Starting phenix.real_space_refine on Fri Jul 3 17:36:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7usw_26741/07_2026/7usw_26741.cif Found real_map, /net/cci-nas-00/data/ceres_data/7usw_26741/07_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_26741/07_2026/7usw_26741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7usw_26741/07_2026/7usw_26741.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7usw_26741/07_2026/7usw_26741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7usw_26741/07_2026/7usw_26741.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7usw_26741/07_2026/7usw_26741.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7usw_26741/07_2026/7usw_26741.cif" } 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-6108/lib/python3.11/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: 74 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: 74 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: 3.53, per 1000 atoms: 0.25 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: 1.46 Conformation dependent library (CDL) restraints added in 618.3 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: 0.48 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: 2.07 Time building geometry restraints manager: 1.80 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 - 21.38: 7800 21.38 - 42.76: 825 42.76 - 64.14: 95 64.14 - 85.52: 9 85.52 - 106.90: 5 Dihedral angle restraints: 8734 sinusoidal: 3788 harmonic: 4946 Sorted by residual: dihedral pdb=" N PEE B1304 " pdb=" C4 PEE B1304 " pdb=" C5 PEE B1304 " pdb=" O4P PEE B1304 " ideal model delta sinusoidal sigma weight residual -56.97 -163.87 106.90 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" N PEE A1303 " pdb=" C4 PEE A1303 " pdb=" C5 PEE A1303 " pdb=" O4P PEE A1303 " ideal model delta sinusoidal sigma weight residual -56.97 -163.82 106.85 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" CA MET D 46 " pdb=" C MET D 46 " pdb=" N ARG D 47 " pdb=" CA ARG D 47 " ideal model delta harmonic sigma weight residual -180.00 -163.65 -16.35 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 8731 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: 5.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.360 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 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 : 15.913 106.901 5516 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/Z covalent geometry : bond 0.00367 / 0.18 (14584) covalent geometry : angle 0.92235 / 0.38 (19510) SS BOND : bond 0.00224 / 0.11 ( 2) SS BOND : angle 0.34699 / 0.19 ( 4) hydrogen bonds : bond 0.11557 / 7.55 ( 901) hydrogen bonds : angle 4.95170 / 3.60 ( 2697) Misc. bond : bond 0.20575 / 15.13 ( 5) link_NAG-ASN : bond 0.05271 / 2.56 ( 2) link_NAG-ASN : angle 10.28961 / 5.23 ( 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 : 0.527 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: 0.1498 time to fit residues: 36.5286 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 : 0.535 ------------------------------------------------------------------------------- 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... 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 = 0.214577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.168220 restraints weight = 14761.774| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 2.81 r_work: 0.3687 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.0638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14593 Z= 0.112 Angle : 0.474 7.474 19520 Z= 0.248 Chirality : 0.038 0.145 2166 Planarity : 0.004 0.064 2342 Dihedral : 7.915 65.824 2329 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.97 % Allowed : 18.78 % 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: 2.46 (0.21), residues: 1660 helix: 2.64 (0.15), residues: 1190 sheet: None (None), residues: 0 loop : -1.14 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 147 TYR 0.014 0.001 TYR A 245 PHE 0.021 0.001 PHE E 105 TRP 0.004 0.001 TRP F 25 HIS 0.004 0.001 HIS B 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (14584) covalent geometry : angle 0.47106 / 0.25 (19510) SS BOND : bond 0.00179 / 0.09 ( 2) SS BOND : angle 0.56554 / 0.31 ( 4) hydrogen bonds : bond 0.03935 / 2.65 ( 901) hydrogen bonds : angle 3.79961 / 2.74 ( 2697) Misc. bond : bond 0.00009 / 0.01 ( 5) link_NAG-ASN : bond 0.00283 / 0.14 ( 2) link_NAG-ASN : angle 2.86634 / 1.60 ( 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 192 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 GLU cc_start: 0.7595 (tt0) cc_final: 0.7266 (tt0) REVERT: A 738 MET cc_start: 0.7877 (mmt) cc_final: 0.7593 (mtm) REVERT: A 846 ARG cc_start: 0.7421 (mtt180) cc_final: 0.5953 (mmt180) REVERT: B 738 MET cc_start: 0.7867 (mmt) cc_final: 0.7569 (mtm) REVERT: B 846 ARG cc_start: 0.7307 (mtt180) cc_final: 0.5920 (mmt180) outliers start: 14 outliers final: 7 residues processed: 186 average time/residue: 0.1490 time to fit residues: 38.6920 Evaluate side-chains 172 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 165 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 371 ILE 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: 0.9980 chunk 145 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 147 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4526 r_free = 0.4526 target = 0.211422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.166029 restraints weight = 14850.019| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 2.99 r_work: 0.3654 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14593 Z= 0.146 Angle : 0.504 7.573 19520 Z= 0.262 Chirality : 0.040 0.150 2166 Planarity : 0.004 0.070 2342 Dihedral : 8.093 65.476 2326 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.21 % Allowed : 18.65 % Favored : 79.14 % 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: 2.31 (0.21), residues: 1660 helix: 2.58 (0.15), residues: 1178 sheet: None (None), residues: 0 loop : -1.26 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 431 TYR 0.018 0.001 TYR A 245 PHE 0.022 0.001 PHE E 105 TRP 0.005 0.001 TRP D 25 HIS 0.003 0.001 HIS B 731 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (14584) covalent geometry : angle 0.50382 / 0.26 (19510) SS BOND : bond 0.00296 / 0.15 ( 2) SS BOND : angle 0.48638 / 0.27 ( 4) hydrogen bonds : bond 0.04249 / 2.88 ( 901) hydrogen bonds : angle 3.76931 / 2.72 ( 2697) Misc. bond : bond 0.00030 / 0.02 ( 5) link_NAG-ASN : bond 0.00057 / 0.03 ( 2) link_NAG-ASN : angle 1.23919 / 0.65 ( 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 200 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 GLU cc_start: 0.7649 (tt0) cc_final: 0.7315 (tt0) REVERT: A 846 ARG cc_start: 0.7539 (mtt180) cc_final: 0.6023 (mmt180) REVERT: B 846 ARG cc_start: 0.7448 (mtt180) cc_final: 0.5952 (mmt180) REVERT: F 26 MET cc_start: 0.7529 (mtm) cc_final: 0.7145 (mtm) outliers start: 32 outliers final: 17 residues processed: 187 average time/residue: 0.1355 time to fit residues: 36.0676 Evaluate side-chains 178 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain F residue 41 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 68 optimal weight: 0.5980 chunk 60 optimal weight: 40.0000 chunk 36 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 129 optimal weight: 0.1980 chunk 28 optimal weight: 0.7980 chunk 67 optimal weight: 0.0370 chunk 2 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4536 r_free = 0.4536 target = 0.212634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.167047 restraints weight = 14860.997| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 3.04 r_work: 0.3646 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14593 Z= 0.110 Angle : 0.471 6.937 19520 Z= 0.246 Chirality : 0.038 0.148 2166 Planarity : 0.004 0.066 2342 Dihedral : 7.847 68.488 2326 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.52 % Allowed : 19.54 % Favored : 78.94 % 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: 2.63 (0.15), residues: 1192 sheet: None (None), residues: 0 loop : -1.17 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 158 TYR 0.013 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/Z covalent geometry : bond 0.00250 / 0.11 (14584) covalent geometry : angle 0.47034 / 0.25 (19510) SS BOND : bond 0.00224 / 0.11 ( 2) SS BOND : angle 0.35311 / 0.20 ( 4) hydrogen bonds : bond 0.03799 / 2.57 ( 901) hydrogen bonds : angle 3.67791 / 2.65 ( 2697) Misc. bond : bond 0.00018 / 0.01 ( 5) link_NAG-ASN : bond 0.00031 / 0.02 ( 2) link_NAG-ASN : angle 1.07773 / 0.52 ( 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 185 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 GLU cc_start: 0.7605 (tt0) cc_final: 0.7264 (tt0) REVERT: A 846 ARG cc_start: 0.7482 (mtt180) cc_final: 0.5946 (mmt180) REVERT: B 846 ARG cc_start: 0.7421 (mtt180) cc_final: 0.5924 (mmt180) REVERT: E 194 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8377 (mm) REVERT: F 26 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7310 (mtt) outliers start: 22 outliers final: 17 residues processed: 176 average time/residue: 0.1405 time to fit residues: 35.0913 Evaluate side-chains 180 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 55 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 141 optimal weight: 0.0050 chunk 135 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 57 optimal weight: 0.0570 chunk 54 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 overall best weight: 0.5312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4539 r_free = 0.4539 target = 0.212980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.165622 restraints weight = 14948.651| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 3.25 r_work: 0.3674 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14593 Z= 0.109 Angle : 0.463 7.033 19520 Z= 0.243 Chirality : 0.038 0.149 2166 Planarity : 0.004 0.066 2342 Dihedral : 7.730 70.899 2326 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.93 % Allowed : 19.75 % Favored : 78.31 % 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: 2.53 (0.21), residues: 1660 helix: 2.70 (0.15), residues: 1190 sheet: None (None), residues: 0 loop : -1.18 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 431 TYR 0.013 0.001 TYR A 245 PHE 0.019 0.001 PHE C 105 TRP 0.007 0.001 TRP D 25 HIS 0.002 0.001 HIS B 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (14584) covalent geometry : angle 0.46296 / 0.24 (19510) SS BOND : bond 0.00228 / 0.11 ( 2) SS BOND : angle 0.32874 / 0.18 ( 4) hydrogen bonds : bond 0.03685 / 2.49 ( 901) hydrogen bonds : angle 3.63453 / 2.62 ( 2697) Misc. bond : bond 0.00019 / 0.01 ( 5) link_NAG-ASN : bond 0.00050 / 0.03 ( 2) link_NAG-ASN : angle 1.09755 / 0.51 ( 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 193 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 GLU cc_start: 0.7608 (tt0) cc_final: 0.7277 (tt0) REVERT: A 846 ARG cc_start: 0.7486 (mtt180) cc_final: 0.5966 (mmt180) REVERT: B 846 ARG cc_start: 0.7460 (mtt180) cc_final: 0.5965 (mmt180) REVERT: E 194 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8384 (mm) REVERT: F 26 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.7305 (mtt) outliers start: 28 outliers final: 20 residues processed: 182 average time/residue: 0.1384 time to fit residues: 35.7232 Evaluate side-chains 186 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 155 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 139 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.211101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.165315 restraints weight = 14922.912| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 3.09 r_work: 0.3659 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14593 Z= 0.139 Angle : 0.493 7.557 19520 Z= 0.257 Chirality : 0.040 0.149 2166 Planarity : 0.004 0.068 2342 Dihedral : 7.987 74.917 2326 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.93 % Allowed : 20.44 % Favored : 77.62 % 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: 2.37 (0.21), residues: 1660 helix: 2.61 (0.15), residues: 1182 sheet: None (None), residues: 0 loop : -1.25 (0.27), residues: 478 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 0.020 0.001 PHE E 105 TRP 0.006 0.001 TRP D 25 HIS 0.003 0.001 HIS B 731 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (14584) covalent geometry : angle 0.49300 / 0.26 (19510) SS BOND : bond 0.00336 / 0.17 ( 2) SS BOND : angle 0.39747 / 0.23 ( 4) hydrogen bonds : bond 0.04014 / 2.72 ( 901) hydrogen bonds : angle 3.67875 / 2.65 ( 2697) Misc. bond : bond 0.00029 / 0.02 ( 5) link_NAG-ASN : bond 0.00061 / 0.03 ( 2) link_NAG-ASN : angle 1.16882 / 0.53 ( 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 196 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 GLU cc_start: 0.7634 (tt0) cc_final: 0.7279 (tt0) REVERT: A 846 ARG cc_start: 0.7510 (mtt180) cc_final: 0.5956 (mmt180) REVERT: B 846 ARG cc_start: 0.7488 (mtt180) cc_final: 0.5973 (mmt180) REVERT: C 26 ASP cc_start: 0.7154 (t0) cc_final: 0.6730 (t0) REVERT: E 26 ASP cc_start: 0.7122 (t0) cc_final: 0.6869 (t0) REVERT: E 194 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8372 (mm) REVERT: F 26 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.7257 (mtt) outliers start: 28 outliers final: 20 residues processed: 186 average time/residue: 0.1345 time to fit residues: 35.8627 Evaluate side-chains 183 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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: 4.9990 chunk 67 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 135 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.211355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.165958 restraints weight = 14878.949| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 2.73 r_work: 0.3655 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1141 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= 0.128 Angle : 0.494 7.648 19520 Z= 0.259 Chirality : 0.039 0.153 2166 Planarity : 0.004 0.068 2342 Dihedral : 7.997 78.248 2326 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % 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: 2.37 (0.21), residues: 1660 helix: 2.61 (0.15), residues: 1182 sheet: None (None), residues: 0 loop : -1.24 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 165 TYR 0.014 0.001 TYR A 245 PHE 0.019 0.001 PHE C 105 TRP 0.007 0.001 TRP D 25 HIS 0.002 0.001 HIS A 731 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (14584) covalent geometry : angle 0.49402 / 0.26 (19510) SS BOND : bond 0.00301 / 0.15 ( 2) SS BOND : angle 0.35451 / 0.20 ( 4) hydrogen bonds : bond 0.03931 / 2.66 ( 901) hydrogen bonds : angle 3.67952 / 2.65 ( 2697) Misc. bond : bond 0.00024 / 0.01 ( 5) link_NAG-ASN : bond 0.00066 / 0.03 ( 2) link_NAG-ASN : angle 1.21488 / 0.55 ( 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 189 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 GLU cc_start: 0.7649 (tt0) cc_final: 0.7443 (tt0) REVERT: A 846 ARG cc_start: 0.7519 (mtt180) cc_final: 0.5965 (mmt180) REVERT: B 846 ARG cc_start: 0.7508 (mtt180) cc_final: 0.5977 (mmt180) REVERT: E 194 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8376 (mm) REVERT: F 26 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7255 (mtt) outliers start: 24 outliers final: 21 residues processed: 180 average time/residue: 0.1306 time to fit residues: 33.3892 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 : 0.585 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 159 optimal weight: 3.9990 chunk 113 optimal weight: 0.0010 chunk 62 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 152 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 overall best weight: 1.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN B 181 ASN B 736 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.210097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.163844 restraints weight = 14992.367| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 3.30 r_work: 0.3647 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14593 Z= 0.155 Angle : 0.521 7.871 19520 Z= 0.272 Chirality : 0.040 0.147 2166 Planarity : 0.004 0.070 2342 Dihedral : 8.262 83.418 2326 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.59 % Allowed : 20.99 % Favored : 77.42 % 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: 2.25 (0.21), residues: 1660 helix: 2.53 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -1.29 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 165 TYR 0.017 0.001 TYR A 245 PHE 0.020 0.001 PHE E 105 TRP 0.007 0.001 TRP D 25 HIS 0.003 0.001 HIS E 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (14584) covalent geometry : angle 0.52055 / 0.27 (19510) SS BOND : bond 0.00374 / 0.19 ( 2) SS BOND : angle 0.42829 / 0.25 ( 4) hydrogen bonds : bond 0.04193 / 2.84 ( 901) hydrogen bonds : angle 3.72346 / 2.68 ( 2697) Misc. bond : bond 0.00033 / 0.02 ( 5) link_NAG-ASN : bond 0.00061 / 0.03 ( 2) link_NAG-ASN : angle 1.20373 / 0.55 ( 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 191 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 GLU cc_start: 0.7613 (tt0) cc_final: 0.7405 (tt0) REVERT: A 846 ARG cc_start: 0.7523 (mtt180) cc_final: 0.5964 (mmt180) REVERT: B 846 ARG cc_start: 0.7520 (mtt180) cc_final: 0.5970 (mmt180) REVERT: C 152 ASP cc_start: 0.7708 (m-30) cc_final: 0.7049 (t70) REVERT: D 52 ARG cc_start: 0.8110 (mtm180) cc_final: 0.7800 (mtm180) REVERT: E 194 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8362 (mm) REVERT: F 26 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7196 (mtt) outliers start: 23 outliers final: 21 residues processed: 182 average time/residue: 0.1374 time to fit residues: 35.7695 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 : 0.466 ------------------------------------------------------------------------------- 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: 0.8980 chunk 3 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 124 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 64 optimal weight: 20.0000 chunk 47 optimal weight: 0.6980 chunk 106 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.211613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.165736 restraints weight = 15028.993| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 3.29 r_work: 0.3683 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 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 0.047 14593 Z= 0.117 Angle : 0.494 8.217 19520 Z= 0.260 Chirality : 0.039 0.147 2166 Planarity : 0.004 0.067 2342 Dihedral : 8.067 86.294 2326 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.80 % Allowed : 21.20 % Favored : 77.00 % 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: 2.41 (0.21), residues: 1660 helix: 2.64 (0.15), residues: 1182 sheet: None (None), residues: 0 loop : -1.23 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 165 TYR 0.013 0.001 TYR B 245 PHE 0.026 0.001 PHE C 161 TRP 0.007 0.001 TRP D 25 HIS 0.002 0.001 HIS A 731 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (14584) covalent geometry : angle 0.49385 / 0.26 (19510) SS BOND : bond 0.00262 / 0.13 ( 2) SS BOND : angle 0.34103 / 0.20 ( 4) hydrogen bonds : bond 0.03815 / 2.58 ( 901) hydrogen bonds : angle 3.65528 / 2.63 ( 2697) Misc. bond : bond 0.00019 / 0.01 ( 5) link_NAG-ASN : bond 0.00043 / 0.02 ( 2) link_NAG-ASN : angle 1.13168 / 0.52 ( 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 189 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 846 ARG cc_start: 0.7530 (mtt180) cc_final: 0.5993 (mmt180) REVERT: B 846 ARG cc_start: 0.7497 (mtt180) cc_final: 0.5951 (mmt180) REVERT: D 52 ARG cc_start: 0.8104 (mtm180) cc_final: 0.7798 (mtm180) REVERT: E 194 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8352 (mm) REVERT: F 26 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7286 (mtt) outliers start: 26 outliers final: 21 residues processed: 179 average time/residue: 0.1366 time to fit residues: 35.0974 Evaluate side-chains 187 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 49 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 78 optimal weight: 0.0060 chunk 158 optimal weight: 0.0980 chunk 14 optimal weight: 0.0470 chunk 51 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 overall best weight: 0.3094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN A 736 GLN B 181 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.213441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.167439 restraints weight = 14893.012| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 3.23 r_work: 0.3735 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 14593 Z= 0.105 Angle : 0.481 9.304 19520 Z= 0.253 Chirality : 0.038 0.169 2166 Planarity : 0.004 0.066 2342 Dihedral : 7.679 88.829 2326 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.31 % Allowed : 21.41 % Favored : 77.28 % 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: 2.59 (0.21), residues: 1660 helix: 2.76 (0.15), residues: 1182 sheet: None (None), residues: 0 loop : -1.11 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 147 TYR 0.010 0.001 TYR B 245 PHE 0.027 0.001 PHE E 161 TRP 0.009 0.001 TRP D 25 HIS 0.003 0.000 HIS B 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (14584) covalent geometry : angle 0.48057 / 0.25 (19510) SS BOND : bond 0.00167 / 0.08 ( 2) SS BOND : angle 0.28487 / 0.16 ( 4) hydrogen bonds : bond 0.03460 / 2.34 ( 901) hydrogen bonds : angle 3.58293 / 2.58 ( 2697) Misc. bond : bond 0.00013 / 0.01 ( 5) link_NAG-ASN : bond 0.00015 / 0.01 ( 2) link_NAG-ASN : angle 1.07594 / 0.47 ( 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 181 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 GLU cc_start: 0.7666 (tt0) cc_final: 0.7463 (tt0) REVERT: A 846 ARG cc_start: 0.7462 (mtt180) cc_final: 0.5931 (mmt180) REVERT: B 846 ARG cc_start: 0.7443 (mtt180) cc_final: 0.5895 (mmt180) REVERT: D 52 ARG cc_start: 0.8102 (mtm180) cc_final: 0.7857 (mtm180) REVERT: E 194 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8286 (mm) REVERT: F 26 MET cc_start: 0.7438 (OUTLIER) cc_final: 0.7187 (mtt) outliers start: 19 outliers final: 14 residues processed: 174 average time/residue: 0.1393 time to fit residues: 34.2326 Evaluate side-chains 175 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 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 841 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 150 THR 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: 0.9990 chunk 32 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 60 optimal weight: 40.0000 chunk 157 optimal weight: 6.9990 chunk 128 optimal weight: 0.4980 chunk 38 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4541 r_free = 0.4541 target = 0.212854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.166125 restraints weight = 14915.337| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 3.22 r_work: 0.3668 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1252 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= 0.111 Angle : 0.484 8.370 19520 Z= 0.255 Chirality : 0.038 0.147 2166 Planarity : 0.004 0.066 2342 Dihedral : 7.635 89.635 2326 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.31 % Allowed : 21.41 % Favored : 77.28 % 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: 2.61 (0.21), residues: 1660 helix: 2.80 (0.15), residues: 1178 sheet: None (None), residues: 0 loop : -1.15 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 147 TYR 0.011 0.001 TYR A 245 PHE 0.028 0.001 PHE C 161 TRP 0.007 0.001 TRP D 25 HIS 0.002 0.000 HIS B 731 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (14584) covalent geometry : angle 0.48364 / 0.26 (19510) SS BOND : bond 0.00205 / 0.10 ( 2) SS BOND : angle 0.29641 / 0.17 ( 4) hydrogen bonds : bond 0.03545 / 2.40 ( 901) hydrogen bonds : angle 3.57966 / 2.57 ( 2697) Misc. bond : bond 0.00018 / 0.01 ( 5) link_NAG-ASN : bond 0.00017 / 0.01 ( 2) link_NAG-ASN : angle 1.08368 / 0.47 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3335.59 seconds wall clock time: 57 minutes 59.07 seconds (3479.07 seconds total)