA A 218 " --> pdb=" O PRO A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 241 Processing helix chain 'A' and resid 242 through 263 Processing helix chain 'A' and resid 263 through 274 removed outlier: 3.941A pdb=" N TRP A 267 " --> pdb=" O TRP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 297 Processing helix chain 'A' and resid 297 through 310 Proline residue: A 303 - end of helix Processing helix chain 'A' and resid 310 through 318 removed outlier: 3.691A pdb=" N ARG A 314 " --> pdb=" O SER A 310 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 302 through 303 removed outlier: 3.974A pdb=" N ALA C 302 " --> pdb=" O VAL C 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 226 through 228 removed outlier: 3.768A pdb=" N LEU C 116 " --> pdb=" O THR C 246 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 172 through 173 Processing sheet with id=AA4, first strand: chain 'C' and resid 250 through 251 Processing sheet with id=AA5, first strand: chain 'C' and resid 534 through 535 removed outlier: 5.681A pdb=" N VAL C 486 " --> pdb=" O VAL C 534 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS C 493 " --> pdb=" O ASP H 218 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP H 218 " --> pdb=" O LYS C 493 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS H 210 " --> pdb=" O THR H 215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.513A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS H 22 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.196A pdb=" N GLY H 10 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY H 33 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 130 through 133 removed outlier: 3.581A pdb=" N LEU H 151 " --> pdb=" O PHE H 132 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP H 154 " --> pdb=" O TYR H 186 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SER H 187 " --> pdb=" O ALA H 178 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA H 178 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER H 189 " --> pdb=" O PHE H 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.622A pdb=" N VAL L 19 " --> pdb=" O ILE L 81 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU L 79 " --> pdb=" O MET L 21 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE L 77 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB2, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.911A pdb=" N LYS L 36 " --> pdb=" O TYR L 31 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 59 through 60 removed outlier: 6.694A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR L 102 " --> pdb=" O GLN L 96 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 119 through 123 removed outlier: 3.527A pdb=" N SER L 119 " --> pdb=" O ASN L 142 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU L 180 " --> pdb=" O LEU L 141 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 151 through 154 removed outlier: 3.599A pdb=" N GLU L 200 " --> pdb=" O GLN L 152 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LYS L 154 " --> pdb=" O ALA L 198 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ALA L 198 " --> pdb=" O LYS L 154 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR L 197 " --> pdb=" O PHE L 214 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 177 through 180 Processing sheet with id=AB7, first strand: chain 'B' and resid 3 through 8 Processing sheet with id=AB8, first strand: chain 'B' and resid 11 through 13 removed outlier: 3.687A pdb=" N ALA B 50 " --> pdb=" O TRP B 37 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG B 39 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N LEU B 48 " --> pdb=" O ARG B 39 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 99 through 100 428 hydrogen bonds defined for protein. 1194 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: 1.61 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2952 1.34 - 1.46: 2328 1.46 - 1.58: 4212 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 9550 Sorted by residual: bond pdb=" C LEU A 264 " pdb=" N PRO A 265 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.72e+00 bond pdb=" C SER L 7 " pdb=" N PRO L 8 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.05e+00 bond pdb=" C TYR A 206 " pdb=" N PRO A 207 " ideal model delta sigma weight residual 1.335 1.349 -0.013 1.36e-02 5.41e+03 9.34e-01 bond pdb=" C LYS B 87 " pdb=" N PRO B 88 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.08e-01 bond pdb=" CA THR B 102 " pdb=" CB THR B 102 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 6.59e-01 ... (remaining 9545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 12538 1.20 - 2.40: 362 2.40 - 3.59: 68 3.59 - 4.79: 21 4.79 - 5.99: 10 Bond angle restraints: 12999 Sorted by residual: angle pdb=" C THR C 287 " pdb=" N ASP C 288 " pdb=" CA ASP C 288 " ideal model delta sigma weight residual 121.54 126.28 -4.74 1.91e+00 2.74e-01 6.15e+00 angle pdb=" N THR C 491 " pdb=" CA THR C 491 " pdb=" C THR C 491 " ideal model delta sigma weight residual 114.56 111.63 2.93 1.27e+00 6.20e-01 5.33e+00 angle pdb=" C ARG B 101 " pdb=" N THR B 102 " pdb=" CA THR B 102 " ideal model delta sigma weight residual 121.54 125.79 -4.25 1.91e+00 2.74e-01 4.94e+00 angle pdb=" N ALA L 57 " pdb=" CA ALA L 57 " pdb=" CB ALA L 57 " ideal model delta sigma weight residual 113.65 110.56 3.09 1.47e+00 4.63e-01 4.42e+00 angle pdb=" N SER L 7 " pdb=" CA SER L 7 " pdb=" C SER L 7 " ideal model delta sigma weight residual 109.81 114.03 -4.22 2.21e+00 2.05e-01 3.64e+00 ... (remaining 12994 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 5089 17.45 - 34.89: 440 34.89 - 52.34: 61 52.34 - 69.78: 16 69.78 - 87.23: 8 Dihedral angle restraints: 5614 sinusoidal: 2084 harmonic: 3530 Sorted by residual: dihedral pdb=" CA LYS A 112 " pdb=" C LYS A 112 " pdb=" N SER A 113 " pdb=" CA SER A 113 " ideal model delta harmonic sigma weight residual -180.00 -162.50 -17.50 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CB MET L 3 " pdb=" CG MET L 3 " pdb=" SD MET L 3 " pdb=" CE MET L 3 " ideal model delta sinusoidal sigma weight residual 60.00 118.50 -58.50 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CG LYS A 318 " pdb=" CD LYS A 318 " pdb=" CE LYS A 318 " pdb=" NZ LYS A 318 " ideal model delta sinusoidal sigma weight residual 180.00 123.17 56.83 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 5611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 929 0.031 - 0.061: 351 0.061 - 0.091: 107 0.091 - 0.122: 78 0.122 - 0.152: 10 Chirality restraints: 1475 Sorted by residual: chirality pdb=" CA ILE C 334 " pdb=" N ILE C 334 " pdb=" C ILE C 334 " pdb=" CB ILE C 334 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" CB THR B 91 " pdb=" CA THR B 91 " pdb=" OG1 THR B 91 " pdb=" CG2 THR B 91 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA VAL C 38 " pdb=" N VAL C 38 " pdb=" C VAL C 38 " pdb=" CB VAL C 38 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 1472 not shown) Planarity restraints: 1642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 168 " -0.036 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO A 169 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 169 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 169 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 49 " 0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO L 50 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO L 50 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 50 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 388 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.24e+00 pdb=" N PRO C 389 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 389 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 389 " -0.021 5.00e-02 4.00e+02 ... (remaining 1639 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 4368 2.98 - 3.46: 8835 3.46 - 3.94: 13997 3.94 - 4.42: 14934 4.42 - 4.90: 26136 Nonbonded interactions: 68270 Sorted by model distance: nonbonded pdb=" O LEU C 281 " pdb=" CB LEU C 285 " model vdw 2.497 3.440 nonbonded pdb=" O ASN C 19 " pdb=" OE1 GLU C 23 " model vdw 2.573 3.040 nonbonded pdb=" N ASP B 34 " pdb=" OD1 ASP B 34 " model vdw 2.595 3.120 nonbonded pdb=" O SER B 85 " pdb=" OG SER B 85 " model vdw 2.600 3.040 nonbonded pdb=" N ASP H 103 " pdb=" OD1 ASP H 103 " model vdw 2.603 3.120 ... (remaining 68265 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 6.190 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: 0.390 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.920 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 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 : 0.003 0.038 9554 Z= 0.125 Angle : 0.527 5.989 13007 Z= 0.273 Chirality : 0.041 0.152 1475 Planarity : 0.004 0.054 1642 Dihedral : 13.482 87.230 3328 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.26), residues: 1184 helix: 1.88 (0.27), residues: 406 sheet: 0.39 (0.31), residues: 299 loop : -1.31 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 19 TYR 0.019 0.001 TYR L 31 PHE 0.013 0.001 PHE A 216 TRP 0.014 0.001 TRP A 267 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 9550) covalent geometry : angle 0.52681 / 0.27 (12999) SS BOND : bond 0.00513 / 0.26 ( 4) SS BOND : angle 0.86135 / 0.38 ( 8) hydrogen bonds : bond 0.20435 / 13.74 ( 428) hydrogen bonds : angle 6.19279 / 4.34 ( 1194) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.431 Fit side-chains REVERT: C 132 GLU cc_start: 0.7268 (tm-30) cc_final: 0.6835 (tm-30) REVERT: C 252 LYS cc_start: 0.7603 (mttp) cc_final: 0.7334 (mttp) REVERT: C 515 ASN cc_start: 0.7535 (t0) cc_final: 0.7253 (t0) REVERT: H 76 LYS cc_start: 0.7891 (mtmm) cc_final: 0.7552 (mtmm) REVERT: L 67 ARG cc_start: 0.7727 (mtm110) cc_final: 0.7466 (mtp180) REVERT: L 136 SER cc_start: 0.8389 (m) cc_final: 0.8091 (t) REVERT: A 43 LEU cc_start: 0.8209 (tt) cc_final: 0.7950 (tt) REVERT: A 161 ILE cc_start: 0.8011 (pt) cc_final: 0.7779 (pt) REVERT: A 164 VAL cc_start: 0.8794 (t) cc_final: 0.8582 (p) REVERT: A 211 PHE cc_start: 0.8406 (t80) cc_final: 0.8142 (t80) REVERT: A 241 LYS cc_start: 0.8381 (mtpt) cc_final: 0.8165 (mtpt) REVERT: B 19 LEU cc_start: 0.8550 (pp) cc_final: 0.8298 (pp) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.0894 time to fit residues: 26.3923 Evaluate side-chains 192 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 517 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.160859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.130633 restraints weight = 15475.744| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.87 r_work: 0.3574 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9554 Z= 0.131 Angle : 0.563 9.563 13007 Z= 0.281 Chirality : 0.042 0.159 1475 Planarity : 0.004 0.063 1642 Dihedral : 3.674 17.649 1292 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.54 % Allowed : 7.79 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.26), residues: 1184 helix: 1.96 (0.27), residues: 411 sheet: 0.60 (0.32), residues: 306 loop : -1.23 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 101 TYR 0.016 0.001 TYR C 156 PHE 0.018 0.001 PHE A 216 TRP 0.011 0.001 TRP H 47 HIS 0.005 0.001 HIS H 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 9550) covalent geometry : angle 0.56287 / 0.28 (12999) SS BOND : bond 0.00605 / 0.31 ( 4) SS BOND : angle 0.85886 / 0.42 ( 8) hydrogen bonds : bond 0.04773 / 3.05 ( 428) hydrogen bonds : angle 4.68403 / 3.28 ( 1194) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 131 GLU cc_start: 0.7510 (mp0) cc_final: 0.7105 (mp0) REVERT: C 132 GLU cc_start: 0.7204 (tm-30) cc_final: 0.6751 (tm-30) REVERT: C 209 THR cc_start: 0.8154 (m) cc_final: 0.7663 (p) REVERT: C 515 ASN cc_start: 0.7508 (t0) cc_final: 0.7225 (t0) REVERT: H 103 ASP cc_start: 0.8414 (p0) cc_final: 0.8126 (p0) REVERT: L 67 ARG cc_start: 0.7671 (mtm110) cc_final: 0.7398 (mtp180) REVERT: L 136 SER cc_start: 0.8206 (m) cc_final: 0.7774 (p) REVERT: A 43 LEU cc_start: 0.8249 (tt) cc_final: 0.7986 (tt) REVERT: A 116 TRP cc_start: 0.7924 (t60) cc_final: 0.7334 (t60) REVERT: A 161 ILE cc_start: 0.8054 (pt) cc_final: 0.7815 (pt) REVERT: A 164 VAL cc_start: 0.8831 (t) cc_final: 0.8625 (p) REVERT: A 211 PHE cc_start: 0.8407 (t80) cc_final: 0.8172 (t80) REVERT: A 219 SER cc_start: 0.8276 (m) cc_final: 0.8046 (t) REVERT: A 220 PHE cc_start: 0.7393 (t80) cc_final: 0.7177 (t80) outliers start: 15 outliers final: 10 residues processed: 197 average time/residue: 0.0901 time to fit residues: 25.4883 Evaluate side-chains 195 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 185 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 13 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 356 GLN C 517 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.159829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.129494 restraints weight = 15421.940| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.88 r_work: 0.3561 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9554 Z= 0.155 Angle : 0.570 10.813 13007 Z= 0.283 Chirality : 0.042 0.151 1475 Planarity : 0.004 0.057 1642 Dihedral : 3.743 17.978 1292 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.95 % Allowed : 10.96 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.26), residues: 1184 helix: 1.88 (0.27), residues: 411 sheet: 0.70 (0.32), residues: 299 loop : -1.24 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 101 TYR 0.018 0.001 TYR C 156 PHE 0.021 0.001 PHE C 251 TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS L 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 9550) covalent geometry : angle 0.56961 / 0.28 (12999) SS BOND : bond 0.00709 / 0.36 ( 4) SS BOND : angle 0.85567 / 0.42 ( 8) hydrogen bonds : bond 0.04768 / 3.03 ( 428) hydrogen bonds : angle 4.46374 / 3.12 ( 1194) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: C 131 GLU cc_start: 0.7501 (mp0) cc_final: 0.7123 (mp0) REVERT: C 132 GLU cc_start: 0.7234 (tm-30) cc_final: 0.6759 (tm-30) REVERT: C 156 TYR cc_start: 0.7314 (m-80) cc_final: 0.6955 (m-80) REVERT: C 252 LYS cc_start: 0.7569 (mttp) cc_final: 0.7319 (mttp) REVERT: C 515 ASN cc_start: 0.7520 (t0) cc_final: 0.7236 (t0) REVERT: A 43 LEU cc_start: 0.8262 (tt) cc_final: 0.8002 (tt) REVERT: A 116 TRP cc_start: 0.7979 (t60) cc_final: 0.7328 (t60) REVERT: A 161 ILE cc_start: 0.8036 (pt) cc_final: 0.7806 (pt) REVERT: A 219 SER cc_start: 0.8343 (m) cc_final: 0.8119 (t) REVERT: A 220 PHE cc_start: 0.7465 (t80) cc_final: 0.7254 (t80) outliers start: 19 outliers final: 13 residues processed: 193 average time/residue: 0.0867 time to fit residues: 24.1173 Evaluate side-chains 201 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 168 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 517 ASN L 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.157810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.127438 restraints weight = 15618.682| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.88 r_work: 0.3537 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9554 Z= 0.189 Angle : 0.594 10.721 13007 Z= 0.299 Chirality : 0.043 0.160 1475 Planarity : 0.004 0.062 1642 Dihedral : 3.944 18.511 1292 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.66 % Allowed : 11.78 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.26), residues: 1184 helix: 1.79 (0.27), residues: 410 sheet: 0.67 (0.32), residues: 299 loop : -1.34 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 101 TYR 0.020 0.002 TYR C 156 PHE 0.018 0.002 PHE C 251 TRP 0.012 0.001 TRP A 270 HIS 0.004 0.001 HIS L 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 ( 9550) covalent geometry : angle 0.59396 / 0.30 (12999) SS BOND : bond 0.00865 / 0.44 ( 4) SS BOND : angle 1.08243 / 0.53 ( 8) hydrogen bonds : bond 0.05095 / 3.21 ( 428) hydrogen bonds : angle 4.45891 / 3.12 ( 1194) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: C 23 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.5934 (mp0) REVERT: C 131 GLU cc_start: 0.7510 (mp0) cc_final: 0.7274 (mp0) REVERT: C 132 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6732 (tm-30) REVERT: C 156 TYR cc_start: 0.7343 (m-80) cc_final: 0.6212 (m-80) REVERT: C 252 LYS cc_start: 0.7548 (mttp) cc_final: 0.7342 (mttp) REVERT: C 515 ASN cc_start: 0.7522 (t0) cc_final: 0.7240 (t0) REVERT: A 43 LEU cc_start: 0.8264 (tt) cc_final: 0.7988 (tt) REVERT: A 60 ILE cc_start: 0.7945 (tt) cc_final: 0.7675 (mt) REVERT: A 116 TRP cc_start: 0.8048 (t60) cc_final: 0.7256 (t60) REVERT: A 117 PHE cc_start: 0.7654 (t80) cc_final: 0.7244 (t80) REVERT: A 120 THR cc_start: 0.8490 (m) cc_final: 0.8277 (m) REVERT: A 295 MET cc_start: 0.8324 (tmm) cc_final: 0.7930 (tmm) outliers start: 26 outliers final: 19 residues processed: 209 average time/residue: 0.0848 time to fit residues: 25.7965 Evaluate side-chains 210 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 190 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 168 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 23 optimal weight: 0.0670 chunk 27 optimal weight: 0.3980 chunk 98 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 112 optimal weight: 0.0870 chunk 39 optimal weight: 0.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- 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 = 0.4124 r_free = 0.4124 target = 0.160749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.130676 restraints weight = 15651.781| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.87 r_work: 0.3577 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9554 Z= 0.112 Angle : 0.539 11.267 13007 Z= 0.266 Chirality : 0.041 0.149 1475 Planarity : 0.004 0.052 1642 Dihedral : 3.684 17.504 1292 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.56 % Allowed : 13.11 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.26), residues: 1184 helix: 1.98 (0.27), residues: 410 sheet: 0.52 (0.31), residues: 319 loop : -1.17 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 250 TYR 0.012 0.001 TYR H 155 PHE 0.019 0.001 PHE A 216 TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 9550) covalent geometry : angle 0.53906 / 0.27 (12999) SS BOND : bond 0.00519 / 0.26 ( 4) SS BOND : angle 0.67414 / 0.31 ( 8) hydrogen bonds : bond 0.03953 / 2.47 ( 428) hydrogen bonds : angle 4.18934 / 2.92 ( 1194) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: C 23 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.5960 (mp0) REVERT: C 131 GLU cc_start: 0.7455 (mp0) cc_final: 0.7230 (mp0) REVERT: C 132 GLU cc_start: 0.7204 (tm-30) cc_final: 0.6659 (tm-30) REVERT: C 154 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7474 (tp30) REVERT: C 515 ASN cc_start: 0.7481 (t0) cc_final: 0.7183 (t0) REVERT: L 4 LEU cc_start: 0.8701 (mp) cc_final: 0.8441 (mt) REVERT: A 43 LEU cc_start: 0.8220 (tt) cc_final: 0.7961 (tt) REVERT: A 60 ILE cc_start: 0.7834 (tt) cc_final: 0.7601 (mt) REVERT: A 116 TRP cc_start: 0.7902 (t60) cc_final: 0.7217 (t60) REVERT: A 295 MET cc_start: 0.8033 (tmm) cc_final: 0.7789 (tmm) outliers start: 25 outliers final: 19 residues processed: 193 average time/residue: 0.0884 time to fit residues: 24.5677 Evaluate side-chains 208 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 168 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 124 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 30 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 8 optimal weight: 6.9990 chunk 13 optimal weight: 0.0010 chunk 98 optimal weight: 0.3980 chunk 108 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 102 optimal weight: 0.5980 overall best weight: 0.4386 ------------------------------------------------------------------------------- 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 = 0.4117 r_free = 0.4117 target = 0.160089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.129987 restraints weight = 15526.960| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.89 r_work: 0.3565 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9554 Z= 0.118 Angle : 0.537 10.147 13007 Z= 0.265 Chirality : 0.041 0.149 1475 Planarity : 0.004 0.051 1642 Dihedral : 3.628 17.153 1292 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.25 % Allowed : 14.04 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.26), residues: 1184 helix: 2.03 (0.27), residues: 410 sheet: 0.59 (0.31), residues: 309 loop : -1.13 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 250 TYR 0.013 0.001 TYR H 155 PHE 0.017 0.001 PHE A 306 TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS H 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 9550) covalent geometry : angle 0.53672 / 0.26 (12999) SS BOND : bond 0.00569 / 0.29 ( 4) SS BOND : angle 0.74855 / 0.35 ( 8) hydrogen bonds : bond 0.03966 / 2.48 ( 428) hydrogen bonds : angle 4.14066 / 2.89 ( 1194) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: C 23 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.5940 (mp0) REVERT: C 131 GLU cc_start: 0.7483 (mp0) cc_final: 0.7247 (mp0) REVERT: C 132 GLU cc_start: 0.7205 (tm-30) cc_final: 0.6625 (tm-30) REVERT: C 154 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7504 (tp30) REVERT: C 515 ASN cc_start: 0.7499 (t0) cc_final: 0.7190 (t0) REVERT: L 4 LEU cc_start: 0.8708 (mp) cc_final: 0.8453 (mt) REVERT: A 43 LEU cc_start: 0.8223 (tt) cc_final: 0.7964 (tt) REVERT: A 116 TRP cc_start: 0.7897 (t60) cc_final: 0.7219 (t60) outliers start: 22 outliers final: 19 residues processed: 200 average time/residue: 0.0848 time to fit residues: 24.5596 Evaluate side-chains 203 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 168 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 124 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 102 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 62 optimal weight: 0.0470 chunk 64 optimal weight: 0.0770 chunk 97 optimal weight: 0.2980 overall best weight: 0.3836 ------------------------------------------------------------------------------- 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 = 0.4128 r_free = 0.4128 target = 0.160895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.130840 restraints weight = 15668.491| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.89 r_work: 0.3583 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9554 Z= 0.111 Angle : 0.544 10.293 13007 Z= 0.265 Chirality : 0.041 0.151 1475 Planarity : 0.004 0.049 1642 Dihedral : 3.586 16.820 1292 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.87 % Allowed : 14.45 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.26), residues: 1184 helix: 2.05 (0.27), residues: 413 sheet: 0.79 (0.30), residues: 320 loop : -1.15 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 250 TYR 0.013 0.001 TYR H 155 PHE 0.020 0.001 PHE C 251 TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS H 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 9550) covalent geometry : angle 0.54387 / 0.27 (12999) SS BOND : bond 0.00519 / 0.26 ( 4) SS BOND : angle 0.72459 / 0.33 ( 8) hydrogen bonds : bond 0.03751 / 2.35 ( 428) hydrogen bonds : angle 4.06260 / 2.83 ( 1194) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: C 23 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.5934 (mp0) REVERT: C 131 GLU cc_start: 0.7477 (mp0) cc_final: 0.7230 (mp0) REVERT: C 132 GLU cc_start: 0.7189 (tm-30) cc_final: 0.6592 (tm-30) REVERT: C 209 THR cc_start: 0.8195 (m) cc_final: 0.7684 (p) REVERT: C 515 ASN cc_start: 0.7466 (t0) cc_final: 0.7186 (t0) REVERT: A 43 LEU cc_start: 0.8215 (tt) cc_final: 0.7960 (tt) REVERT: A 116 TRP cc_start: 0.7885 (t60) cc_final: 0.7215 (t60) outliers start: 28 outliers final: 21 residues processed: 198 average time/residue: 0.0815 time to fit residues: 23.3999 Evaluate side-chains 210 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 124 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 78 optimal weight: 0.9980 chunk 56 optimal weight: 0.0980 chunk 24 optimal weight: 8.9990 chunk 99 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4108 r_free = 0.4108 target = 0.159484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.128791 restraints weight = 15555.910| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.92 r_work: 0.3545 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9554 Z= 0.153 Angle : 0.579 10.229 13007 Z= 0.284 Chirality : 0.042 0.153 1475 Planarity : 0.004 0.052 1642 Dihedral : 3.769 17.283 1292 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.28 % Allowed : 14.86 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.26), residues: 1184 helix: 1.97 (0.27), residues: 413 sheet: 0.61 (0.31), residues: 314 loop : -1.12 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 250 TYR 0.015 0.001 TYR C 156 PHE 0.022 0.001 PHE C 251 TRP 0.012 0.001 TRP A 127 HIS 0.004 0.001 HIS H 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 9550) covalent geometry : angle 0.57860 / 0.28 (12999) SS BOND : bond 0.00738 / 0.38 ( 4) SS BOND : angle 0.94929 / 0.46 ( 8) hydrogen bonds : bond 0.04334 / 2.72 ( 428) hydrogen bonds : angle 4.17737 / 2.91 ( 1194) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: C 23 GLU cc_start: 0.6396 (OUTLIER) cc_final: 0.5952 (mp0) REVERT: C 131 GLU cc_start: 0.7540 (mp0) cc_final: 0.7271 (mp0) REVERT: C 132 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6636 (tm-30) REVERT: C 154 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7567 (tp30) REVERT: C 156 TYR cc_start: 0.7341 (m-80) cc_final: 0.6262 (m-80) REVERT: C 515 ASN cc_start: 0.7511 (t0) cc_final: 0.7244 (t0) REVERT: A 43 LEU cc_start: 0.8228 (tt) cc_final: 0.7976 (tt) REVERT: A 116 TRP cc_start: 0.7941 (t60) cc_final: 0.7262 (t60) outliers start: 32 outliers final: 23 residues processed: 202 average time/residue: 0.0850 time to fit residues: 24.9110 Evaluate side-chains 210 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 168 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 124 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 69 optimal weight: 0.0470 chunk 22 optimal weight: 0.7980 overall best weight: 0.6480 ------------------------------------------------------------------------------- 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 = 0.4107 r_free = 0.4107 target = 0.159047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.128830 restraints weight = 15471.114| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.87 r_work: 0.3555 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9554 Z= 0.145 Angle : 0.587 9.911 13007 Z= 0.287 Chirality : 0.042 0.159 1475 Planarity : 0.004 0.049 1642 Dihedral : 3.793 17.383 1292 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.77 % Allowed : 15.68 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.26), residues: 1184 helix: 1.95 (0.27), residues: 413 sheet: 0.51 (0.30), residues: 324 loop : -1.15 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 101 TYR 0.018 0.001 TYR C 91 PHE 0.020 0.001 PHE C 251 TRP 0.011 0.001 TRP A 127 HIS 0.004 0.001 HIS H 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 9550) covalent geometry : angle 0.58645 / 0.29 (12999) SS BOND : bond 0.00691 / 0.35 ( 4) SS BOND : angle 0.96864 / 0.47 ( 8) hydrogen bonds : bond 0.04279 / 2.67 ( 428) hydrogen bonds : angle 4.19122 / 2.92 ( 1194) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: C 23 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.5976 (mp0) REVERT: C 131 GLU cc_start: 0.7538 (mp0) cc_final: 0.7266 (mp0) REVERT: C 132 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6630 (tm-30) REVERT: C 154 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7555 (tp30) REVERT: C 156 TYR cc_start: 0.7327 (m-80) cc_final: 0.6247 (m-80) REVERT: C 515 ASN cc_start: 0.7486 (t0) cc_final: 0.7209 (t0) REVERT: A 43 LEU cc_start: 0.8232 (tt) cc_final: 0.7977 (tt) REVERT: A 116 TRP cc_start: 0.7941 (t60) cc_final: 0.7290 (t60) REVERT: A 288 ILE cc_start: 0.7665 (mm) cc_final: 0.7353 (mm) outliers start: 27 outliers final: 24 residues processed: 192 average time/residue: 0.0832 time to fit residues: 23.0319 Evaluate side-chains 206 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 168 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 124 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 31 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.4099 r_free = 0.4099 target = 0.158866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.128542 restraints weight = 15480.056| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.86 r_work: 0.3540 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9554 Z= 0.169 Angle : 0.611 9.834 13007 Z= 0.300 Chirality : 0.042 0.172 1475 Planarity : 0.004 0.058 1642 Dihedral : 3.926 17.851 1292 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.66 % Allowed : 15.68 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.26), residues: 1184 helix: 1.85 (0.26), residues: 413 sheet: 0.59 (0.30), residues: 317 loop : -1.25 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 250 TYR 0.017 0.001 TYR C 156 PHE 0.021 0.001 PHE C 251 TRP 0.012 0.001 TRP A 127 HIS 0.005 0.001 HIS H 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 9550) covalent geometry : angle 0.61018 / 0.30 (12999) SS BOND : bond 0.00817 / 0.42 ( 4) SS BOND : angle 1.07197 / 0.52 ( 8) hydrogen bonds : bond 0.04626 / 2.90 ( 428) hydrogen bonds : angle 4.27953 / 2.98 ( 1194) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2368 Ramachandran restraints generated. 1184 Oldfield, 0 Emsley, 1184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: C 23 GLU cc_start: 0.6430 (OUTLIER) cc_final: 0.5992 (mp0) REVERT: C 131 GLU cc_start: 0.7550 (mp0) cc_final: 0.7271 (mp0) REVERT: C 132 GLU cc_start: 0.7277 (tm-30) cc_final: 0.6628 (tm-30) REVERT: C 154 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7560 (tp30) REVERT: C 156 TYR cc_start: 0.7360 (m-80) cc_final: 0.6277 (m-80) REVERT: C 210 ASP cc_start: 0.7553 (t0) cc_final: 0.7286 (t70) REVERT: C 515 ASN cc_start: 0.7477 (t0) cc_final: 0.7194 (t0) REVERT: A 43 LEU cc_start: 0.8233 (tt) cc_final: 0.7978 (tt) REVERT: A 116 TRP cc_start: 0.7980 (t60) cc_final: 0.7213 (t60) REVERT: A 120 THR cc_start: 0.8479 (m) cc_final: 0.8274 (m) REVERT: A 288 ILE cc_start: 0.7735 (mm) cc_final: 0.7428 (mm) outliers start: 26 outliers final: 24 residues processed: 198 average time/residue: 0.0874 time to fit residues: 24.9226 Evaluate side-chains 212 residues out of total 1029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 168 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 ARG Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 124 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.1980 chunk 21 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 95 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.159491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.129160 restraints weight = 15429.992| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.89 r_work: 0.3547 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9554 Z= 0.145 Angle : 0.593 9.772 13007 Z= 0.290 Chirality : 0.042 0.167 1475 Planarity : 0.005 0.070 1642 Dihedral : 3.885 17.710 1292 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.66 % Allowed : 16.09 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.26), residues: 1184 helix: 1.90 (0.26), residues: 413 sheet: 0.49 (0.30), residues: 324 loop : -1.19 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 250 TYR 0.015 0.001 TYR C 156 PHE 0.020 0.001 PHE C 251 TRP 0.010 0.001 TRP A 127 HIS 0.004 0.001 HIS H 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 9550) covalent geometry : angle 0.59218 / 0.29 (12999) SS BOND : bond 0.00696 / 0.36 ( 4) SS BOND : angle 1.01566 / 0.49 ( 8) hydrogen bonds : bond 0.04322 / 2.70 ( 428) hydrogen bonds : angle 4.22604 / 2.94 ( 1194) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2909.73 seconds wall clock time: 50 minutes 24.77 seconds (3024.77 seconds total)