Starting phenix.real_space_refine on Sat Sep 12 00:09:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d2l_27142/09_2026/8d2l_27142.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2l_27142/09_2026/8d2l_27142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d2l_27142/09_2026/8d2l_27142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2l_27142/09_2026/8d2l_27142.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8d2l_27142/09_2026/8d2l_27142.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d2l_27142/09_2026/8d2l_27142.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d2l_27142/09_2026/8d2l_27142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2l_27142/09_2026/8d2l_27142.map" } resolution = 2.21 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 151 5.49 5 Mg 10 5.21 5 S 20 5.16 5 C 6892 2.51 5 N 2199 2.21 5 O 2955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12227 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 8720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8720 Classifications: {'peptide': 1105} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 59, 'TRANS': 1041} Chain breaks: 3 Chain: "B" Number of atoms: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 2080 Unusual residues: {'GTP': 1} Classifications: {'RNAv2': 96, 'undetermined': 1} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 7, 'rna3p_pur': 44, 'rna3p_pyr': 40} Link IDs: {'rna2p': 12, 'rna3p': 83, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" G B 2 " Chain breaks: 1 Chain: "X" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 267 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "T" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 481 Classifications: {'DNA': 24} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 23} Chain: "D" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 12} Chain: "Y" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 180 Classifications: {'water': 180} Link IDs: {None: 179} Chain: "B" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 121 Classifications: {'water': 121} Link IDs: {None: 120} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "T" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.70, per 1000 atoms: 0.22 Number of scatterers: 12227 At special positions: 0 Unit cell: (95.7, 106.425, 129.525, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 20 16.00 P 151 15.00 Mg 10 11.99 O 2955 8.00 N 2199 7.00 C 6892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS A 578 " distance=2.08 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS A 610 " distance=2.12 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS A 613 " distance=1.94 Simple disulfide: pdb=" SG CYS A 578 " - pdb=" SG CYS A 610 " distance=1.94 Simple disulfide: pdb=" SG CYS A 578 " - pdb=" SG CYS A 613 " distance=2.08 Simple disulfide: pdb=" SG CYS A 610 " - pdb=" SG CYS A 613 " distance=2.07 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: 1.11 Conformation dependent library (CDL) restraints added in 481.2 milliseconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 10 sheets defined 50.3% alpha, 10.1% beta 56 base pairs and 96 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 59 through 92 Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 120 through 138 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 180 through 192 Processing helix chain 'A' and resid 221 through 237 Processing helix chain 'A' and resid 239 through 251 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 279 through 293 Processing helix chain 'A' and resid 306 through 319 Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 364 through 377 Processing helix chain 'A' and resid 381 through 391 Processing helix chain 'A' and resid 392 through 405 Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 421 through 430 Processing helix chain 'A' and resid 441 through 455 Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'A' and resid 486 through 508 Processing helix chain 'A' and resid 524 through 552 Processing helix chain 'A' and resid 558 through 571 Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 611 through 618 Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 633 through 643 Processing helix chain 'A' and resid 653 through 669 Processing helix chain 'A' and resid 681 through 703 Processing helix chain 'A' and resid 712 through 722 Processing helix chain 'A' and resid 725 through 730 Processing helix chain 'A' and resid 742 through 747 removed outlier: 3.767A pdb=" N LEU A 745 " --> pdb=" O THR A 742 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ARG A 747 " --> pdb=" O ARG A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 758 Processing helix chain 'A' and resid 761 through 777 Processing helix chain 'A' and resid 797 through 807 Processing helix chain 'A' and resid 809 through 820 Processing helix chain 'A' and resid 856 through 861 Processing helix chain 'A' and resid 864 through 876 Processing helix chain 'A' and resid 957 through 963 Processing helix chain 'A' and resid 981 through 986 Processing helix chain 'A' and resid 988 through 997 Processing helix chain 'A' and resid 1024 through 1033 removed outlier: 3.647A pdb=" N MET A1028 " --> pdb=" O GLY A1024 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR A1032 " --> pdb=" O MET A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1069 removed outlier: 3.721A pdb=" N ALA A1061 " --> pdb=" O SER A1057 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER A1069 " --> pdb=" O ARG A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1086 Processing helix chain 'A' and resid 1094 through 1098 Processing sheet with id=AA1, first strand: chain 'A' and resid 706 through 711 removed outlier: 6.901A pdb=" N TRP A 13 " --> pdb=" O SER A 512 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N VAL A 514 " --> pdb=" O TRP A 13 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU A 15 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N GLU A 516 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL A 17 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE A 24 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL A 43 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU A 26 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA A 41 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ALA A 28 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ILE A 39 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER A 30 " --> pdb=" O LYS A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 266 removed outlier: 5.719A pdb=" N GLN A 272 " --> pdb=" O ASP A 266 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 302 through 304 Processing sheet with id=AA4, first strand: chain 'A' and resid 588 through 591 Processing sheet with id=AA5, first strand: chain 'A' and resid 846 through 849 Processing sheet with id=AA6, first strand: chain 'A' and resid 854 through 855 Processing sheet with id=AA7, first strand: chain 'A' and resid 899 through 900 Processing sheet with id=AA8, first strand: chain 'A' and resid 921 through 924 Processing sheet with id=AA9, first strand: chain 'A' and resid 948 through 956 removed outlier: 3.653A pdb=" N GLY A1004 " --> pdb=" O VAL A 939 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG A 941 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N GLN A1002 " --> pdb=" O ARG A 941 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1090 through 1093 removed outlier: 6.617A pdb=" N ARG A1048 " --> pdb=" O PHE A1043 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N PHE A1043 " --> pdb=" O ARG A1048 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN A1050 " --> pdb=" O THR A1041 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A1011 " --> pdb=" O ILE A1106 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1254 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 141 hydrogen bonds 266 hydrogen bond angles 0 basepair planarities 56 basepair parallelities 96 stacking parallelities Total time for adding SS restraints: 3.20 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2464 1.33 - 1.46: 4671 1.46 - 1.60: 5094 1.60 - 1.73: 176 1.73 - 1.87: 28 Bond restraints: 12433 Sorted by residual: bond pdb=" C1' DC T 21 " pdb=" N1 DC T 21 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.93e+01 bond pdb=" C3' DC X 3 " pdb=" O3' DC X 3 " ideal model delta sigma weight residual 1.435 1.506 -0.071 1.30e-02 5.92e+03 2.95e+01 bond pdb=" C5' DT X 4 " pdb=" C4' DT X 4 " ideal model delta sigma weight residual 1.512 1.548 -0.036 7.00e-03 2.04e+04 2.60e+01 bond pdb=" C1' DT T 22 " pdb=" N1 DT T 22 " ideal model delta sigma weight residual 1.468 1.534 -0.066 1.40e-02 5.10e+03 2.25e+01 bond pdb=" C3' DT D 30 " pdb=" O3' DT D 30 " ideal model delta sigma weight residual 1.435 1.376 0.059 1.30e-02 5.92e+03 2.08e+01 ... (remaining 12428 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.53: 17515 5.53 - 11.07: 38 11.07 - 16.60: 2 16.60 - 22.13: 0 22.13 - 27.67: 1 Bond angle restraints: 17556 Sorted by residual: angle pdb=" CA CYS A 613 " pdb=" CB CYS A 613 " pdb=" SG CYS A 613 " ideal model delta sigma weight residual 114.40 142.07 -27.67 2.30e+00 1.89e-01 1.45e+02 angle pdb=" O4' DC T 21 " pdb=" C1' DC T 21 " pdb=" N1 DC T 21 " ideal model delta sigma weight residual 108.00 113.55 -5.55 7.00e-01 2.04e+00 6.29e+01 angle pdb=" O4' DC X 3 " pdb=" C1' DC X 3 " pdb=" N1 DC X 3 " ideal model delta sigma weight residual 108.00 113.45 -5.45 7.00e-01 2.04e+00 6.07e+01 angle pdb=" O4' DG T 17 " pdb=" C1' DG T 17 " pdb=" N9 DG T 17 " ideal model delta sigma weight residual 108.00 113.27 -5.27 7.00e-01 2.04e+00 5.67e+01 angle pdb=" N CYS A 613 " pdb=" CA CYS A 613 " pdb=" CB CYS A 613 " ideal model delta sigma weight residual 110.16 100.24 9.92 1.48e+00 4.57e-01 4.49e+01 ... (remaining 17551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.25: 6782 33.25 - 66.50: 597 66.50 - 99.75: 62 99.75 - 133.00: 1 133.00 - 166.25: 1 Dihedral angle restraints: 7443 sinusoidal: 4247 harmonic: 3196 Sorted by residual: dihedral pdb=" C4' A B 41 " pdb=" C3' A B 41 " pdb=" C2' A B 41 " pdb=" C1' A B 41 " ideal model delta sinusoidal sigma weight residual 36.34 -39.01 75.36 1 3.10e+00 1.04e-01 7.46e+02 dihedral pdb=" C4' C B 60 " pdb=" C3' C B 60 " pdb=" C2' C B 60 " pdb=" C1' C B 60 " ideal model delta sinusoidal sigma weight residual 36.34 -38.25 74.59 1 3.10e+00 1.04e-01 7.34e+02 dihedral pdb=" C4' U B 76 " pdb=" C3' U B 76 " pdb=" C2' U B 76 " pdb=" C1' U B 76 " ideal model delta sinusoidal sigma weight residual 36.34 -35.85 72.19 1 3.10e+00 1.04e-01 6.93e+02 ... (remaining 7440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1747 0.092 - 0.183: 152 0.183 - 0.275: 105 0.275 - 0.366: 13 0.366 - 0.458: 3 Chirality restraints: 2020 Sorted by residual: chirality pdb=" P C B 88 " pdb=" OP1 C B 88 " pdb=" OP2 C B 88 " pdb=" O5' C B 88 " both_signs ideal model delta sigma weight residual True 2.17 -2.63 -0.46 2.00e-01 2.50e+01 5.24e+00 chirality pdb=" P A B 38 " pdb=" OP1 A B 38 " pdb=" OP2 A B 38 " pdb=" O5' A B 38 " both_signs ideal model delta sigma weight residual True 2.17 -2.56 -0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" P C B 63 " pdb=" OP1 C B 63 " pdb=" OP2 C B 63 " pdb=" O5' C B 63 " both_signs ideal model delta sigma weight residual True 2.17 -2.56 -0.39 2.00e-01 2.50e+01 3.79e+00 ... (remaining 2017 not shown) Planarity restraints: 1738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 363 " 0.026 2.00e-02 2.50e+03 3.28e-02 1.88e+01 pdb=" CG PHE A 363 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE A 363 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 PHE A 363 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 363 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE A 363 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 363 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A1020 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C THR A1020 " -0.059 2.00e-02 2.50e+03 pdb=" O THR A1020 " 0.022 2.00e-02 2.50e+03 pdb=" N THR A1021 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 613 " 0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C CYS A 613 " -0.057 2.00e-02 2.50e+03 pdb=" O CYS A 613 " 0.022 2.00e-02 2.50e+03 pdb=" N ASN A 614 " 0.019 2.00e-02 2.50e+03 ... (remaining 1735 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 327 2.60 - 3.18: 9650 3.18 - 3.75: 24183 3.75 - 4.33: 31757 4.33 - 4.90: 46822 Nonbonded interactions: 112739 Sorted by model distance: nonbonded pdb=" OE2 GLU A 516 " pdb="MG MG A1202 " model vdw 2.031 2.170 nonbonded pdb=" OD1 ASP A 590 " pdb="MG MG A1201 " model vdw 2.045 2.170 nonbonded pdb=" OP2 DT D 28 " pdb="MG MG A1202 " model vdw 2.058 2.170 nonbonded pdb=" O3' DA X 13 " pdb="MG MG A1201 " model vdw 2.066 2.170 nonbonded pdb=" OP1 U B 78 " pdb="MG MG B 205 " model vdw 2.067 2.170 ... (remaining 112734 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.110 Find NCS groups from input model: 0.060 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:5.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 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 : 0.006 0.094 12440 Z= 0.371 Angle : 1.148 35.157 17568 Z= 0.640 Chirality : 0.078 0.458 2020 Planarity : 0.007 0.073 1738 Dihedral : 20.803 166.247 5351 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.15 (0.23), residues: 1097 helix: 0.34 (0.21), residues: 546 sheet: -0.27 (0.60), residues: 76 loop : -0.46 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1048 TYR 0.018 0.003 TYR A 986 PHE 0.071 0.003 PHE A 363 TRP 0.023 0.002 TRP A 721 HIS 0.004 0.001 HIS A 574 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.36 (12433) covalent geometry : angle 0.98210 / 0.57 (17556) SS BOND : bond 0.07162 / 4.58 ( 6) SS BOND : angle 22.79990 / 14.94 ( 12) hydrogen bonds : bond 0.07234 / 5.14 ( 573) hydrogen bonds : angle 4.77559 / 3.45 ( 1520) Misc. bond : bond 0.00085 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.382 Fit side-chains REVERT: A 21 GLU cc_start: 0.7780 (tp30) cc_final: 0.7527 (mm-30) REVERT: A 33 GLU cc_start: 0.6796 (pm20) cc_final: 0.6472 (pm20) REVERT: A 724 ILE cc_start: 0.7914 (mm) cc_final: 0.7690 (mp) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.9728 time to fit residues: 120.1296 Evaluate side-chains 102 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.160695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.122202 restraints weight = 10162.564| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.16 r_work: 0.3154 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 12440 Z= 0.274 Angle : 1.221 28.760 17568 Z= 0.552 Chirality : 0.104 1.533 2020 Planarity : 0.006 0.048 1738 Dihedral : 21.141 164.623 3262 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.31 % Allowed : 6.12 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.73 (0.25), residues: 1097 helix: 1.17 (0.22), residues: 546 sheet: -0.14 (0.58), residues: 81 loop : -0.10 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 137 TYR 0.021 0.002 TYR A 986 PHE 0.025 0.002 PHE A 282 TRP 0.017 0.002 TRP A 161 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.26 (12433) covalent geometry : angle 1.07500 / 0.48 (17556) SS BOND : bond 0.08368 / 5.44 ( 6) SS BOND : angle 22.15449 / 14.04 ( 12) hydrogen bonds : bond 0.06817 / 4.82 ( 573) hydrogen bonds : angle 4.24061 / 3.08 ( 1520) Misc. bond : bond 0.00057 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7171 (pm20) cc_final: 0.6868 (pp20) REVERT: A 230 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7662 (mpt-90) REVERT: A 724 ILE cc_start: 0.7851 (mm) cc_final: 0.7593 (mp) outliers start: 12 outliers final: 3 residues processed: 110 average time/residue: 0.9907 time to fit residues: 114.9688 Evaluate side-chains 103 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 1048 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 111 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.162724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.126009 restraints weight = 10389.747| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.20 r_work: 0.3179 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 12440 Z= 0.208 Angle : 1.053 30.852 17568 Z= 0.484 Chirality : 0.084 1.579 2020 Planarity : 0.004 0.043 1738 Dihedral : 21.160 165.817 3262 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.87 % Allowed : 7.43 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 1.10 (0.25), residues: 1097 helix: 1.53 (0.22), residues: 546 sheet: -0.15 (0.58), residues: 81 loop : 0.04 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 137 TYR 0.017 0.002 TYR A 986 PHE 0.020 0.002 PHE A 282 TRP 0.015 0.002 TRP A 161 HIS 0.004 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.19 (12433) covalent geometry : angle 0.88227 / 0.40 (17556) SS BOND : bond 0.08451 / 5.47 ( 6) SS BOND : angle 21.97690 / 13.64 ( 12) hydrogen bonds : bond 0.06070 / 4.31 ( 573) hydrogen bonds : angle 4.05544 / 2.96 ( 1520) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7066 (pm20) cc_final: 0.6726 (pp20) REVERT: A 724 ILE cc_start: 0.7818 (mm) cc_final: 0.7545 (mp) REVERT: A 864 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7685 (mp0) outliers start: 8 outliers final: 4 residues processed: 110 average time/residue: 0.9937 time to fit residues: 115.3543 Evaluate side-chains 103 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 1048 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 37 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.158370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.120061 restraints weight = 10294.426| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.23 r_work: 0.3110 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.125 12440 Z= 0.344 Angle : 1.157 33.788 17568 Z= 0.536 Chirality : 0.089 1.588 2020 Planarity : 0.006 0.048 1738 Dihedral : 21.334 174.796 3262 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.31 % Allowed : 8.52 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.94 (0.25), residues: 1097 helix: 1.38 (0.22), residues: 545 sheet: -0.13 (0.57), residues: 81 loop : -0.03 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1107 TYR 0.024 0.003 TYR A 986 PHE 0.029 0.003 PHE A 282 TRP 0.017 0.003 TRP A 161 HIS 0.007 0.002 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.33 (12433) covalent geometry : angle 0.99514 / 0.46 (17556) SS BOND : bond 0.07980 / 4.97 ( 6) SS BOND : angle 22.62608 / 14.29 ( 12) hydrogen bonds : bond 0.07281 / 5.07 ( 573) hydrogen bonds : angle 4.31992 / 3.14 ( 1520) Misc. bond : bond 0.00022 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 137 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.6324 (mtt180) REVERT: A 149 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8407 (ttmt) REVERT: A 230 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7662 (mpt-90) REVERT: A 724 ILE cc_start: 0.7731 (mm) cc_final: 0.7452 (mp) outliers start: 12 outliers final: 6 residues processed: 110 average time/residue: 0.9349 time to fit residues: 108.5896 Evaluate side-chains 107 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 1048 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 80 optimal weight: 0.0570 chunk 91 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.159102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.122086 restraints weight = 10368.314| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.28 r_work: 0.3115 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.128 12440 Z= 0.295 Angle : 1.073 32.203 17568 Z= 0.502 Chirality : 0.081 1.601 2020 Planarity : 0.006 0.048 1738 Dihedral : 21.483 177.351 3262 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.53 % Allowed : 8.74 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.98 (0.25), residues: 1097 helix: 1.44 (0.22), residues: 545 sheet: -0.15 (0.57), residues: 81 loop : -0.04 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 631 TYR 0.022 0.002 TYR A 986 PHE 0.025 0.002 PHE A 282 TRP 0.017 0.002 TRP A 161 HIS 0.007 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.28 (12433) covalent geometry : angle 0.90121 / 0.42 (17556) SS BOND : bond 0.08541 / 5.45 ( 6) SS BOND : angle 22.31713 / 13.92 ( 12) hydrogen bonds : bond 0.06753 / 4.72 ( 573) hydrogen bonds : angle 4.23332 / 3.09 ( 1520) Misc. bond : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 137 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.6310 (mtt180) REVERT: A 149 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8328 (ttmt) REVERT: A 230 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7682 (mpt-90) REVERT: A 365 GLU cc_start: 0.8120 (tt0) cc_final: 0.7411 (pt0) REVERT: A 372 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6835 (tt0) REVERT: A 724 ILE cc_start: 0.7761 (mm) cc_final: 0.7477 (mp) outliers start: 14 outliers final: 7 residues processed: 109 average time/residue: 0.9282 time to fit residues: 107.1489 Evaluate side-chains 108 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 1048 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 82 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.157823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.120670 restraints weight = 10324.887| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.28 r_work: 0.3096 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.137 12440 Z= 0.353 Angle : 1.139 32.742 17568 Z= 0.532 Chirality : 0.084 1.508 2020 Planarity : 0.006 0.050 1738 Dihedral : 21.569 175.321 3262 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.53 % Allowed : 9.07 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.82 (0.25), residues: 1097 helix: 1.29 (0.22), residues: 545 sheet: -0.13 (0.57), residues: 81 loop : -0.11 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 137 TYR 0.025 0.003 TYR A 986 PHE 0.029 0.003 PHE A 282 TRP 0.018 0.003 TRP A 161 HIS 0.008 0.002 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00724 / 0.34 (12433) covalent geometry : angle 0.97239 / 0.45 (17556) SS BOND : bond 0.07859 / 4.92 ( 6) SS BOND : angle 22.68697 / 14.27 ( 12) hydrogen bonds : bond 0.07341 / 5.09 ( 573) hydrogen bonds : angle 4.36140 / 3.18 ( 1520) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 137 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.6348 (mtt180) REVERT: A 149 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8380 (ttmt) REVERT: A 230 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7696 (mpt-90) REVERT: A 365 GLU cc_start: 0.8101 (tt0) cc_final: 0.7387 (pt0) REVERT: A 372 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6846 (tt0) REVERT: A 679 GLN cc_start: 0.5119 (tt0) cc_final: 0.4798 (tt0) REVERT: A 724 ILE cc_start: 0.7775 (mm) cc_final: 0.7485 (mp) outliers start: 14 outliers final: 7 residues processed: 108 average time/residue: 0.9388 time to fit residues: 107.3935 Evaluate side-chains 107 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 1048 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 81 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.158765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.122496 restraints weight = 10312.441| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.22 r_work: 0.3115 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 12440 Z= 0.296 Angle : 1.079 32.589 17568 Z= 0.504 Chirality : 0.080 1.522 2020 Planarity : 0.006 0.040 1738 Dihedral : 21.524 173.198 3262 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.53 % Allowed : 9.73 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 0.97 (0.25), residues: 1097 helix: 1.42 (0.22), residues: 545 sheet: -0.10 (0.57), residues: 81 loop : -0.04 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 137 TYR 0.023 0.002 TYR A 986 PHE 0.026 0.002 PHE A 282 TRP 0.017 0.002 TRP A 161 HIS 0.007 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.28 (12433) covalent geometry : angle 0.90523 / 0.42 (17556) SS BOND : bond 0.08269 / 5.25 ( 6) SS BOND : angle 22.46349 / 14.02 ( 12) hydrogen bonds : bond 0.06832 / 4.77 ( 573) hydrogen bonds : angle 4.25927 / 3.11 ( 1520) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 137 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.6344 (mtt180) REVERT: A 149 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8326 (ttmt) REVERT: A 230 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7687 (mpt-90) REVERT: A 365 GLU cc_start: 0.8083 (tt0) cc_final: 0.7409 (pt0) REVERT: A 372 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6870 (tt0) REVERT: A 679 GLN cc_start: 0.5136 (tt0) cc_final: 0.4744 (tt0) REVERT: A 724 ILE cc_start: 0.7824 (mm) cc_final: 0.7536 (mp) outliers start: 14 outliers final: 8 residues processed: 110 average time/residue: 0.8939 time to fit residues: 104.2436 Evaluate side-chains 108 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 1048 ARG Chi-restraints excluded: chain A residue 1074 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 76 optimal weight: 0.1980 chunk 91 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.3845 r_free = 0.3845 target = 0.161897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.125091 restraints weight = 10441.339| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.24 r_work: 0.3168 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 12440 Z= 0.201 Angle : 0.986 31.471 17568 Z= 0.462 Chirality : 0.073 1.525 2020 Planarity : 0.004 0.034 1738 Dihedral : 21.413 171.547 3262 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.09 % Allowed : 10.05 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 1.25 (0.25), residues: 1097 helix: 1.68 (0.22), residues: 546 sheet: -0.10 (0.58), residues: 81 loop : 0.08 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 631 TYR 0.020 0.002 TYR A 986 PHE 0.019 0.002 PHE A 282 TRP 0.016 0.002 TRP A 161 HIS 0.005 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 (12433) covalent geometry : angle 0.79743 / 0.37 (17556) SS BOND : bond 0.08405 / 5.43 ( 6) SS BOND : angle 22.17347 / 13.75 ( 12) hydrogen bonds : bond 0.05992 / 4.24 ( 573) hydrogen bonds : angle 4.06293 / 2.98 ( 1520) Misc. bond : bond 0.00009 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 149 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8271 (mttp) REVERT: A 230 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7666 (mpt-90) REVERT: A 365 GLU cc_start: 0.8018 (tt0) cc_final: 0.7343 (pt0) REVERT: A 724 ILE cc_start: 0.7835 (mm) cc_final: 0.7544 (mp) outliers start: 10 outliers final: 4 residues processed: 108 average time/residue: 0.8835 time to fit residues: 101.1265 Evaluate side-chains 103 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 1048 ARG Chi-restraints excluded: chain A residue 1074 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 6 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 63 optimal weight: 0.5980 chunk 104 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 13 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 28 optimal weight: 0.6980 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.162151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.125233 restraints weight = 10379.419| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.25 r_work: 0.3167 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 12440 Z= 0.202 Angle : 0.972 31.150 17568 Z= 0.456 Chirality : 0.071 1.427 2020 Planarity : 0.004 0.035 1738 Dihedral : 21.367 170.669 3262 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.87 % Allowed : 10.60 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 1.32 (0.25), residues: 1097 helix: 1.76 (0.22), residues: 546 sheet: -0.04 (0.58), residues: 81 loop : 0.09 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 631 TYR 0.020 0.002 TYR A 986 PHE 0.020 0.002 PHE A 282 TRP 0.016 0.002 TRP A 161 HIS 0.004 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 (12433) covalent geometry : angle 0.78215 / 0.36 (17556) SS BOND : bond 0.08555 / 5.52 ( 6) SS BOND : angle 22.08504 / 13.70 ( 12) hydrogen bonds : bond 0.05936 / 4.19 ( 573) hydrogen bonds : angle 3.99168 / 2.93 ( 1520) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7877 (tp30) cc_final: 0.7660 (mm-30) REVERT: A 230 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7664 (mpt-90) REVERT: A 365 GLU cc_start: 0.8018 (tt0) cc_final: 0.7347 (pt0) REVERT: A 724 ILE cc_start: 0.7858 (mm) cc_final: 0.7566 (mp) outliers start: 8 outliers final: 5 residues processed: 106 average time/residue: 0.8670 time to fit residues: 97.6561 Evaluate side-chains 106 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 1048 ARG Chi-restraints excluded: chain A residue 1074 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 96 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.160481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.123132 restraints weight = 10381.722| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.25 r_work: 0.3142 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 12440 Z= 0.246 Angle : 1.010 31.758 17568 Z= 0.474 Chirality : 0.073 1.373 2020 Planarity : 0.005 0.036 1738 Dihedral : 21.404 170.710 3262 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.87 % Allowed : 10.71 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 1.26 (0.25), residues: 1097 helix: 1.69 (0.22), residues: 547 sheet: -0.07 (0.58), residues: 81 loop : 0.07 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 631 TYR 0.021 0.002 TYR A 986 PHE 0.023 0.002 PHE A 282 TRP 0.016 0.002 TRP A 387 HIS 0.006 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.23 (12433) covalent geometry : angle 0.82771 / 0.39 (17556) SS BOND : bond 0.08511 / 5.48 ( 6) SS BOND : angle 22.18208 / 13.78 ( 12) hydrogen bonds : bond 0.06289 / 4.41 ( 573) hydrogen bonds : angle 4.08773 / 3.00 ( 1520) Misc. bond : bond 0.00007 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7900 (tp30) cc_final: 0.7673 (mm-30) REVERT: A 230 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7673 (mpt-90) REVERT: A 365 GLU cc_start: 0.8048 (tt0) cc_final: 0.7349 (pt0) REVERT: A 724 ILE cc_start: 0.7829 (mm) cc_final: 0.7538 (mp) outliers start: 8 outliers final: 5 residues processed: 106 average time/residue: 0.8299 time to fit residues: 93.6122 Evaluate side-chains 105 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 1048 ARG Chi-restraints excluded: chain A residue 1074 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 85 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.163327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.126844 restraints weight = 10410.075| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.19 r_work: 0.3187 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 12440 Z= 0.183 Angle : 0.965 31.458 17568 Z= 0.453 Chirality : 0.069 1.362 2020 Planarity : 0.004 0.034 1738 Dihedral : 21.355 170.122 3262 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.55 % Allowed : 11.04 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % 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: 1.35 (0.25), residues: 1097 helix: 1.80 (0.22), residues: 546 sheet: -0.23 (0.56), residues: 86 loop : 0.12 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 631 TYR 0.018 0.002 TYR A 986 PHE 0.017 0.001 PHE A 282 TRP 0.020 0.002 TRP A 387 HIS 0.005 0.001 HIS A 574 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (12433) covalent geometry : angle 0.76292 / 0.36 (17556) SS BOND : bond 0.07935 / 4.92 ( 6) SS BOND : angle 22.60964 / 14.34 ( 12) hydrogen bonds : bond 0.05714 / 4.07 ( 573) hydrogen bonds : angle 3.97107 / 2.92 ( 1520) Misc. bond : bond 0.00018 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5413.40 seconds wall clock time: 92 minutes 45.22 seconds (5565.22 seconds total)