Starting phenix.real_space_refine on Wed Mar 4 17:55:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7usw_26741/03_2026/7usw_26741.cif Found real_map, /net/cci-nas-00/data/ceres_data/7usw_26741/03_2026/7usw_26741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7usw_26741/03_2026/7usw_26741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7usw_26741/03_2026/7usw_26741.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7usw_26741/03_2026/7usw_26741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7usw_26741/03_2026/7usw_26741.map" } resolution = 3.1 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= 0.000 sd= 1.000 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: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 P 4 5.49 5 S 78 5.16 5 C 9572 2.51 5 N 2282 2.21 5 O 2378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14322 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4897 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 18, 'TRANS': 589} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 4, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "B" Number of atoms: 4897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4897 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 18, 'TRANS': 589} Chain breaks: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 4, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "C" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1536 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "D" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 343 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1536 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 176} Chain: "F" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 343 Classifications: {'peptide': 46} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 328 Unusual residues: {' CA': 2, '3PE': 1, 'CLR': 1, 'D12': 6, 'NAG': 1, 'PEE': 1, 'R16': 1, 'ZFC': 14} Classifications: {'undetermined': 27} Link IDs: {None: 26} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 360 Unusual residues: {' CA': 2, '3PE': 1, 'CLR': 1, 'D12': 6, 'NAG': 1, 'PEE': 1, 'R16': 3, 'ZFC': 14} Classifications: {'undetermined': 29} Link IDs: {None: 28} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 39 Unusual residues: {'PLM': 1, 'ZFC': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 39 Unusual residues: {'PLM': 1, 'ZFC': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 3.09, per 1000 atoms: 0.22 Number of scatterers: 14322 At special positions: 0 Unit cell: (133.401, 108.231, 108.231, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 8 19.99 S 78 16.00 P 4 15.00 O 2378 8.00 N 2282 7.00 C 9572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 667 " - pdb=" SG CYS A 816 " distance=2.03 Simple disulfide: pdb=" SG CYS B 667 " - pdb=" SG CYS B 816 " 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=5, symmetry=0 Links applied NAG-ASN " NAG A1327 " - " ASN A 209 " " NAG B1329 " - " ASN B 209 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 649.9 milliseconds 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3212 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 2 sheets defined 75.2% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 75 through 93 Processing helix chain 'A' and resid 99 through 118 Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 122 through 147 Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 152 through 164 removed outlier: 3.651A pdb=" N ILE A 156 " --> pdb=" O TRP A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 191 removed outlier: 4.202A pdb=" N TYR A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE A 191 " --> pdb=" O ILE A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 204 through 216 removed outlier: 4.915A pdb=" N THR A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ARG A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 4.133A pdb=" N VAL A 223 " --> pdb=" O ALA A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.532A pdb=" N TYR A 248 " --> pdb=" O TYR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 290 removed outlier: 3.607A pdb=" N PHE A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 318 through 343 removed outlier: 3.585A pdb=" N LYS A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 381 removed outlier: 3.591A pdb=" N CYS A 364 " --> pdb=" O ASN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 417 removed outlier: 3.806A pdb=" N SER A 397 " --> pdb=" O ASN A 393 " (cutoff:3.500A) Proline residue: A 407 - end of helix removed outlier: 3.785A pdb=" N MET A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 459 Processing helix chain 'A' and resid 667 through 695 Processing helix chain 'A' and resid 695 through 706 Processing helix chain 'A' and resid 724 through 743 Processing helix chain 'A' and resid 748 through 771 removed outlier: 3.801A pdb=" N ILE A 755 " --> pdb=" O ALA A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 809 Proline residue: A 802 - end of helix Processing helix chain 'A' and resid 826 through 834 removed outlier: 3.904A pdb=" N GLU A 832 " --> pdb=" O VAL A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 847 removed outlier: 3.828A pdb=" N HIS A 847 " --> pdb=" O SER A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 886 Proline residue: A 856 - end of helix Processing helix chain 'B' and resid 76 through 93 Processing helix chain 'B' and resid 99 through 118 Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' Processing helix chain 'B' and resid 122 through 147 Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 152 through 164 removed outlier: 3.623A pdb=" N ILE B 156 " --> pdb=" O TRP B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 191 removed outlier: 4.206A pdb=" N TYR B 170 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE B 191 " --> pdb=" O ILE B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 202 Processing helix chain 'B' and resid 204 through 216 removed outlier: 4.895A pdb=" N THR B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ARG B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 223 removed outlier: 4.148A pdb=" N VAL B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 removed outlier: 3.573A pdb=" N TYR B 248 " --> pdb=" O TYR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 290 removed outlier: 3.604A pdb=" N PHE B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 309 Processing helix chain 'B' and resid 318 through 343 removed outlier: 3.556A pdb=" N LYS B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 381 removed outlier: 3.581A pdb=" N CYS B 364 " --> pdb=" O ASN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 417 removed outlier: 3.809A pdb=" N SER B 397 " --> pdb=" O ASN B 393 " (cutoff:3.500A) Proline residue: B 407 - end of helix removed outlier: 3.768A pdb=" N MET B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 459 Processing helix chain 'B' and resid 667 through 695 Processing helix chain 'B' and resid 695 through 706 Processing helix chain 'B' and resid 724 through 743 Processing helix chain 'B' and resid 748 through 771 removed outlier: 3.802A pdb=" N ILE B 755 " --> pdb=" O ALA B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 809 Proline residue: B 802 - end of helix Processing helix chain 'B' and resid 826 through 834 removed outlier: 3.915A pdb=" N GLU B 832 " --> pdb=" O VAL B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 838 through 847 removed outlier: 3.870A pdb=" N HIS B 847 " --> pdb=" O SER B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 886 Proline residue: B 856 - end of helix Processing helix chain 'C' and resid 21 through 32 Processing helix chain 'C' and resid 35 through 50 removed outlier: 3.713A pdb=" N ASN C 50 " --> pdb=" O PHE C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 66 removed outlier: 3.752A pdb=" N ILE C 65 " --> pdb=" O ASN C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 75 Processing helix chain 'C' and resid 76 through 81 removed outlier: 4.703A pdb=" N GLU C 81 " --> pdb=" O PRO C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 93 Processing helix chain 'C' and resid 102 through 112 Processing helix chain 'C' and resid 117 through 130 Processing helix chain 'C' and resid 138 through 151 Processing helix chain 'C' and resid 155 through 170 Processing helix chain 'C' and resid 179 through 188 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'D' and resid 23 through 44 Processing helix chain 'D' and resid 53 through 63 Processing helix chain 'E' and resid 21 through 32 Processing helix chain 'E' and resid 35 through 50 removed outlier: 3.714A pdb=" N ASN E 50 " --> pdb=" O PHE E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 66 removed outlier: 3.750A pdb=" N ILE E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 75 Processing helix chain 'E' and resid 76 through 81 removed outlier: 4.697A pdb=" N GLU E 81 " --> pdb=" O PRO E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 93 Processing helix chain 'E' and resid 102 through 112 Processing helix chain 'E' and resid 117 through 130 Processing helix chain 'E' and resid 138 through 150 Processing helix chain 'E' and resid 155 through 170 Processing helix chain 'E' and resid 179 through 188 Processing helix chain 'E' and resid 192 through 197 Processing helix chain 'F' and resid 23 through 43 Processing helix chain 'F' and resid 53 through 63 Processing sheet with id=AA1, first strand: chain 'C' and resid 67 through 69 Processing sheet with id=AA2, first strand: chain 'E' and resid 67 through 69 901 hydrogen bonds defined for protein. 2697 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2100 1.31 - 1.43: 3931 1.43 - 1.56: 8415 1.56 - 1.69: 8 1.69 - 1.81: 130 Bond restraints: 14584 Sorted by residual: bond pdb=" C21 3PE B1305 " pdb=" O21 3PE B1305 " ideal model delta sigma weight residual 1.316 1.397 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C21 3PE A1304 " pdb=" O21 3PE A1304 " ideal model delta sigma weight residual 1.316 1.397 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C30 PEE A1303 " pdb=" O3 PEE A1303 " ideal model delta sigma weight residual 1.327 1.397 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C30 PEE B1304 " pdb=" O3 PEE B1304 " ideal model delta sigma weight residual 1.327 1.397 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C10 PEE B1304 " pdb=" O2 PEE B1304 " ideal model delta sigma weight residual 1.332 1.401 -0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 14579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 18963 3.27 - 6.53: 517 6.53 - 9.80: 23 9.80 - 13.07: 3 13.07 - 16.33: 4 Bond angle restraints: 19510 Sorted by residual: angle pdb=" O3P PEE A1303 " pdb=" P PEE A1303 " pdb=" O4P PEE A1303 " ideal model delta sigma weight residual 92.91 109.24 -16.33 3.00e+00 1.11e-01 2.96e+01 angle pdb=" O3P PEE B1304 " pdb=" P PEE B1304 " pdb=" O4P PEE B1304 " ideal model delta sigma weight residual 92.91 109.20 -16.29 3.00e+00 1.11e-01 2.95e+01 angle pdb=" O12 3PE A1304 " pdb=" P 3PE A1304 " pdb=" O14 3PE A1304 " ideal model delta sigma weight residual 123.79 109.30 14.49 3.00e+00 1.11e-01 2.33e+01 angle pdb=" O12 3PE B1305 " pdb=" P 3PE B1305 " pdb=" O14 3PE B1305 " ideal model delta sigma weight residual 123.79 109.32 14.47 3.00e+00 1.11e-01 2.33e+01 angle pdb=" O1P PEE A1303 " pdb=" P PEE A1303 " pdb=" O2P PEE A1303 " ideal model delta sigma weight residual 119.43 109.35 10.08 3.00e+00 1.11e-01 1.13e+01 ... (remaining 19505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.71: 8632 34.71 - 69.42: 278 69.42 - 104.12: 14 104.12 - 138.83: 2 138.83 - 173.54: 6 Dihedral angle restraints: 8932 sinusoidal: 3986 harmonic: 4946 Sorted by residual: dihedral pdb=" C4 PEE A1303 " pdb=" O4P PEE A1303 " pdb=" P PEE A1303 " pdb=" O1P PEE A1303 " ideal model delta sinusoidal sigma weight residual 57.28 -129.18 -173.54 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C4 PEE B1304 " pdb=" O4P PEE B1304 " pdb=" P PEE B1304 " pdb=" O1P PEE B1304 " ideal model delta sinusoidal sigma weight residual 57.28 -129.44 -173.28 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O2 PEE A1303 " pdb=" C1 PEE A1303 " pdb=" C2 PEE A1303 " pdb=" O3P PEE A1303 " ideal model delta sinusoidal sigma weight residual -59.96 96.31 -156.27 1 3.00e+01 1.11e-03 2.04e+01 ... (remaining 8929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2026 0.074 - 0.148: 134 0.148 - 0.222: 4 0.222 - 0.296: 1 0.296 - 0.371: 1 Chirality restraints: 2166 Sorted by residual: chirality pdb=" C1 NAG B1329 " pdb=" ND2 ASN B 209 " pdb=" C2 NAG B1329 " pdb=" O5 NAG B1329 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" C1 NAG A1327 " pdb=" ND2 ASN A 209 " pdb=" C2 NAG A1327 " pdb=" O5 NAG A1327 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C2 PEE B1304 " pdb=" C1 PEE B1304 " pdb=" C3 PEE B1304 " pdb=" O2 PEE B1304 " both_signs ideal model delta sigma weight residual False -2.33 -2.53 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 2163 not shown) Planarity restraints: 2344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1329 " -0.276 2.00e-02 2.50e+03 2.35e-01 6.93e+02 pdb=" C7 NAG B1329 " 0.060 2.00e-02 2.50e+03 pdb=" C8 NAG B1329 " 0.023 2.00e-02 2.50e+03 pdb=" N2 NAG B1329 " 0.395 2.00e-02 2.50e+03 pdb=" O7 NAG B1329 " -0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1327 " 0.275 2.00e-02 2.50e+03 2.35e-01 6.92e+02 pdb=" C7 NAG A1327 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG A1327 " -0.023 2.00e-02 2.50e+03 pdb=" N2 NAG A1327 " -0.395 2.00e-02 2.50e+03 pdb=" O7 NAG A1327 " 0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 209 " 0.096 2.00e-02 2.50e+03 1.21e-01 1.83e+02 pdb=" CG ASN A 209 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN A 209 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 209 " -0.205 2.00e-02 2.50e+03 pdb=" C1 NAG A1327 " 0.143 2.00e-02 2.50e+03 ... (remaining 2341 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3177 2.78 - 3.31: 13130 3.31 - 3.84: 23433 3.84 - 4.37: 25989 4.37 - 4.90: 47422 Nonbonded interactions: 113151 Sorted by model distance: nonbonded pdb=" O TYR C 28 " pdb=" OG1 THR C 32 " model vdw 2.254 3.040 nonbonded pdb=" O TYR E 28 " pdb=" OG1 THR E 32 " model vdw 2.277 3.040 nonbonded pdb=" SG CYS F 44 " pdb=" C1 PLM F 204 " model vdw 2.286 3.630 nonbonded pdb=" OE2 GLU B 196 " pdb=" NZ LYS B 215 " model vdw 2.286 3.120 nonbonded pdb=" OE2 GLU A 196 " pdb=" NZ LYS A 215 " model vdw 2.288 3.120 ... (remaining 113146 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 75 through 886 or resid 1302 or resid 1306 or resid 1308 t \ hrough 1309 or resid 1316 through 1319 or (resid 1320 through 1321 and (name C1 \ or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 )) or resid 13 \ 22 through 1323 or resid 1325)) selection = (chain 'B' and (resid 75 through 886 or resid 1302 or resid 1306 or resid 1308 t \ hrough 1309 or (resid 1316 and (name C1 or name C2 or name C3 or name C4 or name \ C5 or name C6 or name C7 or name C8 or name C9 )) or resid 1317 or (resid 1318 \ and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 ) \ ) or (resid 1319 and (name C1 or name C2 or name C3 or name C4 or name C5 or nam \ e C6 or name C7 or name C8 )) or (resid 1320 through 1321 and (name C1 or name C \ 2 or name C3 or name C4 or name C5 or name C6 or name C7 )) or (resid 1322 and ( \ name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or nam \ e C8 )) or resid 1323 or resid 1325)) } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' 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: 5.000 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 12.590 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 : 0.005 0.460 14593 Z= 0.421 Angle : 0.940 16.930 19520 Z= 0.382 Chirality : 0.040 0.371 2166 Planarity : 0.008 0.235 2342 Dihedral : 17.023 173.541 5714 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.21 % Allowed : 19.54 % Favored : 80.25 % 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: 2.17 (0.21), residues: 1660 helix: 2.54 (0.15), residues: 1160 sheet: None (None), residues: 0 loop : -1.37 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 23 TYR 0.012 0.001 TYR A 245 PHE 0.038 0.001 PHE C 161 TRP 0.008 0.001 TRP F 25 HIS 0.002 0.000 HIS A 731 Details of bonding type rmsd covalent geometry : bond 0.00367 (14584) covalent geometry : angle 0.92235 (19510) SS BOND : bond 0.00224 ( 2) SS BOND : angle 0.34699 ( 4) hydrogen bonds : bond 0.11557 ( 901) hydrogen bonds : angle 4.95170 ( 2697) Misc. bond : bond 0.20575 ( 5) link_NAG-ASN : bond 0.05271 ( 2) link_NAG-ASN : angle 10.28961 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 174 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 738 MET cc_start: 0.7439 (mmt) cc_final: 0.7234 (mtm) REVERT: A 846 ARG cc_start: 0.7430 (mtt180) cc_final: 0.6375 (mmt180) REVERT: B 738 MET cc_start: 0.7428 (mmt) cc_final: 0.7202 (mtm) REVERT: B 846 ARG cc_start: 0.7328 (mtt180) cc_final: 0.6272 (mmt180) outliers start: 3 outliers final: 2 residues processed: 174 average time/residue: 0.1500 time to fit residues: 35.9712 Evaluate side-chains 170 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 168 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain D residue 41 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 0.1980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN E 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.214616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.167729 restraints weight = 14766.799| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 2.89 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.0613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14593 Z= 0.113 Angle : 0.476 7.439 19520 Z= 0.249 Chirality : 0.038 0.152 2166 Planarity : 0.004 0.064 2342 Dihedral : 11.637 173.914 2527 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.90 % Allowed : 18.85 % Favored : 80.25 % 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: 2.48 (0.21), residues: 1660 helix: 2.64 (0.15), residues: 1190 sheet: None (None), residues: 0 loop : -1.13 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 147 TYR 0.013 0.001 TYR A 245 PHE 0.021 0.001 PHE E 105 TRP 0.005 0.001 TRP F 25 HIS 0.004 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00248 (14584) covalent geometry : angle 0.47324 (19510) SS BOND : bond 0.00171 ( 2) SS BOND : angle 0.55948 ( 4) hydrogen bonds : bond 0.03951 ( 901) hydrogen bonds : angle 3.81094 ( 2697) Misc. bond : bond 0.00010 ( 5) link_NAG-ASN : bond 0.00180 ( 2) link_NAG-ASN : angle 2.94162 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 GLU cc_start: 0.7019 (tt0) cc_final: 0.6695 (tt0) REVERT: A 846 ARG cc_start: 0.7122 (mtt180) cc_final: 0.5929 (mmt180) REVERT: B 205 GLU cc_start: 0.7120 (tt0) cc_final: 0.6916 (tt0) REVERT: B 846 ARG cc_start: 0.6985 (mtt180) cc_final: 0.5897 (mmt180) outliers start: 13 outliers final: 7 residues processed: 184 average time/residue: 0.1397 time to fit residues: 36.0056 Evaluate side-chains 171 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 164 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 194 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 119 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 133 optimal weight: 0.0040 chunk 147 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 736 GLN B 181 ASN B 736 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.212537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.166428 restraints weight = 14910.823| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 3.06 r_work: 0.3673 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14593 Z= 0.127 Angle : 0.481 7.048 19520 Z= 0.251 Chirality : 0.039 0.157 2166 Planarity : 0.004 0.069 2342 Dihedral : 10.438 163.771 2524 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.00 % Allowed : 18.92 % Favored : 79.07 % 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: 2.44 (0.21), residues: 1660 helix: 2.62 (0.15), residues: 1190 sheet: None (None), residues: 0 loop : -1.16 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 431 TYR 0.016 0.001 TYR A 245 PHE 0.021 0.001 PHE E 105 TRP 0.005 0.001 TRP D 25 HIS 0.003 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00301 (14584) covalent geometry : angle 0.48061 (19510) SS BOND : bond 0.00261 ( 2) SS BOND : angle 0.46885 ( 4) hydrogen bonds : bond 0.04009 ( 901) hydrogen bonds : angle 3.73061 ( 2697) Misc. bond : bond 0.00023 ( 5) link_NAG-ASN : bond 0.00121 ( 2) link_NAG-ASN : angle 1.33126 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 GLU cc_start: 0.7601 (tt0) cc_final: 0.7277 (tt0) REVERT: A 846 ARG cc_start: 0.7522 (mtt180) cc_final: 0.6013 (mmt180) REVERT: B 205 GLU cc_start: 0.7589 (tt0) cc_final: 0.7036 (tt0) REVERT: B 846 ARG cc_start: 0.7449 (mtt180) cc_final: 0.5957 (mmt180) REVERT: E 194 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8386 (mm) REVERT: F 26 MET cc_start: 0.7554 (mtm) cc_final: 0.7181 (mtm) outliers start: 29 outliers final: 15 residues processed: 188 average time/residue: 0.1462 time to fit residues: 38.4313 Evaluate side-chains 179 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 194 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 68 optimal weight: 0.6980 chunk 60 optimal weight: 40.0000 chunk 36 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 129 optimal weight: 0.0970 chunk 28 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN B 181 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.212504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.166053 restraints weight = 14901.408| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 3.02 r_work: 0.3640 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14593 Z= 0.121 Angle : 0.476 7.093 19520 Z= 0.248 Chirality : 0.039 0.151 2166 Planarity : 0.004 0.068 2342 Dihedral : 10.064 159.063 2524 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.66 % Allowed : 19.82 % Favored : 78.52 % 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: 2.45 (0.21), residues: 1660 helix: 2.62 (0.15), residues: 1192 sheet: None (None), residues: 0 loop : -1.16 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 158 TYR 0.015 0.001 TYR B 245 PHE 0.020 0.001 PHE E 105 TRP 0.005 0.001 TRP D 25 HIS 0.003 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00286 (14584) covalent geometry : angle 0.47618 (19510) SS BOND : bond 0.00265 ( 2) SS BOND : angle 0.38881 ( 4) hydrogen bonds : bond 0.03877 ( 901) hydrogen bonds : angle 3.68546 ( 2697) Misc. bond : bond 0.00023 ( 5) link_NAG-ASN : bond 0.00057 ( 2) link_NAG-ASN : angle 1.10330 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 GLU cc_start: 0.7648 (tt0) cc_final: 0.7317 (tt0) REVERT: A 846 ARG cc_start: 0.7499 (mtt180) cc_final: 0.5962 (mmt180) REVERT: B 205 GLU cc_start: 0.7647 (tt0) cc_final: 0.7091 (tt0) REVERT: B 846 ARG cc_start: 0.7435 (mtt180) cc_final: 0.5946 (mmt180) REVERT: E 194 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8396 (mm) REVERT: F 26 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.7341 (mtt) outliers start: 24 outliers final: 16 residues processed: 177 average time/residue: 0.1354 time to fit residues: 33.6574 Evaluate side-chains 180 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 771 CYS Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 48 optimal weight: 0.8980 chunk 55 optimal weight: 0.0970 chunk 84 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 147 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN B 181 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.212541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.166987 restraints weight = 14981.049| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 3.03 r_work: 0.3662 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14593 Z= 0.120 Angle : 0.474 7.439 19520 Z= 0.247 Chirality : 0.039 0.148 2166 Planarity : 0.004 0.067 2342 Dihedral : 9.938 157.459 2524 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.86 % Allowed : 19.75 % Favored : 78.38 % 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: 2.47 (0.21), residues: 1660 helix: 2.64 (0.15), residues: 1194 sheet: None (None), residues: 0 loop : -1.16 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 431 TYR 0.014 0.001 TYR A 245 PHE 0.020 0.001 PHE C 105 TRP 0.006 0.001 TRP D 25 HIS 0.002 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00283 (14584) covalent geometry : angle 0.47376 (19510) SS BOND : bond 0.00267 ( 2) SS BOND : angle 0.36330 ( 4) hydrogen bonds : bond 0.03816 ( 901) hydrogen bonds : angle 3.65985 ( 2697) Misc. bond : bond 0.00022 ( 5) link_NAG-ASN : bond 0.00054 ( 2) link_NAG-ASN : angle 1.01812 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 GLU cc_start: 0.7595 (tt0) cc_final: 0.7252 (tt0) REVERT: A 846 ARG cc_start: 0.7480 (mtt180) cc_final: 0.5957 (mmt180) REVERT: B 205 GLU cc_start: 0.7584 (tt0) cc_final: 0.7346 (tt0) REVERT: B 846 ARG cc_start: 0.7476 (mtt180) cc_final: 0.5976 (mmt180) REVERT: E 194 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8373 (mm) REVERT: F 26 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7229 (mtt) outliers start: 27 outliers final: 22 residues processed: 181 average time/residue: 0.1300 time to fit residues: 33.5736 Evaluate side-chains 183 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 771 CYS Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 155 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 98 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN B 181 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.211821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.166182 restraints weight = 14946.180| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 3.18 r_work: 0.3625 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14593 Z= 0.129 Angle : 0.484 7.499 19520 Z= 0.252 Chirality : 0.039 0.149 2166 Planarity : 0.004 0.067 2342 Dihedral : 9.949 158.333 2524 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.93 % Allowed : 20.37 % Favored : 77.69 % 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: 2.43 (0.21), residues: 1660 helix: 2.66 (0.15), residues: 1182 sheet: None (None), residues: 0 loop : -1.22 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 158 TYR 0.015 0.001 TYR A 245 PHE 0.020 0.001 PHE E 105 TRP 0.007 0.001 TRP D 25 HIS 0.002 0.001 HIS A 731 Details of bonding type rmsd covalent geometry : bond 0.00310 (14584) covalent geometry : angle 0.48424 (19510) SS BOND : bond 0.00302 ( 2) SS BOND : angle 0.38091 ( 4) hydrogen bonds : bond 0.03912 ( 901) hydrogen bonds : angle 3.66559 ( 2697) Misc. bond : bond 0.00025 ( 5) link_NAG-ASN : bond 0.00061 ( 2) link_NAG-ASN : angle 0.98993 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 GLU cc_start: 0.7624 (tt0) cc_final: 0.7250 (tt0) REVERT: A 846 ARG cc_start: 0.7529 (mtt180) cc_final: 0.5970 (mmt180) REVERT: B 128 MET cc_start: 0.4411 (tpt) cc_final: 0.4091 (tpt) REVERT: B 205 GLU cc_start: 0.7613 (tt0) cc_final: 0.7374 (tt0) REVERT: B 846 ARG cc_start: 0.7497 (mtt180) cc_final: 0.5983 (mmt180) REVERT: C 26 ASP cc_start: 0.7192 (t0) cc_final: 0.6787 (t0) REVERT: E 26 ASP cc_start: 0.7190 (t0) cc_final: 0.6811 (t0) REVERT: E 194 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8397 (mm) REVERT: F 26 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7281 (mtt) outliers start: 28 outliers final: 20 residues processed: 188 average time/residue: 0.1360 time to fit residues: 35.9709 Evaluate side-chains 187 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 771 CYS Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 75 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 135 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 78 optimal weight: 0.0670 chunk 35 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 736 GLN B 181 ASN B 736 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.212326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.166312 restraints weight = 14881.168| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 3.31 r_work: 0.3680 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14593 Z= 0.118 Angle : 0.483 7.744 19520 Z= 0.254 Chirality : 0.039 0.148 2166 Planarity : 0.004 0.067 2342 Dihedral : 9.888 161.175 2524 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.73 % Allowed : 20.72 % Favored : 77.56 % 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: 2.47 (0.21), residues: 1660 helix: 2.68 (0.15), residues: 1182 sheet: None (None), residues: 0 loop : -1.19 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 165 TYR 0.014 0.001 TYR A 245 PHE 0.019 0.001 PHE E 105 TRP 0.008 0.001 TRP D 25 HIS 0.002 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00273 (14584) covalent geometry : angle 0.48284 (19510) SS BOND : bond 0.00255 ( 2) SS BOND : angle 0.34209 ( 4) hydrogen bonds : bond 0.03780 ( 901) hydrogen bonds : angle 3.65952 ( 2697) Misc. bond : bond 0.00020 ( 5) link_NAG-ASN : bond 0.00050 ( 2) link_NAG-ASN : angle 0.97429 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 GLU cc_start: 0.7585 (tt0) cc_final: 0.7228 (tt0) REVERT: A 846 ARG cc_start: 0.7492 (mtt180) cc_final: 0.5943 (mmt180) REVERT: B 205 GLU cc_start: 0.7594 (tt0) cc_final: 0.7366 (tt0) REVERT: B 846 ARG cc_start: 0.7473 (mtt180) cc_final: 0.5944 (mmt180) REVERT: D 52 ARG cc_start: 0.8098 (mtm180) cc_final: 0.7779 (mtm180) REVERT: E 194 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8382 (mm) REVERT: F 26 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7249 (mtt) outliers start: 25 outliers final: 20 residues processed: 184 average time/residue: 0.1303 time to fit residues: 33.7724 Evaluate side-chains 184 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 771 CYS Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 159 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN B 181 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.211148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.165492 restraints weight = 15033.301| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 3.25 r_work: 0.3661 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14593 Z= 0.138 Angle : 0.504 7.964 19520 Z= 0.264 Chirality : 0.040 0.148 2166 Planarity : 0.004 0.068 2342 Dihedral : 9.987 165.686 2524 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.86 % Allowed : 20.65 % Favored : 77.49 % 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: 2.38 (0.21), residues: 1660 helix: 2.61 (0.15), residues: 1182 sheet: None (None), residues: 0 loop : -1.22 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 165 TYR 0.015 0.001 TYR B 245 PHE 0.019 0.001 PHE E 105 TRP 0.008 0.001 TRP D 25 HIS 0.003 0.001 HIS E 198 Details of bonding type rmsd covalent geometry : bond 0.00333 (14584) covalent geometry : angle 0.50417 (19510) SS BOND : bond 0.00331 ( 2) SS BOND : angle 0.39014 ( 4) hydrogen bonds : bond 0.03992 ( 901) hydrogen bonds : angle 3.68473 ( 2697) Misc. bond : bond 0.00027 ( 5) link_NAG-ASN : bond 0.00057 ( 2) link_NAG-ASN : angle 0.98425 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 GLU cc_start: 0.7545 (tt0) cc_final: 0.7329 (tt0) REVERT: A 846 ARG cc_start: 0.7507 (mtt180) cc_final: 0.5955 (mmt180) REVERT: B 205 GLU cc_start: 0.7539 (tt0) cc_final: 0.7303 (tt0) REVERT: B 846 ARG cc_start: 0.7488 (mtt180) cc_final: 0.5972 (mmt180) REVERT: C 152 ASP cc_start: 0.7684 (m-30) cc_final: 0.7028 (t70) REVERT: E 194 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8373 (mm) REVERT: F 26 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7232 (mtt) outliers start: 27 outliers final: 21 residues processed: 182 average time/residue: 0.1366 time to fit residues: 34.9604 Evaluate side-chains 186 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 771 CYS Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 124 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 64 optimal weight: 20.0000 chunk 47 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN B 181 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.211653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.166429 restraints weight = 15062.710| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 3.17 r_work: 0.3653 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14593 Z= 0.123 Angle : 0.496 8.217 19520 Z= 0.261 Chirality : 0.039 0.147 2166 Planarity : 0.004 0.067 2342 Dihedral : 9.967 171.059 2524 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.66 % Allowed : 20.79 % Favored : 77.56 % 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: 2.44 (0.21), residues: 1660 helix: 2.66 (0.15), residues: 1182 sheet: None (None), residues: 0 loop : -1.20 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 165 TYR 0.014 0.001 TYR A 245 PHE 0.025 0.001 PHE C 161 TRP 0.007 0.001 TRP D 25 HIS 0.002 0.001 HIS B 731 Details of bonding type rmsd covalent geometry : bond 0.00288 (14584) covalent geometry : angle 0.49572 (19510) SS BOND : bond 0.00281 ( 2) SS BOND : angle 0.34918 ( 4) hydrogen bonds : bond 0.03848 ( 901) hydrogen bonds : angle 3.65568 ( 2697) Misc. bond : bond 0.00022 ( 5) link_NAG-ASN : bond 0.00047 ( 2) link_NAG-ASN : angle 0.97085 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 GLU cc_start: 0.7599 (tt0) cc_final: 0.7390 (tt0) REVERT: A 846 ARG cc_start: 0.7523 (mtt180) cc_final: 0.5974 (mmt180) REVERT: B 205 GLU cc_start: 0.7611 (tt0) cc_final: 0.7059 (tt0) REVERT: B 846 ARG cc_start: 0.7472 (mtt180) cc_final: 0.5929 (mmt180) REVERT: C 152 ASP cc_start: 0.7686 (m-30) cc_final: 0.7072 (t70) REVERT: D 52 ARG cc_start: 0.8092 (mtm180) cc_final: 0.7858 (mtm180) REVERT: E 194 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8373 (mm) REVERT: F 26 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7211 (mtt) outliers start: 24 outliers final: 21 residues processed: 181 average time/residue: 0.1420 time to fit residues: 36.0423 Evaluate side-chains 185 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 771 CYS Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 49 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 78 optimal weight: 0.0040 chunk 158 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN B 181 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.212346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.167001 restraints weight = 14924.126| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 3.16 r_work: 0.3671 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14593 Z= 0.115 Angle : 0.493 8.654 19520 Z= 0.259 Chirality : 0.039 0.175 2166 Planarity : 0.004 0.066 2342 Dihedral : 9.907 176.642 2524 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.52 % Allowed : 20.93 % Favored : 77.56 % 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: 2.51 (0.21), residues: 1660 helix: 2.73 (0.15), residues: 1178 sheet: None (None), residues: 0 loop : -1.20 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 158 TYR 0.013 0.001 TYR A 245 PHE 0.031 0.001 PHE E 161 TRP 0.009 0.001 TRP D 25 HIS 0.002 0.001 HIS B 731 Details of bonding type rmsd covalent geometry : bond 0.00262 (14584) covalent geometry : angle 0.49292 (19510) SS BOND : bond 0.00234 ( 2) SS BOND : angle 0.33226 ( 4) hydrogen bonds : bond 0.03694 ( 901) hydrogen bonds : angle 3.61857 ( 2697) Misc. bond : bond 0.00018 ( 5) link_NAG-ASN : bond 0.00051 ( 2) link_NAG-ASN : angle 0.95389 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 GLU cc_start: 0.7577 (tt0) cc_final: 0.7364 (tt0) REVERT: A 846 ARG cc_start: 0.7494 (mtt180) cc_final: 0.5952 (mmt180) REVERT: B 205 GLU cc_start: 0.7623 (tt0) cc_final: 0.7078 (tt0) REVERT: B 846 ARG cc_start: 0.7464 (mtt180) cc_final: 0.5911 (mmt180) REVERT: D 52 ARG cc_start: 0.8088 (mtm180) cc_final: 0.7849 (mtm180) REVERT: E 194 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8356 (mm) REVERT: F 26 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.7224 (mtt) outliers start: 22 outliers final: 20 residues processed: 180 average time/residue: 0.1484 time to fit residues: 37.2695 Evaluate side-chains 188 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 771 CYS Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 188 SER Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 35 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 60 optimal weight: 40.0000 chunk 157 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN B 181 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.211370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.165723 restraints weight = 14985.894| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 2.99 r_work: 0.3662 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14593 Z= 0.132 Angle : 0.505 8.356 19520 Z= 0.265 Chirality : 0.039 0.149 2166 Planarity : 0.004 0.067 2342 Dihedral : 9.997 179.455 2524 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.66 % Allowed : 20.99 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.21), residues: 1660 helix: 2.65 (0.15), residues: 1182 sheet: None (None), residues: 0 loop : -1.21 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 165 TYR 0.015 0.001 TYR A 245 PHE 0.028 0.001 PHE C 161 TRP 0.008 0.001 TRP D 25 HIS 0.002 0.001 HIS A 731 Details of bonding type rmsd covalent geometry : bond 0.00317 (14584) covalent geometry : angle 0.50469 (19510) SS BOND : bond 0.00315 ( 2) SS BOND : angle 0.38283 ( 4) hydrogen bonds : bond 0.03882 ( 901) hydrogen bonds : angle 3.64296 ( 2697) Misc. bond : bond 0.00024 ( 5) link_NAG-ASN : bond 0.00058 ( 2) link_NAG-ASN : angle 0.96123 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3317.43 seconds wall clock time: 57 minutes 31.50 seconds (3451.50 seconds total)