Starting phenix.real_space_refine on Tue Dec 31 09:29:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7usw_26741/12_2024/7usw_26741.cif Found real_map, /net/cci-nas-00/data/ceres_data/7usw_26741/12_2024/7usw_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7usw_26741/12_2024/7usw_26741.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7usw_26741/12_2024/7usw_26741.map" model { file = "/net/cci-nas-00/data/ceres_data/7usw_26741/12_2024/7usw_26741.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7usw_26741/12_2024/7usw_26741.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 5, '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: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 5, '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: 9.88, per 1000 atoms: 0.69 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: 3.84 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.25 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: 4.12 Time building geometry restraints manager: 4.34 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: 6.560 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: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 33.410 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.320 ------------------------------------------------------------------------------- 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 : 0.004 0.081 14584 Z= 0.234 Angle : 0.922 16.332 19510 Z= 0.377 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 : 7.09 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.008 0.001 TRP F 25 HIS 0.002 0.000 HIS A 731 PHE 0.038 0.001 PHE C 161 TYR 0.012 0.001 TYR A 245 ARG 0.004 0.000 ARG D 23 *********************** 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 : 1.404 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: 0.3284 time to fit residues: 79.3634 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 : 1.673 ------------------------------------------------------------------------------- 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 138 optimal weight: 2.9990 chunk 124 optimal weight: 0.2980 chunk 68 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 49 optimal weight: 0.0270 chunk 78 optimal weight: 0.0970 chunk 95 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 overall best weight: 0.3836 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.0676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14584 Z= 0.145 Angle : 0.464 7.440 19510 Z= 0.243 Chirality : 0.038 0.126 2166 Planarity : 0.004 0.063 2342 Dihedral : 11.455 174.886 2527 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.69 % Allowed : 19.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.21), residues: 1660 helix: 2.66 (0.15), residues: 1190 sheet: None (None), residues: 0 loop : -1.11 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 25 HIS 0.004 0.000 HIS B 420 PHE 0.021 0.001 PHE E 105 TYR 0.013 0.001 TYR A 245 ARG 0.004 0.000 ARG C 147 *********************** 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 187 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 177 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7876 (tp) REVERT: A 846 ARG cc_start: 0.7396 (mtt180) cc_final: 0.6297 (mmt180) REVERT: B 738 MET cc_start: 0.7458 (mmt) cc_final: 0.7093 (mtm) REVERT: B 846 ARG cc_start: 0.7290 (mtt180) cc_final: 0.6264 (mmt180) outliers start: 10 outliers final: 6 residues processed: 184 average time/residue: 0.3258 time to fit residues: 84.0597 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 : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LEU 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 194 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 6.9990 chunk 46 optimal weight: 0.3980 chunk 123 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14584 Z= 0.232 Angle : 0.503 7.482 19510 Z= 0.261 Chirality : 0.040 0.143 2166 Planarity : 0.004 0.071 2342 Dihedral : 10.513 161.300 2524 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.14 % Allowed : 18.85 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.21), residues: 1660 helix: 2.59 (0.15), residues: 1178 sheet: None (None), residues: 0 loop : -1.23 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 25 HIS 0.003 0.001 HIS A 731 PHE 0.021 0.001 PHE E 105 TYR 0.018 0.001 TYR A 245 ARG 0.004 0.000 ARG B 431 *********************** 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 198 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 GLU cc_start: 0.7228 (tt0) cc_final: 0.6999 (tt0) REVERT: A 846 ARG cc_start: 0.7553 (mtt180) cc_final: 0.6358 (mmt180) REVERT: B 738 MET cc_start: 0.7548 (mmt) cc_final: 0.7328 (mtm) REVERT: B 846 ARG cc_start: 0.7447 (mtt180) cc_final: 0.6277 (mmt180) REVERT: F 26 MET cc_start: 0.7878 (mtm) cc_final: 0.7626 (mtm) outliers start: 31 outliers final: 16 residues processed: 185 average time/residue: 0.3255 time to fit residues: 84.4593 Evaluate side-chains 178 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 452 THR Chi-restraints excluded: chain B residue 138 MET 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 D residue 41 ILE 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 147 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 149 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14584 Z= 0.190 Angle : 0.478 7.124 19510 Z= 0.249 Chirality : 0.039 0.124 2166 Planarity : 0.004 0.069 2342 Dihedral : 10.030 154.219 2524 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.07 % Allowed : 19.13 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.21), residues: 1660 helix: 2.62 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -1.22 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 25 HIS 0.002 0.001 HIS B 420 PHE 0.021 0.001 PHE E 105 TYR 0.015 0.001 TYR A 245 ARG 0.003 0.000 ARG A 431 *********************** 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 195 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.4064 (OUTLIER) cc_final: 0.3741 (tpt) REVERT: A 415 LYS cc_start: 0.6751 (mttm) cc_final: 0.6424 (mttt) REVERT: A 846 ARG cc_start: 0.7489 (mtt180) cc_final: 0.6283 (mmt180) REVERT: B 128 MET cc_start: 0.4593 (OUTLIER) cc_final: 0.4162 (tpt) REVERT: B 415 LYS cc_start: 0.6849 (mttm) cc_final: 0.6509 (mttt) REVERT: B 738 MET cc_start: 0.7543 (mmt) cc_final: 0.7259 (mtm) REVERT: B 846 ARG cc_start: 0.7482 (mtt180) cc_final: 0.6287 (mmt180) REVERT: E 194 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8402 (mm) REVERT: F 26 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7613 (mtt) outliers start: 30 outliers final: 17 residues processed: 184 average time/residue: 0.3389 time to fit residues: 88.1133 Evaluate side-chains 181 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 MET 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 A residue 841 VAL Chi-restraints excluded: chain B residue 128 MET 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 135 optimal weight: 8.9990 chunk 109 optimal weight: 0.9980 chunk 0 optimal weight: 40.0000 chunk 80 optimal weight: 0.7980 chunk 142 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14584 Z= 0.201 Angle : 0.488 7.402 19510 Z= 0.253 Chirality : 0.039 0.128 2166 Planarity : 0.004 0.069 2342 Dihedral : 10.032 155.291 2524 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.00 % Allowed : 19.96 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.21), residues: 1660 helix: 2.60 (0.15), residues: 1182 sheet: None (None), residues: 0 loop : -1.24 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 25 HIS 0.003 0.001 HIS B 731 PHE 0.020 0.001 PHE E 105 TYR 0.015 0.001 TYR A 245 ARG 0.003 0.000 ARG A 431 *********************** 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 195 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.4065 (OUTLIER) cc_final: 0.3747 (tpt) REVERT: A 415 LYS cc_start: 0.6708 (mttm) cc_final: 0.6310 (mttt) REVERT: A 846 ARG cc_start: 0.7512 (mtt180) cc_final: 0.6282 (mmt180) REVERT: B 128 MET cc_start: 0.4589 (OUTLIER) cc_final: 0.4329 (tpt) REVERT: B 131 MET cc_start: 0.5939 (tmm) cc_final: 0.5660 (ttm) REVERT: B 415 LYS cc_start: 0.6744 (mttm) cc_final: 0.6351 (mttt) REVERT: B 738 MET cc_start: 0.7545 (mmt) cc_final: 0.7276 (mtm) REVERT: B 846 ARG cc_start: 0.7509 (mtt180) cc_final: 0.6288 (mmt180) REVERT: E 194 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8398 (mm) REVERT: F 26 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7605 (mtt) outliers start: 29 outliers final: 19 residues processed: 182 average time/residue: 0.3215 time to fit residues: 83.3913 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 : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 MET 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 128 MET 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 452 THR 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 53 optimal weight: 0.4980 chunk 142 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14584 Z= 0.196 Angle : 0.491 7.359 19510 Z= 0.255 Chirality : 0.039 0.125 2166 Planarity : 0.004 0.068 2342 Dihedral : 10.007 156.779 2524 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.00 % Allowed : 20.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.21), residues: 1660 helix: 2.61 (0.15), residues: 1182 sheet: None (None), residues: 0 loop : -1.23 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 25 HIS 0.002 0.001 HIS B 731 PHE 0.019 0.001 PHE E 105 TYR 0.015 0.001 TYR A 245 ARG 0.003 0.000 ARG B 158 *********************** 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 194 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.4117 (OUTLIER) cc_final: 0.3810 (tpt) REVERT: A 846 ARG cc_start: 0.7514 (mtt180) cc_final: 0.6273 (mmt180) REVERT: B 128 MET cc_start: 0.4602 (OUTLIER) cc_final: 0.4178 (tpt) REVERT: B 738 MET cc_start: 0.7544 (mmt) cc_final: 0.7269 (mtm) REVERT: B 846 ARG cc_start: 0.7517 (mtt180) cc_final: 0.6275 (mmt180) REVERT: C 26 ASP cc_start: 0.6952 (t0) cc_final: 0.6707 (t0) REVERT: E 194 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8394 (mm) REVERT: F 26 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7603 (mtt) outliers start: 29 outliers final: 21 residues processed: 183 average time/residue: 0.3204 time to fit residues: 83.8269 Evaluate side-chains 188 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 MET 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 128 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 90 optimal weight: 0.0870 chunk 115 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 133 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 158 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 72 optimal weight: 0.0060 overall best weight: 0.4574 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 14584 Z= 0.154 Angle : 0.478 7.678 19510 Z= 0.250 Chirality : 0.038 0.122 2166 Planarity : 0.004 0.066 2342 Dihedral : 9.829 160.774 2524 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.21), residues: 1660 helix: 2.74 (0.15), residues: 1178 sheet: None (None), residues: 0 loop : -1.20 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 25 HIS 0.002 0.000 HIS B 420 PHE 0.018 0.001 PHE C 105 TYR 0.012 0.001 TYR A 245 ARG 0.004 0.000 ARG C 165 *********************** 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 197 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.4122 (OUTLIER) cc_final: 0.3816 (tpt) REVERT: A 846 ARG cc_start: 0.7503 (mtt180) cc_final: 0.6258 (mmt180) REVERT: B 128 MET cc_start: 0.4551 (OUTLIER) cc_final: 0.4304 (tpt) REVERT: B 131 MET cc_start: 0.5915 (tmm) cc_final: 0.5636 (ttm) REVERT: B 738 MET cc_start: 0.7525 (mmt) cc_final: 0.7185 (mtm) REVERT: B 846 ARG cc_start: 0.7491 (mtt180) cc_final: 0.6273 (mmt180) REVERT: C 152 ASP cc_start: 0.7114 (m-30) cc_final: 0.6825 (t70) REVERT: F 26 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7644 (mtt) outliers start: 24 outliers final: 18 residues processed: 187 average time/residue: 0.3168 time to fit residues: 83.5769 Evaluate side-chains 187 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 MET 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 128 MET 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 C residue 188 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 188 SER 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 97 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 94 optimal weight: 0.0980 chunk 47 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 0.0070 chunk 100 optimal weight: 0.5980 chunk 107 optimal weight: 0.1980 chunk 78 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 124 optimal weight: 0.0270 overall best weight: 0.1856 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14584 Z= 0.129 Angle : 0.462 7.932 19510 Z= 0.243 Chirality : 0.037 0.129 2166 Planarity : 0.004 0.065 2342 Dihedral : 9.503 166.599 2524 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.59 % Allowed : 21.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.21), residues: 1660 helix: 2.80 (0.15), residues: 1194 sheet: None (None), residues: 0 loop : -1.00 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 25 HIS 0.001 0.000 HIS B 404 PHE 0.023 0.001 PHE E 161 TYR 0.008 0.001 TYR A 245 ARG 0.003 0.000 ARG E 165 *********************** 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: 23 poor density : 169 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.4118 (OUTLIER) cc_final: 0.3826 (tpt) REVERT: A 846 ARG cc_start: 0.7487 (mtt180) cc_final: 0.6277 (mmt180) REVERT: B 128 MET cc_start: 0.4518 (OUTLIER) cc_final: 0.4274 (tpt) REVERT: B 131 MET cc_start: 0.5882 (tmm) cc_final: 0.5587 (ttm) REVERT: B 846 ARG cc_start: 0.7433 (mtt180) cc_final: 0.6231 (mmt180) outliers start: 23 outliers final: 16 residues processed: 181 average time/residue: 0.3320 time to fit residues: 85.2458 Evaluate side-chains 185 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 MET 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 B residue 128 MET 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 363 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 194 ILE 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 143 optimal weight: 0.7980 chunk 151 optimal weight: 0.5980 chunk 138 optimal weight: 0.6980 chunk 147 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 64 optimal weight: 20.0000 chunk 115 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 133 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14584 Z= 0.178 Angle : 0.489 8.322 19510 Z= 0.255 Chirality : 0.039 0.138 2166 Planarity : 0.004 0.066 2342 Dihedral : 9.634 170.735 2524 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.52 % Allowed : 21.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.21), residues: 1660 helix: 2.78 (0.15), residues: 1190 sheet: None (None), residues: 0 loop : -1.09 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 25 HIS 0.002 0.001 HIS B 731 PHE 0.026 0.001 PHE C 161 TYR 0.014 0.001 TYR A 245 ARG 0.009 0.000 ARG C 165 *********************** 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 188 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.4082 (OUTLIER) cc_final: 0.3779 (tpt) REVERT: A 846 ARG cc_start: 0.7502 (mtt180) cc_final: 0.6289 (mmt180) REVERT: B 128 MET cc_start: 0.4539 (OUTLIER) cc_final: 0.4279 (tpt) REVERT: B 131 MET cc_start: 0.5886 (tmm) cc_final: 0.5580 (ttm) REVERT: B 846 ARG cc_start: 0.7472 (mtt180) cc_final: 0.6244 (mmt180) outliers start: 22 outliers final: 18 residues processed: 180 average time/residue: 0.3216 time to fit residues: 81.2116 Evaluate side-chains 184 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 MET 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 B residue 128 MET 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 363 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 D residue 48 ILE 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 96 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 163 optimal weight: 0.0570 chunk 150 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 B 736 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14584 Z= 0.167 Angle : 0.487 8.789 19510 Z= 0.254 Chirality : 0.039 0.153 2166 Planarity : 0.004 0.066 2342 Dihedral : 9.693 176.426 2524 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.38 % Allowed : 21.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.21), residues: 1660 helix: 2.81 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -1.14 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 25 HIS 0.002 0.001 HIS A 731 PHE 0.022 0.001 PHE E 161 TYR 0.013 0.001 TYR A 245 ARG 0.004 0.000 ARG E 165 ********************** 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 190 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.4086 (OUTLIER) cc_final: 0.3784 (tpt) REVERT: A 846 ARG cc_start: 0.7501 (mtt180) cc_final: 0.6273 (mmt180) REVERT: B 128 MET cc_start: 0.4549 (OUTLIER) cc_final: 0.4143 (tpt) REVERT: B 846 ARG cc_start: 0.7499 (mtt180) cc_final: 0.6253 (mmt180) outliers start: 20 outliers final: 17 residues processed: 184 average time/residue: 0.3164 time to fit residues: 82.2540 Evaluate side-chains 187 residues out of total 1506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 MET 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 B residue 128 MET 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 363 ILE Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 771 CYS Chi-restraints excluded: chain B residue 841 VAL Chi-restraints excluded: chain D residue 48 ILE 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 103 optimal weight: 1.9990 chunk 138 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 133 optimal weight: 0.0370 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.4540 r_free = 0.4540 target = 0.212859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.167395 restraints weight = 14826.178| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 3.03 r_work: 0.3700 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14584 Z= 0.171 Angle : 0.493 8.839 19510 Z= 0.256 Chirality : 0.039 0.181 2166 Planarity : 0.004 0.066 2342 Dihedral : 9.736 179.093 2524 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.45 % Allowed : 20.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.21), residues: 1660 helix: 2.81 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -1.14 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 25 HIS 0.002 0.001 HIS A 731 PHE 0.031 0.001 PHE C 161 TYR 0.013 0.001 TYR A 245 ARG 0.004 0.000 ARG E 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2879.68 seconds wall clock time: 53 minutes 41.82 seconds (3221.82 seconds total)