Starting phenix.real_space_refine on Fri Oct 23 07:46:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6n9u_0379/10_2026/6n9u_0379.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n9u_0379/10_2026/6n9u_0379.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n9u_0379/10_2026/6n9u_0379.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n9u_0379/10_2026/6n9u_0379.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6n9u_0379/10_2026/6n9u_0379.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6n9u_0379/10_2026/6n9u_0379.cif" model { file = "/net/cci-nas-00/data/ceres_data/6n9u_0379/10_2026/6n9u_0379.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n9u_0379/10_2026/6n9u_0379.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 20 5.49 5 Mg 2 5.21 5 S 47 5.16 5 C 5527 2.51 5 N 1531 2.21 5 O 1694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8822 Number of models: 1 Model: "" Number of chains: 7 Chain: "E" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1740 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1538 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 4, 'TRANS': 191} Chain: "H" Number of atoms: 5144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5144 Classifications: {'peptide': 645} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 622} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "P" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 122 Unusual residues: {'DOC': 1} Classifications: {'RNAv2': 5, 'undetermined': 1} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna3p': 4, None: 1} Not linked: pdbres=" G P 5 " pdbres="DOC P 6 " Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 246 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {' MG': 2, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 69 SG CYS E 17 59.453 36.079 46.143 1.00 84.80 S ATOM 91 SG CYS E 20 58.126 33.933 44.451 1.00 85.19 S ATOM 204 SG CYS E 36 56.118 35.082 46.849 1.00 66.69 S ATOM 229 SG CYS E 39 58.279 32.837 47.885 1.00 69.94 S Time building chain proxies: 2.06, per 1000 atoms: 0.23 Number of scatterers: 8822 At special positions: 0 Unit cell: (86.86, 100.62, 121.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 47 16.00 P 20 15.00 Mg 2 11.99 O 1694 8.00 N 1531 7.00 C 5527 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 235 " - pdb=" SG CYS F 241 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 306.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 601 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 17 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 39 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 36 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 20 " Number of angles added : 6 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1950 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 13 sheets defined 36.0% alpha, 11.7% beta 5 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'E' and resid 87 through 95 removed outlier: 4.132A pdb=" N CYS E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 104 removed outlier: 4.066A pdb=" N GLY E 103 " --> pdb=" O LYS E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 170 Processing helix chain 'E' and resid 187 through 192 removed outlier: 3.888A pdb=" N ASN E 192 " --> pdb=" O THR E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 199 removed outlier: 3.789A pdb=" N PHE E 199 " --> pdb=" O PHE E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 243 removed outlier: 3.502A pdb=" N CYS E 241 " --> pdb=" O ASP E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 246 No H-bonds generated for 'chain 'E' and resid 244 through 246' Processing helix chain 'E' and resid 247 through 256 removed outlier: 4.048A pdb=" N GLN E 253 " --> pdb=" O GLU E 249 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TRP E 255 " --> pdb=" O MET E 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 95 removed outlier: 3.731A pdb=" N CYS F 91 " --> pdb=" O SER F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 169 removed outlier: 3.797A pdb=" N LEU F 163 " --> pdb=" O GLU F 159 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL F 165 " --> pdb=" O ASP F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 191 removed outlier: 3.647A pdb=" N ALA F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 220 Processing helix chain 'F' and resid 237 through 244 removed outlier: 3.600A pdb=" N CYS F 241 " --> pdb=" O ASP F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 254 removed outlier: 3.688A pdb=" N VAL F 254 " --> pdb=" O ILE F 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 52 Processing helix chain 'H' and resid 64 through 76 removed outlier: 3.527A pdb=" N LYS H 74 " --> pdb=" O THR H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 99 Processing helix chain 'H' and resid 124 through 132 Processing helix chain 'H' and resid 138 through 151 Processing helix chain 'H' and resid 164 through 186 removed outlier: 4.187A pdb=" N MET H 168 " --> pdb=" O ASN H 164 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS H 184 " --> pdb=" O ALA H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 231 removed outlier: 3.635A pdb=" N GLU H 217 " --> pdb=" O ALA H 213 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS H 218 " --> pdb=" O VAL H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 246 removed outlier: 3.917A pdb=" N LEU H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 259 removed outlier: 4.008A pdb=" N GLU H 259 " --> pdb=" O ARG H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 348 Processing helix chain 'H' and resid 378 through 400 removed outlier: 4.509A pdb=" N ASP H 384 " --> pdb=" O GLN H 380 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU H 385 " --> pdb=" O ALA H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 409 removed outlier: 3.612A pdb=" N ARG H 408 " --> pdb=" O ALA H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 448 through 453 Processing helix chain 'H' and resid 478 through 488 removed outlier: 3.642A pdb=" N ALA H 485 " --> pdb=" O LEU H 481 " (cutoff:3.500A) Processing helix chain 'H' and resid 504 through 514 removed outlier: 3.989A pdb=" N LYS H 508 " --> pdb=" O ASP H 504 " (cutoff:3.500A) Processing helix chain 'H' and resid 517 through 530 removed outlier: 3.722A pdb=" N TYR H 526 " --> pdb=" O LYS H 522 " (cutoff:3.500A) Processing helix chain 'H' and resid 544 through 555 removed outlier: 4.054A pdb=" N LYS H 552 " --> pdb=" O GLY H 548 " (cutoff:3.500A) Processing helix chain 'H' and resid 561 through 573 Processing helix chain 'H' and resid 608 through 637 removed outlier: 4.130A pdb=" N SER H 616 " --> pdb=" O THR H 612 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA H 617 " --> pdb=" O LEU H 613 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU H 620 " --> pdb=" O SER H 616 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE H 621 " --> pdb=" O ALA H 617 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N CYS H 622 " --> pdb=" O GLY H 618 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE H 627 " --> pdb=" O LYS H 623 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU H 630 " --> pdb=" O ILE H 626 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU H 633 " --> pdb=" O THR H 629 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU H 635 " --> pdb=" O GLU H 631 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY H 637 " --> pdb=" O LEU H 633 " (cutoff:3.500A) Processing helix chain 'H' and resid 662 through 684 removed outlier: 4.577A pdb=" N GLN H 674 " --> pdb=" O ILE H 670 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU H 675 " --> pdb=" O GLU H 671 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TRP H 684 " --> pdb=" O VAL H 680 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 11 through 15 removed outlier: 3.667A pdb=" N TYR E 13 " --> pdb=" O LEU E 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 96 through 99 removed outlier: 3.740A pdb=" N SER E 120 " --> pdb=" O TYR E 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 141 through 142 removed outlier: 3.526A pdb=" N SER E 177 " --> pdb=" O PHE E 142 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE E 202 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY E 258 " --> pdb=" O VAL E 230 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 97 through 100 removed outlier: 4.018A pdb=" N SER F 120 " --> pdb=" O TYR F 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 141 through 142 Processing sheet with id=AA6, first strand: chain 'F' and resid 153 through 155 removed outlier: 6.364A pdb=" N ILE F 153 " --> pdb=" O ILE F 203 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE F 202 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL F 230 " --> pdb=" O GLY F 258 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY F 258 " --> pdb=" O VAL F 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'H' and resid 32 through 34 removed outlier: 4.188A pdb=" N GLY H 21 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE H 2 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE H 56 " --> pdb=" O ILE H 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 232 through 233 Processing sheet with id=AA9, first strand: chain 'H' and resid 264 through 267 Processing sheet with id=AB1, first strand: chain 'H' and resid 419 through 421 Processing sheet with id=AB2, first strand: chain 'H' and resid 646 through 651 removed outlier: 7.065A pdb=" N GLN H 657 " --> pdb=" O MET H 649 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 574 through 579 removed outlier: 3.877A pdb=" N SER H 576 " --> pdb=" O LYS H 587 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 592 through 594 283 hydrogen bonds defined for protein. 804 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for OD residue (no planarity definition) Restraints generated for nucleic acids: 13 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 9 stacking parallelities Total time for adding SS restraints: 1.48 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1466 1.31 - 1.44: 2556 1.44 - 1.56: 4926 1.56 - 1.69: 37 1.69 - 1.82: 72 Bond restraints: 9057 Sorted by residual: bond pdb=" C6 TTP H 801 " pdb=" N1 TTP H 801 " ideal model delta sigma weight residual 1.337 1.424 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" N1 DOC P 6 " pdb=" C2 DOC P 6 " ideal model delta sigma weight residual 1.405 1.489 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" P DOC P 6 " pdb=" O5' DOC P 6 " ideal model delta sigma weight residual 1.730 1.660 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C2 TTP H 801 " pdb=" N1 TTP H 801 " ideal model delta sigma weight residual 1.410 1.480 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C2 TTP H 801 " pdb=" O2 TTP H 801 " ideal model delta sigma weight residual 1.250 1.182 0.068 2.00e-02 2.50e+03 1.15e+01 ... (remaining 9052 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 11809 1.89 - 3.77: 443 3.77 - 5.66: 46 5.66 - 7.54: 14 7.54 - 9.43: 11 Bond angle restraints: 12323 Sorted by residual: angle pdb=" N3 DT T2007 " pdb=" C4 DT T2007 " pdb=" O4 DT T2007 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.06e+01 angle pdb=" N ILE H 464 " pdb=" CA ILE H 464 " pdb=" C ILE H 464 " ideal model delta sigma weight residual 113.71 109.54 4.17 9.50e-01 1.11e+00 1.93e+01 angle pdb=" N3 DT T2013 " pdb=" C4 DT T2013 " pdb=" O4 DT T2013 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT T2010 " pdb=" C4 DT T2010 " pdb=" O4 DT T2010 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT T2002 " pdb=" C4 DT T2002 " pdb=" O4 DT T2002 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 ... (remaining 12318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.27: 5183 33.27 - 66.54: 99 66.54 - 99.81: 9 99.81 - 133.07: 0 133.07 - 166.34: 1 Dihedral angle restraints: 5292 sinusoidal: 2245 harmonic: 3047 Sorted by residual: dihedral pdb=" C2 TTP H 801 " pdb=" C1' TTP H 801 " pdb=" N1 TTP H 801 " pdb=" O4' TTP H 801 " ideal model delta sinusoidal sigma weight residual 301.68 135.34 166.34 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" CA TYR H 64 " pdb=" C TYR H 64 " pdb=" N ASP H 65 " pdb=" CA ASP H 65 " ideal model delta harmonic sigma weight residual -180.00 -153.26 -26.74 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" C5' TTP H 801 " pdb=" O5' TTP H 801 " pdb=" PA TTP H 801 " pdb=" O3A TTP H 801 " ideal model delta sinusoidal sigma weight residual 179.97 84.34 95.63 1 2.00e+01 2.50e-03 2.64e+01 ... (remaining 5289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1001 0.062 - 0.124: 262 0.124 - 0.187: 34 0.187 - 0.249: 9 0.249 - 0.311: 1 Chirality restraints: 1307 Sorted by residual: chirality pdb=" C4' TTP H 801 " pdb=" C3' TTP H 801 " pdb=" C5' TTP H 801 " pdb=" O4' TTP H 801 " both_signs ideal model delta sigma weight residual False -2.50 -2.81 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" P C P 2 " pdb=" OP1 C P 2 " pdb=" OP2 C P 2 " pdb=" O5' C P 2 " both_signs ideal model delta sigma weight residual True 2.17 -2.40 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB ILE H 505 " pdb=" CA ILE H 505 " pdb=" CG1 ILE H 505 " pdb=" CG2 ILE H 505 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1304 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 700 " 0.024 2.00e-02 2.50e+03 2.01e-02 1.01e+01 pdb=" CG TRP H 700 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP H 700 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP H 700 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 700 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP H 700 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP H 700 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 700 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 700 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP H 700 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 97 " 0.017 2.00e-02 2.50e+03 1.84e-02 8.46e+00 pdb=" CG TRP F 97 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP F 97 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP F 97 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 97 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP F 97 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 97 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 97 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 97 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP F 97 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 147 " 0.020 2.00e-02 2.50e+03 1.79e-02 7.97e+00 pdb=" CG TRP E 147 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP E 147 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP E 147 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 147 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 147 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP E 147 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 147 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 147 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP E 147 " 0.003 2.00e-02 2.50e+03 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 791 2.74 - 3.28: 7689 3.28 - 3.82: 13900 3.82 - 4.36: 15938 4.36 - 4.90: 27831 Nonbonded interactions: 66149 Sorted by model distance: nonbonded pdb=" OD2 ASP H 654 " pdb="MG MG H 802 " model vdw 2.205 2.170 nonbonded pdb=" O GLY F 158 " pdb=" OG SER F 177 " model vdw 2.254 3.040 nonbonded pdb=" O ALA H 476 " pdb="MG MG H 802 " model vdw 2.274 2.170 nonbonded pdb=" O2B TTP H 801 " pdb="MG MG H 802 " model vdw 2.283 2.170 nonbonded pdb=" OD2 ASP H 197 " pdb=" OG1 THR H 199 " model vdw 2.293 3.040 ... (remaining 66144 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.260 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 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 : 0.007 0.280 9063 Z= 0.314 Angle : 0.936 30.956 12331 Z= 0.485 Chirality : 0.057 0.311 1307 Planarity : 0.006 0.059 1526 Dihedral : 12.942 166.343 3339 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.34 % Allowed : 4.35 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.67 (0.20), residues: 1049 helix: -3.21 (0.18), residues: 422 sheet: -2.67 (0.40), residues: 142 loop : -3.04 (0.23), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 96 TYR 0.016 0.002 TYR H 648 PHE 0.027 0.003 PHE E 142 TRP 0.053 0.004 TRP H 700 HIS 0.007 0.001 HIS H 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.28 ( 9057) covalent geometry : angle 0.85889 / 0.48 (12323) SS BOND : bond 0.00407 / 0.21 ( 1) SS BOND : angle 1.72546 / 0.91 ( 2) hydrogen bonds : bond 0.12644 / 8.78 ( 296) hydrogen bonds : angle 6.19472 / 4.26 ( 830) metal coordination : bond 0.20289 / 10.27 ( 4) metal coordination : angle 16.87513 / 8.81 ( 6) Misc. bond : bond 0.00035 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 237 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 42 TRP cc_start: 0.8713 (t60) cc_final: 0.8494 (t60) REVERT: E 137 LYS cc_start: 0.8340 (mptt) cc_final: 0.7996 (mmmm) REVERT: E 151 LYS cc_start: 0.8601 (tttm) cc_final: 0.8361 (ttmm) REVERT: F 69 TRP cc_start: 0.6550 (m-10) cc_final: 0.6336 (m-10) REVERT: H 144 LYS cc_start: 0.8006 (tmmt) cc_final: 0.7707 (tttt) REVERT: H 146 MET cc_start: 0.6523 (tpp) cc_final: 0.6291 (mtt) REVERT: H 326 TYR cc_start: 0.6030 (t80) cc_final: 0.5237 (m-80) REVERT: H 346 LEU cc_start: 0.8714 (mt) cc_final: 0.8457 (mt) REVERT: H 450 GLN cc_start: 0.8231 (mt0) cc_final: 0.7745 (mm110) REVERT: H 639 LYS cc_start: 0.8393 (tptp) cc_final: 0.8187 (tttm) outliers start: 3 outliers final: 0 residues processed: 237 average time/residue: 0.1153 time to fit residues: 35.2776 Evaluate side-chains 136 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 100, 38, 61] chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 0.0770 chunk 61 optimal weight: 0.5980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 67 ASN E 70 ASN E 129 ASN E 169 GLN E 201 GLN E 244 ASN E 253 GLN E 256 ASN F 136 HIS H 62 HIS H 150 GLN H 439 GLN H 520 ASN H 615 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.141399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.123052 restraints weight = 13032.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.125737 restraints weight = 7983.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.127453 restraints weight = 5619.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.128491 restraints weight = 4440.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.129338 restraints weight = 3803.052| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9063 Z= 0.136 Angle : 0.628 10.958 12331 Z= 0.328 Chirality : 0.044 0.212 1307 Planarity : 0.005 0.046 1526 Dihedral : 12.114 170.684 1356 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.49 % Allowed : 12.01 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.23), residues: 1049 helix: -1.85 (0.23), residues: 422 sheet: -2.30 (0.41), residues: 140 loop : -2.65 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 145 TYR 0.017 0.001 TYR F 193 PHE 0.018 0.002 PHE H 528 TRP 0.027 0.002 TRP E 147 HIS 0.003 0.001 HIS H 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 9057) covalent geometry : angle 0.62179 / 0.33 (12323) SS BOND : bond 0.00112 / 0.06 ( 1) SS BOND : angle 1.00302 / 0.54 ( 2) hydrogen bonds : bond 0.04592 / 3.02 ( 296) hydrogen bonds : angle 4.97714 / 3.40 ( 830) metal coordination : bond 0.00632 / 0.28 ( 4) metal coordination : angle 4.11489 / 2.18 ( 6) Misc. bond : bond 0.00062 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: E 42 TRP cc_start: 0.8687 (t60) cc_final: 0.8346 (t60) REVERT: F 251 MET cc_start: 0.7563 (tpp) cc_final: 0.7182 (ttm) REVERT: H 101 ASN cc_start: 0.8735 (p0) cc_final: 0.8461 (p0) REVERT: H 144 LYS cc_start: 0.8097 (tmmt) cc_final: 0.7881 (tttt) REVERT: H 168 MET cc_start: 0.6579 (OUTLIER) cc_final: 0.5499 (tmm) REVERT: H 326 TYR cc_start: 0.6003 (t80) cc_final: 0.5361 (m-80) REVERT: H 351 TRP cc_start: 0.7397 (t60) cc_final: 0.7062 (t60) REVERT: H 450 GLN cc_start: 0.8147 (mt0) cc_final: 0.7679 (mm-40) outliers start: 13 outliers final: 10 residues processed: 161 average time/residue: 0.1136 time to fit residues: 24.2033 Evaluate side-chains 136 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 168 MET Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 383 ILE Chi-restraints excluded: chain H residue 443 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: [17, 83, 73, 10, 39, 55, 38, 96, 79, 0, 63] chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 239 ASN ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 439 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.138169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.119753 restraints weight = 13200.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.122293 restraints weight = 8133.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.123864 restraints weight = 5808.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.125077 restraints weight = 4639.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.125626 restraints weight = 3942.062| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9063 Z= 0.158 Angle : 0.595 9.745 12331 Z= 0.313 Chirality : 0.045 0.211 1307 Planarity : 0.004 0.043 1526 Dihedral : 11.953 172.136 1356 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.40 % Allowed : 13.04 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.24), residues: 1049 helix: -1.27 (0.24), residues: 424 sheet: -2.17 (0.39), residues: 155 loop : -2.47 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 248 TYR 0.015 0.001 TYR F 193 PHE 0.013 0.001 PHE H 528 TRP 0.020 0.001 TRP E 147 HIS 0.003 0.001 HIS H 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 9057) covalent geometry : angle 0.58959 / 0.31 (12323) SS BOND : bond 0.00155 / 0.08 ( 1) SS BOND : angle 0.72144 / 0.39 ( 2) hydrogen bonds : bond 0.04346 / 2.89 ( 296) hydrogen bonds : angle 4.77706 / 3.26 ( 830) metal coordination : bond 0.00769 / 0.34 ( 4) metal coordination : angle 3.53741 / 1.93 ( 6) Misc. bond : bond 0.00065 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.317 Fit side-chains REVERT: E 42 TRP cc_start: 0.8730 (t60) cc_final: 0.8441 (t60) REVERT: H 144 LYS cc_start: 0.8076 (tmmt) cc_final: 0.7833 (tttt) REVERT: H 168 MET cc_start: 0.6731 (OUTLIER) cc_final: 0.5760 (tmm) REVERT: H 326 TYR cc_start: 0.5998 (t80) cc_final: 0.5343 (m-80) REVERT: H 351 TRP cc_start: 0.7477 (t60) cc_final: 0.7258 (t60) REVERT: H 450 GLN cc_start: 0.8169 (mt0) cc_final: 0.7685 (mm-40) REVERT: H 474 ILE cc_start: 0.9154 (mt) cc_final: 0.8922 (mt) outliers start: 21 outliers final: 14 residues processed: 151 average time/residue: 0.1129 time to fit residues: 22.5870 Evaluate side-chains 138 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 168 MET Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 383 ILE Chi-restraints excluded: chain H residue 443 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: [28, 12, 45, 71, 66, 36, 81, 53, 85, 38, 33] chunk 28 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 81 optimal weight: 0.2980 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 398 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.138960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.120548 restraints weight = 13249.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.123100 restraints weight = 8160.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.124722 restraints weight = 5822.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.125896 restraints weight = 4610.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.126734 restraints weight = 3905.551| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9063 Z= 0.150 Angle : 0.577 9.071 12331 Z= 0.303 Chirality : 0.045 0.225 1307 Planarity : 0.004 0.062 1526 Dihedral : 11.876 172.500 1356 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.75 % Allowed : 13.62 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.25), residues: 1049 helix: -0.84 (0.25), residues: 425 sheet: -2.14 (0.39), residues: 155 loop : -2.29 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 547 TYR 0.014 0.001 TYR F 193 PHE 0.014 0.001 PHE F 71 TRP 0.013 0.001 TRP E 147 HIS 0.003 0.001 HIS F 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 9057) covalent geometry : angle 0.57295 / 0.30 (12323) SS BOND : bond 0.00185 / 0.10 ( 1) SS BOND : angle 0.61421 / 0.33 ( 2) hydrogen bonds : bond 0.04204 / 2.82 ( 296) hydrogen bonds : angle 4.61284 / 3.15 ( 830) metal coordination : bond 0.00500 / 0.22 ( 4) metal coordination : angle 3.06384 / 1.67 ( 6) Misc. bond : bond 0.00070 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: E 42 TRP cc_start: 0.8720 (t60) cc_final: 0.8450 (t60) REVERT: E 67 ASN cc_start: 0.7156 (OUTLIER) cc_final: 0.6929 (p0) REVERT: E 84 ARG cc_start: 0.7814 (mtp85) cc_final: 0.7603 (mtp85) REVERT: F 147 TRP cc_start: 0.6243 (m100) cc_final: 0.6002 (m100) REVERT: H 144 LYS cc_start: 0.8062 (tmmt) cc_final: 0.7856 (tttt) REVERT: H 168 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.5823 (tmm) REVERT: H 351 TRP cc_start: 0.7455 (t60) cc_final: 0.7233 (t60) REVERT: H 450 GLN cc_start: 0.8209 (mt0) cc_final: 0.7721 (mm-40) REVERT: H 474 ILE cc_start: 0.9183 (mt) cc_final: 0.8953 (mt) outliers start: 24 outliers final: 17 residues processed: 144 average time/residue: 0.1005 time to fit residues: 19.5568 Evaluate side-chains 141 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 168 MET Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 383 ILE Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: [16, 81, 72, 47, 24, 99, 49, 97, 10, 54, 14] chunk 16 optimal weight: 0.0070 chunk 81 optimal weight: 1.9990 chunk 72 optimal weight: 0.0270 chunk 47 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 0.2980 chunk 97 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 0.0870 chunk 14 optimal weight: 0.7980 overall best weight: 0.2034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 19 ASN E 201 GLN ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.142522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.124271 restraints weight = 12984.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.126906 restraints weight = 7920.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.128602 restraints weight = 5591.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.129670 restraints weight = 4395.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.130538 restraints weight = 3742.106| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9063 Z= 0.098 Angle : 0.533 9.055 12331 Z= 0.277 Chirality : 0.043 0.242 1307 Planarity : 0.004 0.066 1526 Dihedral : 11.723 171.653 1356 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.40 % Allowed : 14.42 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.26), residues: 1049 helix: -0.37 (0.26), residues: 423 sheet: -1.95 (0.39), residues: 161 loop : -2.00 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 248 TYR 0.013 0.001 TYR F 193 PHE 0.017 0.001 PHE F 196 TRP 0.012 0.001 TRP E 147 HIS 0.003 0.000 HIS H 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 ( 9057) covalent geometry : angle 0.53001 / 0.28 (12323) SS BOND : bond 0.00081 / 0.04 ( 1) SS BOND : angle 0.58716 / 0.32 ( 2) hydrogen bonds : bond 0.03370 / 2.26 ( 296) hydrogen bonds : angle 4.35670 / 2.97 ( 830) metal coordination : bond 0.00333 / 0.14 ( 4) metal coordination : angle 2.67199 / 1.45 ( 6) Misc. bond : bond 0.00033 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: E 42 TRP cc_start: 0.8673 (t60) cc_final: 0.8465 (t60) REVERT: E 84 ARG cc_start: 0.7666 (mtp85) cc_final: 0.7395 (mtp85) REVERT: F 147 TRP cc_start: 0.6299 (m100) cc_final: 0.6054 (m100) REVERT: H 144 LYS cc_start: 0.8097 (tmmt) cc_final: 0.7897 (tttt) REVERT: H 168 MET cc_start: 0.6692 (OUTLIER) cc_final: 0.5737 (tmm) REVERT: H 351 TRP cc_start: 0.7404 (t60) cc_final: 0.7173 (t60) REVERT: H 450 GLN cc_start: 0.8181 (mt0) cc_final: 0.7693 (mm-40) REVERT: H 474 ILE cc_start: 0.9164 (mt) cc_final: 0.8948 (mt) outliers start: 21 outliers final: 13 residues processed: 156 average time/residue: 0.1030 time to fit residues: 21.6711 Evaluate side-chains 136 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 168 MET Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 498 HIS Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: [79, 18, 53, 14, 23, 58, 45, 32, 48, 90, 43] chunk 79 optimal weight: 0.0870 chunk 18 optimal weight: 0.0170 chunk 53 optimal weight: 2.9990 chunk 14 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 19 ASN E 169 GLN ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.141868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.123501 restraints weight = 13077.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.126152 restraints weight = 7934.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.127906 restraints weight = 5594.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.129061 restraints weight = 4360.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.129693 restraints weight = 3702.729| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9063 Z= 0.105 Angle : 0.535 9.727 12331 Z= 0.276 Chirality : 0.043 0.207 1307 Planarity : 0.004 0.069 1526 Dihedral : 11.645 171.369 1356 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.52 % Allowed : 15.10 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.26), residues: 1049 helix: -0.11 (0.27), residues: 423 sheet: -1.88 (0.39), residues: 168 loop : -1.83 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 248 TYR 0.012 0.001 TYR F 193 PHE 0.009 0.001 PHE F 142 TRP 0.014 0.001 TRP E 147 HIS 0.004 0.001 HIS H 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 9057) covalent geometry : angle 0.53196 / 0.28 (12323) SS BOND : bond 0.00072 / 0.04 ( 1) SS BOND : angle 0.42166 / 0.23 ( 2) hydrogen bonds : bond 0.03328 / 2.24 ( 296) hydrogen bonds : angle 4.23162 / 2.88 ( 830) metal coordination : bond 0.00321 / 0.13 ( 4) metal coordination : angle 2.55511 / 1.38 ( 6) Misc. bond : bond 0.00033 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.338 Fit side-chains REVERT: E 42 TRP cc_start: 0.8647 (t60) cc_final: 0.8433 (t60) REVERT: E 84 ARG cc_start: 0.7620 (mtp85) cc_final: 0.7353 (mtp85) REVERT: E 167 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7282 (tt0) REVERT: F 205 MET cc_start: 0.8521 (tpp) cc_final: 0.7969 (ttp) REVERT: H 109 LEU cc_start: 0.8648 (tp) cc_final: 0.8310 (tp) REVERT: H 144 LYS cc_start: 0.8082 (tmmt) cc_final: 0.7866 (tttt) REVERT: H 168 MET cc_start: 0.6763 (OUTLIER) cc_final: 0.5828 (tmm) REVERT: H 351 TRP cc_start: 0.7363 (t60) cc_final: 0.7144 (t60) REVERT: H 450 GLN cc_start: 0.8192 (mt0) cc_final: 0.7704 (mm-40) REVERT: H 474 ILE cc_start: 0.9188 (mt) cc_final: 0.8802 (mt) outliers start: 22 outliers final: 16 residues processed: 146 average time/residue: 0.1072 time to fit residues: 20.9211 Evaluate side-chains 141 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 168 MET Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 498 HIS Chi-restraints excluded: chain H residue 614 LEU Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: [104, 37, 88, 65, 36, 93, 102, 60, 1, 35, 25] chunk 104 optimal weight: 1.9990 chunk 37 optimal weight: 0.0870 chunk 88 optimal weight: 0.0050 chunk 65 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.4572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 145 HIS ** 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 = 0.3594 r_free = 0.3594 target = 0.141855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.123436 restraints weight = 12779.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.126004 restraints weight = 7839.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.127718 restraints weight = 5558.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.128736 restraints weight = 4377.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.129604 restraints weight = 3740.185| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9063 Z= 0.115 Angle : 0.659 31.334 12331 Z= 0.285 Chirality : 0.043 0.201 1307 Planarity : 0.004 0.071 1526 Dihedral : 11.609 171.101 1356 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.75 % Allowed : 16.13 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.26), residues: 1049 helix: 0.01 (0.27), residues: 423 sheet: -1.87 (0.39), residues: 168 loop : -1.80 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 248 TYR 0.011 0.001 TYR F 193 PHE 0.010 0.001 PHE F 142 TRP 0.014 0.001 TRP F 147 HIS 0.002 0.001 HIS H 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 9057) covalent geometry : angle 0.53678 / 0.28 (12323) SS BOND : bond 0.00116 / 0.06 ( 1) SS BOND : angle 0.37819 / 0.20 ( 2) hydrogen bonds : bond 0.03402 / 2.29 ( 296) hydrogen bonds : angle 4.18177 / 2.84 ( 830) metal coordination : bond 0.01256 / 0.63 ( 4) metal coordination : angle 17.34719 / 9.03 ( 6) Misc. bond : bond 0.00043 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.329 Fit side-chains REVERT: E 42 TRP cc_start: 0.8659 (t60) cc_final: 0.8450 (t60) REVERT: E 84 ARG cc_start: 0.7624 (mtp85) cc_final: 0.7354 (mtp85) REVERT: E 167 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7246 (tt0) REVERT: F 205 MET cc_start: 0.8550 (tpp) cc_final: 0.7966 (ttp) REVERT: H 109 LEU cc_start: 0.8653 (tp) cc_final: 0.8300 (tp) REVERT: H 144 LYS cc_start: 0.8086 (tmmt) cc_final: 0.7872 (tttt) REVERT: H 168 MET cc_start: 0.6799 (OUTLIER) cc_final: 0.5876 (tmm) REVERT: H 351 TRP cc_start: 0.7393 (t60) cc_final: 0.7181 (t60) REVERT: H 450 GLN cc_start: 0.8194 (mt0) cc_final: 0.7702 (mm-40) REVERT: H 474 ILE cc_start: 0.9196 (mt) cc_final: 0.8802 (mt) outliers start: 24 outliers final: 19 residues processed: 143 average time/residue: 0.1032 time to fit residues: 19.8971 Evaluate side-chains 145 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 132 THR Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 168 MET Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 498 HIS Chi-restraints excluded: chain H residue 614 LEU Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: [58, 37, 21, 3, 99, 4, 28, 17, 15, 2, 80] chunk 58 optimal weight: 0.9990 chunk 37 optimal weight: 0.0040 chunk 21 optimal weight: 0.5980 chunk 3 optimal weight: 0.0980 chunk 99 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 0.0070 chunk 2 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 overall best weight: 0.3210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 145 HIS ** 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 = 0.3604 r_free = 0.3604 target = 0.142393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.123981 restraints weight = 12636.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.126555 restraints weight = 7779.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.128269 restraints weight = 5529.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.129422 restraints weight = 4362.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.129949 restraints weight = 3698.563| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9063 Z= 0.102 Angle : 0.579 18.198 12331 Z= 0.275 Chirality : 0.043 0.181 1307 Planarity : 0.004 0.071 1526 Dihedral : 11.507 170.451 1356 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.52 % Allowed : 16.36 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.27), residues: 1049 helix: 0.23 (0.27), residues: 422 sheet: -1.76 (0.40), residues: 168 loop : -1.75 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 248 TYR 0.010 0.001 TYR F 193 PHE 0.008 0.001 PHE F 142 TRP 0.015 0.001 TRP F 147 HIS 0.002 0.000 HIS H 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 9057) covalent geometry : angle 0.52796 / 0.27 (12323) SS BOND : bond 0.00098 / 0.05 ( 1) SS BOND : angle 0.43803 / 0.23 ( 2) hydrogen bonds : bond 0.03207 / 2.16 ( 296) hydrogen bonds : angle 4.06791 / 2.76 ( 830) metal coordination : bond 0.00953 / 0.47 ( 4) metal coordination : angle 10.77104 / 5.63 ( 6) Misc. bond : bond 0.00042 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.202 Fit side-chains REVERT: E 42 TRP cc_start: 0.8730 (t60) cc_final: 0.8489 (t60) REVERT: E 84 ARG cc_start: 0.7560 (mtp85) cc_final: 0.7297 (mtp85) REVERT: E 167 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7382 (tt0) REVERT: F 205 MET cc_start: 0.8528 (tpp) cc_final: 0.7968 (ttp) REVERT: F 218 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7183 (mm-30) REVERT: H 109 LEU cc_start: 0.8709 (tp) cc_final: 0.8344 (tp) REVERT: H 168 MET cc_start: 0.6815 (OUTLIER) cc_final: 0.5928 (tmm) REVERT: H 351 TRP cc_start: 0.7439 (t60) cc_final: 0.7220 (t60) REVERT: H 450 GLN cc_start: 0.8185 (mt0) cc_final: 0.7708 (mm-40) outliers start: 22 outliers final: 15 residues processed: 146 average time/residue: 0.1019 time to fit residues: 20.1068 Evaluate side-chains 136 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 168 MET Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 498 HIS Chi-restraints excluded: chain H residue 614 LEU Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: [33, 12, 68, 83, 89, 38, 4, 35, 62, 45, 85] chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 85 optimal weight: 0.0060 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.141782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.123297 restraints weight = 12611.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.125838 restraints weight = 7856.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.127525 restraints weight = 5613.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.128500 restraints weight = 4443.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.129402 restraints weight = 3816.462| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9063 Z= 0.120 Angle : 0.589 17.696 12331 Z= 0.283 Chirality : 0.044 0.200 1307 Planarity : 0.004 0.071 1526 Dihedral : 11.471 170.372 1356 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.40 % Allowed : 17.16 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.27), residues: 1049 helix: 0.24 (0.27), residues: 423 sheet: -1.79 (0.39), residues: 168 loop : -1.74 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 248 TYR 0.010 0.001 TYR F 193 PHE 0.009 0.001 PHE F 71 TRP 0.019 0.001 TRP F 147 HIS 0.002 0.001 HIS H 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 9057) covalent geometry : angle 0.54596 / 0.28 (12323) SS BOND : bond 0.00152 / 0.08 ( 1) SS BOND : angle 0.41328 / 0.22 ( 2) hydrogen bonds : bond 0.03461 / 2.32 ( 296) hydrogen bonds : angle 4.12415 / 2.81 ( 830) metal coordination : bond 0.01043 / 0.51 ( 4) metal coordination : angle 10.01360 / 5.23 ( 6) Misc. bond : bond 0.00055 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: E 84 ARG cc_start: 0.7586 (mtp85) cc_final: 0.7320 (mtp85) REVERT: F 205 MET cc_start: 0.8569 (tpp) cc_final: 0.8023 (ttp) REVERT: H 109 LEU cc_start: 0.8697 (tp) cc_final: 0.8338 (tp) REVERT: H 168 MET cc_start: 0.6848 (OUTLIER) cc_final: 0.5949 (tmm) REVERT: H 351 TRP cc_start: 0.7454 (t60) cc_final: 0.7238 (t60) REVERT: H 450 GLN cc_start: 0.8195 (mt0) cc_final: 0.7705 (mm-40) outliers start: 21 outliers final: 18 residues processed: 135 average time/residue: 0.0996 time to fit residues: 18.4268 Evaluate side-chains 135 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 168 MET Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 498 HIS Chi-restraints excluded: chain H residue 614 LEU Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: [76, 61, 92, 44, 3, 14, 47, 8, 19, 34, 24] chunk 76 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 0.0050 chunk 47 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.141086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.122495 restraints weight = 12659.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.125031 restraints weight = 7891.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.126705 restraints weight = 5639.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.127706 restraints weight = 4470.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.128477 restraints weight = 3837.357| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9063 Z= 0.126 Angle : 0.583 15.451 12331 Z= 0.285 Chirality : 0.044 0.184 1307 Planarity : 0.004 0.072 1526 Dihedral : 11.446 170.232 1356 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.29 % Allowed : 17.39 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.27), residues: 1049 helix: 0.24 (0.27), residues: 424 sheet: -1.79 (0.39), residues: 168 loop : -1.71 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 248 TYR 0.010 0.001 TYR F 193 PHE 0.014 0.001 PHE F 142 TRP 0.017 0.001 TRP F 147 HIS 0.002 0.001 HIS H 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 9057) covalent geometry : angle 0.55000 / 0.28 (12323) SS BOND : bond 0.00171 / 0.09 ( 1) SS BOND : angle 0.47251 / 0.25 ( 2) hydrogen bonds : bond 0.03616 / 2.40 ( 296) hydrogen bonds : angle 4.13486 / 2.80 ( 830) metal coordination : bond 0.00991 / 0.48 ( 4) metal coordination : angle 8.79208 / 4.60 ( 6) Misc. bond : bond 0.00060 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.250 Fit side-chains REVERT: E 84 ARG cc_start: 0.7584 (mtp85) cc_final: 0.7335 (mtp85) REVERT: F 205 MET cc_start: 0.8585 (tpp) cc_final: 0.8032 (ttp) REVERT: H 109 LEU cc_start: 0.8708 (tp) cc_final: 0.8343 (tp) REVERT: H 168 MET cc_start: 0.6893 (OUTLIER) cc_final: 0.5968 (tmm) REVERT: H 351 TRP cc_start: 0.7450 (t60) cc_final: 0.7230 (t60) REVERT: H 450 GLN cc_start: 0.8198 (mt0) cc_final: 0.7687 (mm-40) outliers start: 20 outliers final: 18 residues processed: 133 average time/residue: 0.0997 time to fit residues: 18.2143 Evaluate side-chains 135 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 160 ILE Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 164 ASN Chi-restraints excluded: chain H residue 168 MET Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 498 HIS Chi-restraints excluded: chain H residue 614 LEU Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: [5, 84, 65, 94, 30, 78, 40, 88, 43, 4, 7] chunk 5 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 30 optimal weight: 0.0070 chunk 78 optimal weight: 0.0570 chunk 40 optimal weight: 0.0670 chunk 88 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 overall best weight: 0.2854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.142129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.123552 restraints weight = 12578.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.126072 restraints weight = 7834.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.127775 restraints weight = 5611.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.128942 restraints weight = 4427.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.129578 restraints weight = 3760.447| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9063 Z= 0.103 Angle : 0.572 13.388 12331 Z= 0.280 Chirality : 0.043 0.175 1307 Planarity : 0.004 0.071 1526 Dihedral : 11.394 170.035 1356 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.63 % Allowed : 17.05 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.27), residues: 1049 helix: 0.37 (0.27), residues: 425 sheet: -1.74 (0.41), residues: 161 loop : -1.62 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 248 TYR 0.011 0.001 TYR F 193 PHE 0.013 0.001 PHE F 142 TRP 0.020 0.001 TRP F 147 HIS 0.002 0.000 HIS F 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 9057) covalent geometry : angle 0.54562 / 0.28 (12323) SS BOND : bond 0.00102 / 0.05 ( 1) SS BOND : angle 0.46483 / 0.25 ( 2) hydrogen bonds : bond 0.03304 / 2.19 ( 296) hydrogen bonds : angle 4.06105 / 2.75 ( 830) metal coordination : bond 0.00876 / 0.43 ( 4) metal coordination : angle 7.77700 / 4.04 ( 6) Misc. bond : bond 0.00047 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1519.20 seconds wall clock time: 26 minutes 54.01 seconds (1614.01 seconds total)