Starting phenix.real_space_refine on Thu Jul 31 05:14:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g2y_29684/07_2025/8g2y_29684_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g2y_29684/07_2025/8g2y_29684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g2y_29684/07_2025/8g2y_29684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g2y_29684/07_2025/8g2y_29684.map" model { file = "/net/cci-nas-00/data/ceres_data/8g2y_29684/07_2025/8g2y_29684_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g2y_29684/07_2025/8g2y_29684_neut.cif" } resolution = 3.44 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= 0.031 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 P 1 5.49 5 S 45 5.16 5 C 4340 2.51 5 N 1123 2.21 5 O 1168 1.98 5 H 6342 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13019 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2951 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 189} Chain breaks: 3 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 4062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 4062 Classifications: {'peptide': 291} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 286} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 7, 'ASN:plan1': 3, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 93 Chain: "G" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 452 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "N" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1647 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 33 Chain: "R" Number of atoms: 3876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 3876 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain breaks: 4 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "R" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'LPC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.06, per 1000 atoms: 0.54 Number of scatterers: 13019 At special positions: 0 Unit cell: (75.075, 86.625, 119.625, 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) S 45 16.00 P 1 15.00 O 1168 8.00 N 1123 7.00 C 4340 6.00 H 6342 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 657 " - pdb=" SG CYS R 733 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.46 Conformation dependent library (CDL) restraints added in 1.1 seconds 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1666 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 11 sheets defined 37.9% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 25 through 40 removed outlier: 3.621A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 278 removed outlier: 4.044A pdb=" N GLN A 267 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.510A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.915A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'G' and resid 14 through 24 removed outlier: 3.809A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.540A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 569 through 573 Processing helix chain 'R' and resid 582 through 608 Processing helix chain 'R' and resid 619 through 647 removed outlier: 3.607A pdb=" N VAL R 647 " --> pdb=" O VAL R 643 " (cutoff:3.500A) Processing helix chain 'R' and resid 656 through 688 removed outlier: 3.572A pdb=" N PHE R 662 " --> pdb=" O THR R 658 " (cutoff:3.500A) Processing helix chain 'R' and resid 694 through 722 removed outlier: 4.822A pdb=" N CYS R 709 " --> pdb=" O LEU R 705 " (cutoff:3.500A) Proline residue: R 710 - end of helix Processing helix chain 'R' and resid 740 through 770 Proline residue: R 750 - end of helix Processing helix chain 'R' and resid 786 through 801 removed outlier: 3.894A pdb=" N GLY R 790 " --> pdb=" O ILE R 786 " (cutoff:3.500A) Proline residue: R 798 - end of helix Processing helix chain 'R' and resid 802 through 805 Processing helix chain 'R' and resid 806 through 811 removed outlier: 3.706A pdb=" N THR R 810 " --> pdb=" O PHE R 806 " (cutoff:3.500A) Processing helix chain 'R' and resid 817 through 829 Processing helix chain 'R' and resid 829 through 838 Processing helix chain 'R' and resid 842 through 848 Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.724A pdb=" N MET A 221 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR A 210 " --> pdb=" O MET A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 47 removed outlier: 6.196A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.138A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 62 removed outlier: 7.007A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 93 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 105 removed outlier: 5.893A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.671A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.782A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.837A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.245A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 296 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 4 Processing sheet with id=AB2, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.612A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 326 hydrogen bonds defined for protein. 924 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: 4.58 Time building geometry restraints manager: 4.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6308 1.03 - 1.23: 47 1.23 - 1.42: 2885 1.42 - 1.62: 3861 1.62 - 1.81: 63 Bond restraints: 13164 Sorted by residual: bond pdb=" N ARG N 57 " pdb=" H ARG N 57 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N LEU A 272 " pdb=" H LEU A 272 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" CG LEU A 272 " pdb=" HG LEU A 272 " ideal model delta sigma weight residual 0.970 1.111 -0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" CB LEU A 272 " pdb=" HB3 LEU A 272 " ideal model delta sigma weight residual 0.970 1.108 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" CB LEU A 272 " pdb=" HB2 LEU A 272 " ideal model delta sigma weight residual 0.970 1.108 -0.138 2.00e-02 2.50e+03 4.77e+01 ... (remaining 13159 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 22901 1.80 - 3.60: 599 3.60 - 5.40: 84 5.40 - 7.19: 12 7.19 - 8.99: 4 Bond angle restraints: 23600 Sorted by residual: angle pdb=" CA VAL N 48 " pdb=" C VAL N 48 " pdb=" O VAL N 48 " ideal model delta sigma weight residual 120.32 114.09 6.23 1.10e+00 8.26e-01 3.21e+01 angle pdb=" CA TRP N 47 " pdb=" C TRP N 47 " pdb=" O TRP N 47 " ideal model delta sigma weight residual 120.54 115.32 5.22 1.13e+00 7.83e-01 2.13e+01 angle pdb=" C VAL N 48 " pdb=" CA VAL N 48 " pdb=" CB VAL N 48 " ideal model delta sigma weight residual 111.55 106.67 4.88 1.15e+00 7.56e-01 1.80e+01 angle pdb=" N ASP B 170 " pdb=" CA ASP B 170 " pdb=" C ASP B 170 " ideal model delta sigma weight residual 109.50 102.86 6.64 1.58e+00 4.01e-01 1.77e+01 angle pdb=" CA THR N 61 " pdb=" C THR N 61 " pdb=" O THR N 61 " ideal model delta sigma weight residual 122.03 117.31 4.72 1.13e+00 7.83e-01 1.74e+01 ... (remaining 23595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 5457 16.81 - 33.61: 573 33.61 - 50.42: 167 50.42 - 67.22: 69 67.22 - 84.03: 13 Dihedral angle restraints: 6279 sinusoidal: 3157 harmonic: 3122 Sorted by residual: dihedral pdb=" CA TYR B 289 " pdb=" C TYR B 289 " pdb=" N ASP B 290 " pdb=" CA ASP B 290 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA GLY R 838 " pdb=" C GLY R 838 " pdb=" N ILE R 839 " pdb=" CA ILE R 839 " ideal model delta harmonic sigma weight residual -180.00 -161.23 -18.77 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" C THR N 61 " pdb=" N THR N 61 " pdb=" CA THR N 61 " pdb=" CB THR N 61 " ideal model delta harmonic sigma weight residual -122.00 -112.69 -9.31 0 2.50e+00 1.60e-01 1.39e+01 ... (remaining 6276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 702 0.036 - 0.071: 289 0.071 - 0.107: 72 0.107 - 0.142: 35 0.142 - 0.178: 6 Chirality restraints: 1104 Sorted by residual: chirality pdb=" CA ILE B 81 " pdb=" N ILE B 81 " pdb=" C ILE B 81 " pdb=" CB ILE B 81 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.11e-01 chirality pdb=" CB VAL N 48 " pdb=" CA VAL N 48 " pdb=" CG1 VAL N 48 " pdb=" CG2 VAL N 48 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.06e-01 ... (remaining 1101 not shown) Planarity restraints: 1996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN R 816 " -0.248 2.00e-02 2.50e+03 3.67e-01 2.02e+03 pdb=" CG ASN R 816 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN R 816 " 0.242 2.00e-02 2.50e+03 pdb=" ND2 ASN R 816 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN R 816 " -0.593 2.00e-02 2.50e+03 pdb="HD22 ASN R 816 " 0.581 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL N 48 " 0.025 2.00e-02 2.50e+03 4.79e-02 2.30e+01 pdb=" N SER N 49 " -0.083 2.00e-02 2.50e+03 pdb=" CA SER N 49 " 0.022 2.00e-02 2.50e+03 pdb=" H SER N 49 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 84 " 0.020 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" N TYR B 85 " -0.067 2.00e-02 2.50e+03 pdb=" CA TYR B 85 " 0.017 2.00e-02 2.50e+03 pdb=" H TYR B 85 " 0.029 2.00e-02 2.50e+03 ... (remaining 1993 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 1394 2.25 - 2.83: 27900 2.83 - 3.42: 33224 3.42 - 4.01: 45162 4.01 - 4.60: 69319 Nonbonded interactions: 176999 Sorted by model distance: nonbonded pdb="HH21 ARG A 231 " pdb="HD21 LEU A 272 " model vdw 1.657 2.270 nonbonded pdb=" O GLY R 809 " pdb=" H ASP R 813 " model vdw 1.722 2.450 nonbonded pdb=" O GLU B 226 " pdb="HH12 ARG N 98 " model vdw 1.730 2.450 nonbonded pdb=" O LEU A 291 " pdb="HE21 GLN A 294 " model vdw 1.732 2.450 nonbonded pdb=" OE2 GLU A 344 " pdb="HH21 ARG A 347 " model vdw 1.747 2.450 ... (remaining 176994 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 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: 0.260 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.560 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 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 0.051 6825 Z= 0.242 Angle : 0.764 8.993 9298 Z= 0.432 Chirality : 0.045 0.178 1104 Planarity : 0.005 0.073 1142 Dihedral : 15.564 84.025 2252 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 20.80 % Favored : 79.20 % 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: -1.42 (0.29), residues: 861 helix: 0.72 (0.30), residues: 320 sheet: -2.52 (0.32), residues: 211 loop : -1.35 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP N 47 HIS 0.003 0.001 HIS R 665 PHE 0.014 0.001 PHE R 672 TYR 0.009 0.001 TYR R 684 ARG 0.002 0.000 ARG N 118 Details of bonding type rmsd hydrogen bonds : bond 0.14450 ( 326) hydrogen bonds : angle 6.38784 ( 924) SS BOND : bond 0.00114 ( 3) SS BOND : angle 1.32801 ( 6) covalent geometry : bond 0.00445 ( 6822) covalent geometry : angle 0.76323 ( 9292) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue THR 369 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue SER 265 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue SER 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue VAL 584 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue MET 693 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue SER 741 is missing expected H atoms. Skipping. Residue THR 785 is missing expected H atoms. Skipping. Residue SER 814 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 TRP cc_start: 0.7661 (m100) cc_final: 0.7420 (m100) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.3933 time to fit residues: 64.6342 Evaluate side-chains 110 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.2980 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 50 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.164879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.129370 restraints weight = 21408.612| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.32 r_work: 0.3453 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6825 Z= 0.115 Angle : 0.489 5.799 9298 Z= 0.262 Chirality : 0.039 0.141 1104 Planarity : 0.004 0.061 1142 Dihedral : 6.289 56.515 963 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.38 % Allowed : 19.72 % Favored : 78.90 % 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: -1.12 (0.29), residues: 861 helix: 1.33 (0.30), residues: 326 sheet: -2.53 (0.32), residues: 208 loop : -1.54 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 47 HIS 0.005 0.001 HIS A 41 PHE 0.010 0.001 PHE R 747 TYR 0.010 0.001 TYR B 105 ARG 0.002 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.03481 ( 326) hydrogen bonds : angle 5.16119 ( 924) SS BOND : bond 0.00326 ( 3) SS BOND : angle 1.69362 ( 6) covalent geometry : bond 0.00253 ( 6822) covalent geometry : angle 0.48775 ( 9292) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue THR 369 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue SER 265 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue SER 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue VAL 584 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue MET 693 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue SER 741 is missing expected H atoms. Skipping. Residue THR 785 is missing expected H atoms. Skipping. Residue SER 814 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 336 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7428 (mp) REVERT: R 721 THR cc_start: 0.5573 (t) cc_final: 0.5274 (t) outliers start: 9 outliers final: 5 residues processed: 112 average time/residue: 0.3665 time to fit residues: 55.8043 Evaluate side-chains 112 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 657 CYS Chi-restraints excluded: chain R residue 735 LEU Chi-restraints excluded: chain R residue 836 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 10 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.161091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.125742 restraints weight = 21881.055| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.33 r_work: 0.3305 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6825 Z= 0.161 Angle : 0.494 5.768 9298 Z= 0.269 Chirality : 0.039 0.150 1104 Planarity : 0.004 0.060 1142 Dihedral : 5.601 54.773 963 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.14 % Allowed : 19.88 % Favored : 77.98 % 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: -1.06 (0.29), residues: 861 helix: 1.48 (0.30), residues: 327 sheet: -2.61 (0.32), residues: 208 loop : -1.57 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 47 HIS 0.003 0.001 HIS B 91 PHE 0.010 0.001 PHE R 747 TYR 0.010 0.001 TYR R 684 ARG 0.003 0.000 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 326) hydrogen bonds : angle 5.00236 ( 924) SS BOND : bond 0.00169 ( 3) SS BOND : angle 1.44352 ( 6) covalent geometry : bond 0.00364 ( 6822) covalent geometry : angle 0.49314 ( 9292) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue THR 369 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue SER 265 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue SER 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue VAL 584 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue MET 693 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue SER 741 is missing expected H atoms. Skipping. Residue THR 785 is missing expected H atoms. Skipping. Residue SER 814 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 721 THR cc_start: 0.5506 (t) cc_final: 0.5206 (t) outliers start: 14 outliers final: 12 residues processed: 122 average time/residue: 0.4460 time to fit residues: 74.3978 Evaluate side-chains 119 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 642 ILE Chi-restraints excluded: chain R residue 657 CYS Chi-restraints excluded: chain R residue 836 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 64 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.161100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.125785 restraints weight = 21695.095| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.33 r_work: 0.3434 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6825 Z= 0.147 Angle : 0.479 5.612 9298 Z= 0.261 Chirality : 0.039 0.144 1104 Planarity : 0.003 0.058 1142 Dihedral : 5.522 57.739 963 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.75 % Allowed : 18.96 % Favored : 78.29 % 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: -1.00 (0.29), residues: 861 helix: 1.59 (0.30), residues: 327 sheet: -2.63 (0.32), residues: 208 loop : -1.55 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.002 0.001 HIS B 91 PHE 0.009 0.001 PHE R 747 TYR 0.009 0.001 TYR R 684 ARG 0.003 0.000 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.03226 ( 326) hydrogen bonds : angle 4.91587 ( 924) SS BOND : bond 0.00325 ( 3) SS BOND : angle 1.85170 ( 6) covalent geometry : bond 0.00330 ( 6822) covalent geometry : angle 0.47719 ( 9292) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue THR 369 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue SER 265 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue SER 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue VAL 584 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue MET 693 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue SER 741 is missing expected H atoms. Skipping. Residue THR 785 is missing expected H atoms. Skipping. Residue SER 814 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8523 (tp) REVERT: B 163 ASP cc_start: 0.8147 (t0) cc_final: 0.7899 (t70) REVERT: R 721 THR cc_start: 0.5643 (t) cc_final: 0.5357 (t) outliers start: 18 outliers final: 15 residues processed: 118 average time/residue: 0.4871 time to fit residues: 79.2096 Evaluate side-chains 121 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 642 ILE Chi-restraints excluded: chain R residue 657 CYS Chi-restraints excluded: chain R residue 735 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.159488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.124035 restraints weight = 21874.785| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.36 r_work: 0.3279 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6825 Z= 0.188 Angle : 0.509 5.536 9298 Z= 0.278 Chirality : 0.040 0.147 1104 Planarity : 0.004 0.057 1142 Dihedral : 5.682 57.617 963 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.98 % Allowed : 18.65 % Favored : 77.37 % 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: -1.15 (0.29), residues: 861 helix: 1.48 (0.30), residues: 327 sheet: -2.73 (0.32), residues: 208 loop : -1.65 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.002 0.001 HIS B 91 PHE 0.010 0.001 PHE R 747 TYR 0.009 0.001 TYR R 684 ARG 0.003 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 326) hydrogen bonds : angle 4.95294 ( 924) SS BOND : bond 0.00302 ( 3) SS BOND : angle 1.85460 ( 6) covalent geometry : bond 0.00429 ( 6822) covalent geometry : angle 0.50732 ( 9292) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue THR 369 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue SER 265 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue SER 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue VAL 584 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue MET 693 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue SER 741 is missing expected H atoms. Skipping. Residue THR 785 is missing expected H atoms. Skipping. Residue SER 814 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.5552 (p0) cc_final: 0.5349 (p0) REVERT: B 97 SER cc_start: 0.8602 (OUTLIER) cc_final: 0.8359 (p) REVERT: B 163 ASP cc_start: 0.8310 (t0) cc_final: 0.8067 (t70) REVERT: R 684 TYR cc_start: 0.7901 (OUTLIER) cc_final: 0.7404 (t80) REVERT: R 721 THR cc_start: 0.5511 (t) cc_final: 0.5228 (t) REVERT: R 819 TRP cc_start: 0.7449 (m100) cc_final: 0.7235 (m100) outliers start: 26 outliers final: 21 residues processed: 127 average time/residue: 0.4040 time to fit residues: 71.4611 Evaluate side-chains 130 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 642 ILE Chi-restraints excluded: chain R residue 657 CYS Chi-restraints excluded: chain R residue 684 TYR Chi-restraints excluded: chain R residue 735 LEU Chi-restraints excluded: chain R residue 836 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 68 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.157148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.121836 restraints weight = 22303.160| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.36 r_work: 0.3276 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6825 Z= 0.177 Angle : 0.500 5.426 9298 Z= 0.273 Chirality : 0.039 0.149 1104 Planarity : 0.004 0.057 1142 Dihedral : 5.732 58.211 963 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.98 % Allowed : 18.81 % Favored : 77.22 % 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: -1.15 (0.29), residues: 861 helix: 1.55 (0.30), residues: 327 sheet: -2.77 (0.32), residues: 208 loop : -1.70 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.003 0.001 HIS B 91 PHE 0.010 0.001 PHE R 747 TYR 0.009 0.001 TYR R 707 ARG 0.004 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03315 ( 326) hydrogen bonds : angle 4.91233 ( 924) SS BOND : bond 0.00205 ( 3) SS BOND : angle 1.42248 ( 6) covalent geometry : bond 0.00400 ( 6822) covalent geometry : angle 0.49931 ( 9292) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue THR 369 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue SER 265 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue SER 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue VAL 584 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue MET 693 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue SER 741 is missing expected H atoms. Skipping. Residue THR 785 is missing expected H atoms. Skipping. Residue SER 814 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 SER cc_start: 0.8596 (OUTLIER) cc_final: 0.8348 (p) REVERT: B 163 ASP cc_start: 0.8353 (t0) cc_final: 0.8152 (t70) REVERT: R 684 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.7396 (t80) REVERT: R 721 THR cc_start: 0.5485 (t) cc_final: 0.5202 (t) outliers start: 26 outliers final: 19 residues processed: 126 average time/residue: 0.3299 time to fit residues: 58.1343 Evaluate side-chains 126 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 568 SER Chi-restraints excluded: chain R residue 642 ILE Chi-restraints excluded: chain R residue 657 CYS Chi-restraints excluded: chain R residue 684 TYR Chi-restraints excluded: chain R residue 735 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 42 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 19 optimal weight: 0.0980 chunk 59 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.160967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.125670 restraints weight = 21738.081| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.34 r_work: 0.3311 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6825 Z= 0.131 Angle : 0.479 5.326 9298 Z= 0.259 Chirality : 0.039 0.147 1104 Planarity : 0.003 0.057 1142 Dihedral : 5.527 57.077 963 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.67 % Allowed : 19.11 % Favored : 77.22 % 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: -1.09 (0.29), residues: 861 helix: 1.63 (0.30), residues: 327 sheet: -2.79 (0.32), residues: 208 loop : -1.65 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.003 0.001 HIS B 142 PHE 0.009 0.001 PHE B 199 TYR 0.008 0.001 TYR R 707 ARG 0.004 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03163 ( 326) hydrogen bonds : angle 4.83401 ( 924) SS BOND : bond 0.00228 ( 3) SS BOND : angle 1.72912 ( 6) covalent geometry : bond 0.00292 ( 6822) covalent geometry : angle 0.47671 ( 9292) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue THR 369 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue SER 265 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue SER 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue VAL 584 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue MET 693 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue SER 741 is missing expected H atoms. Skipping. Residue THR 785 is missing expected H atoms. Skipping. Residue SER 814 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 138 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7712 (tt0) REVERT: B 163 ASP cc_start: 0.8318 (t0) cc_final: 0.8113 (t70) REVERT: R 684 TYR cc_start: 0.7884 (OUTLIER) cc_final: 0.7417 (t80) REVERT: R 721 THR cc_start: 0.5552 (t) cc_final: 0.5278 (t) outliers start: 24 outliers final: 21 residues processed: 127 average time/residue: 0.4556 time to fit residues: 81.3879 Evaluate side-chains 130 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 568 SER Chi-restraints excluded: chain R residue 642 ILE Chi-restraints excluded: chain R residue 657 CYS Chi-restraints excluded: chain R residue 684 TYR Chi-restraints excluded: chain R residue 735 LEU Chi-restraints excluded: chain R residue 797 THR Chi-restraints excluded: chain R residue 836 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.160170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.124951 restraints weight = 21915.567| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.35 r_work: 0.3302 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6825 Z= 0.154 Angle : 0.493 5.256 9298 Z= 0.268 Chirality : 0.039 0.143 1104 Planarity : 0.004 0.057 1142 Dihedral : 5.519 57.700 963 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.28 % Allowed : 18.81 % Favored : 76.91 % 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: -1.11 (0.29), residues: 861 helix: 1.61 (0.30), residues: 327 sheet: -2.83 (0.32), residues: 208 loop : -1.64 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 47 HIS 0.004 0.001 HIS B 142 PHE 0.009 0.001 PHE B 199 TYR 0.008 0.001 TYR N 60 ARG 0.006 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03219 ( 326) hydrogen bonds : angle 4.83924 ( 924) SS BOND : bond 0.00303 ( 3) SS BOND : angle 1.95524 ( 6) covalent geometry : bond 0.00350 ( 6822) covalent geometry : angle 0.49106 ( 9292) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue THR 369 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue SER 265 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue SER 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue VAL 584 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue MET 693 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue SER 741 is missing expected H atoms. Skipping. Residue THR 785 is missing expected H atoms. Skipping. Residue SER 814 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 2.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.5516 (p0) cc_final: 0.5270 (p0) REVERT: B 97 SER cc_start: 0.8605 (OUTLIER) cc_final: 0.8372 (p) REVERT: B 120 ILE cc_start: 0.8783 (mm) cc_final: 0.8243 (tt) REVERT: B 163 ASP cc_start: 0.8333 (t0) cc_final: 0.8120 (t70) REVERT: R 627 MET cc_start: 0.7898 (mmm) cc_final: 0.7575 (mmm) REVERT: R 684 TYR cc_start: 0.7903 (OUTLIER) cc_final: 0.7434 (t80) REVERT: R 721 THR cc_start: 0.5494 (t) cc_final: 0.5210 (t) outliers start: 28 outliers final: 23 residues processed: 128 average time/residue: 0.5037 time to fit residues: 89.8601 Evaluate side-chains 129 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 568 SER Chi-restraints excluded: chain R residue 642 ILE Chi-restraints excluded: chain R residue 657 CYS Chi-restraints excluded: chain R residue 684 TYR Chi-restraints excluded: chain R residue 735 LEU Chi-restraints excluded: chain R residue 797 THR Chi-restraints excluded: chain R residue 836 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 24 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 64 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.162315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.127040 restraints weight = 21663.523| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.35 r_work: 0.3418 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6825 Z= 0.102 Angle : 0.463 5.133 9298 Z= 0.250 Chirality : 0.038 0.149 1104 Planarity : 0.004 0.057 1142 Dihedral : 5.322 57.953 963 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.91 % Allowed : 20.49 % Favored : 76.61 % 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: -0.99 (0.30), residues: 861 helix: 1.70 (0.30), residues: 327 sheet: -2.74 (0.32), residues: 208 loop : -1.58 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.002 0.001 HIS B 142 PHE 0.008 0.001 PHE B 199 TYR 0.007 0.001 TYR N 60 ARG 0.009 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03001 ( 326) hydrogen bonds : angle 4.71032 ( 924) SS BOND : bond 0.00196 ( 3) SS BOND : angle 1.53480 ( 6) covalent geometry : bond 0.00226 ( 6822) covalent geometry : angle 0.46115 ( 9292) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue THR 369 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue SER 265 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue SER 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue VAL 584 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue MET 693 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue SER 741 is missing expected H atoms. Skipping. Residue THR 785 is missing expected H atoms. Skipping. Residue SER 814 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.5552 (p0) cc_final: 0.5331 (p0) REVERT: R 627 MET cc_start: 0.7915 (mmm) cc_final: 0.7615 (mmm) REVERT: R 684 TYR cc_start: 0.7884 (OUTLIER) cc_final: 0.7442 (t80) REVERT: R 721 THR cc_start: 0.5532 (t) cc_final: 0.5267 (t) outliers start: 19 outliers final: 16 residues processed: 121 average time/residue: 0.3146 time to fit residues: 53.6400 Evaluate side-chains 123 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 568 SER Chi-restraints excluded: chain R residue 642 ILE Chi-restraints excluded: chain R residue 657 CYS Chi-restraints excluded: chain R residue 684 TYR Chi-restraints excluded: chain R residue 735 LEU Chi-restraints excluded: chain R residue 797 THR Chi-restraints excluded: chain R residue 836 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 2 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.161339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.125696 restraints weight = 21852.371| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.40 r_work: 0.3285 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6825 Z= 0.132 Angle : 0.481 5.155 9298 Z= 0.261 Chirality : 0.039 0.140 1104 Planarity : 0.004 0.056 1142 Dihedral : 5.348 58.879 963 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.52 % Allowed : 19.88 % Favored : 76.61 % 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: -1.01 (0.30), residues: 861 helix: 1.65 (0.30), residues: 328 sheet: -2.71 (0.32), residues: 209 loop : -1.59 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 47 HIS 0.003 0.001 HIS B 142 PHE 0.016 0.001 PHE R 837 TYR 0.007 0.001 TYR R 684 ARG 0.006 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03078 ( 326) hydrogen bonds : angle 4.70246 ( 924) SS BOND : bond 0.00262 ( 3) SS BOND : angle 2.02793 ( 6) covalent geometry : bond 0.00299 ( 6822) covalent geometry : angle 0.47822 ( 9292) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue THR 369 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue SER 265 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue SER 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue VAL 584 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue MET 693 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue SER 741 is missing expected H atoms. Skipping. Residue THR 785 is missing expected H atoms. Skipping. Residue SER 814 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 ASP cc_start: 0.5431 (p0) cc_final: 0.5204 (p0) REVERT: R 627 MET cc_start: 0.7828 (mmm) cc_final: 0.7529 (mmm) REVERT: R 684 TYR cc_start: 0.7878 (OUTLIER) cc_final: 0.7360 (t80) REVERT: R 721 THR cc_start: 0.5380 (t) cc_final: 0.5114 (t) outliers start: 23 outliers final: 21 residues processed: 121 average time/residue: 0.3366 time to fit residues: 56.6383 Evaluate side-chains 126 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 568 SER Chi-restraints excluded: chain R residue 642 ILE Chi-restraints excluded: chain R residue 657 CYS Chi-restraints excluded: chain R residue 684 TYR Chi-restraints excluded: chain R residue 735 LEU Chi-restraints excluded: chain R residue 797 THR Chi-restraints excluded: chain R residue 836 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 68 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 55 optimal weight: 0.4980 chunk 78 optimal weight: 0.3980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.161460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.125855 restraints weight = 21870.527| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.41 r_work: 0.3286 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6825 Z= 0.127 Angle : 0.476 5.139 9298 Z= 0.258 Chirality : 0.039 0.141 1104 Planarity : 0.003 0.056 1142 Dihedral : 5.310 59.550 963 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.21 % Allowed : 20.34 % Favored : 76.45 % 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: -0.95 (0.30), residues: 861 helix: 1.69 (0.30), residues: 328 sheet: -2.67 (0.32), residues: 209 loop : -1.55 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 47 HIS 0.003 0.001 HIS B 142 PHE 0.009 0.001 PHE B 199 TYR 0.007 0.001 TYR N 60 ARG 0.005 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03055 ( 326) hydrogen bonds : angle 4.67518 ( 924) SS BOND : bond 0.00211 ( 3) SS BOND : angle 2.13091 ( 6) covalent geometry : bond 0.00286 ( 6822) covalent geometry : angle 0.47356 ( 9292) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7662.21 seconds wall clock time: 137 minutes 32.76 seconds (8252.76 seconds total)