Starting phenix.real_space_refine on Wed Jul 30 14:29:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d2l_27142/07_2025/8d2l_27142.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2l_27142/07_2025/8d2l_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d2l_27142/07_2025/8d2l_27142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2l_27142/07_2025/8d2l_27142.map" model { file = "/net/cci-nas-00/data/ceres_data/8d2l_27142/07_2025/8d2l_27142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2l_27142/07_2025/8d2l_27142.cif" } resolution = 2.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'RNA': 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: 7.98, per 1000 atoms: 0.65 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: 3.53 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 6.06 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: 6.83 Time building geometry restraints manager: 4.18 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=" C3' DC X 3 " pdb=" O3' DC X 3 " ideal model delta sigma weight residual 1.422 1.506 -0.084 3.00e-02 1.11e+03 7.78e+00 bond pdb=" C1' DC T 21 " pdb=" N1 DC T 21 " ideal model delta sigma weight residual 1.490 1.556 -0.066 3.00e-02 1.11e+03 4.80e+00 bond pdb=" CA GLU A 33 " pdb=" CB GLU A 33 " ideal model delta sigma weight residual 1.530 1.567 -0.037 1.69e-02 3.50e+03 4.68e+00 bond pdb=" CA ASP A 53 " pdb=" CB ASP A 53 " ideal model delta sigma weight residual 1.530 1.565 -0.035 1.69e-02 3.50e+03 4.32e+00 bond pdb=" O5' DA D 31 " pdb=" C5' DA D 31 " ideal model delta sigma weight residual 1.423 1.364 0.059 3.00e-02 1.11e+03 3.80e+00 ... (remaining 12428 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.53: 17522 5.53 - 11.07: 31 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=" 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 angle pdb=" CA GLU A 33 " pdb=" CB GLU A 33 " pdb=" CG GLU A 33 " ideal model delta sigma weight residual 114.10 126.44 -12.34 2.00e+00 2.50e-01 3.81e+01 angle pdb=" N PRO A 892 " pdb=" CD PRO A 892 " pdb=" CG PRO A 892 " ideal model delta sigma weight residual 103.20 95.50 7.70 1.50e+00 4.44e-01 2.64e+01 angle pdb=" C CYS A 613 " pdb=" CA CYS A 613 " pdb=" CB CYS A 613 " ideal model delta sigma weight residual 110.85 118.09 -7.24 1.70e+00 3.46e-01 1.81e+01 ... (remaining 17551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.25: 6948 33.25 - 66.50: 521 66.50 - 99.75: 54 99.75 - 133.00: 3 133.00 - 166.25: 1 Dihedral angle restraints: 7527 sinusoidal: 4331 harmonic: 3196 Sorted by residual: dihedral pdb=" CB CYS A 578 " pdb=" SG CYS A 578 " pdb=" SG CYS A 610 " pdb=" CB CYS A 610 " ideal model delta sinusoidal sigma weight residual -86.00 -172.88 86.88 1 1.00e+01 1.00e-02 9.08e+01 dihedral pdb=" CA ASP A 590 " pdb=" C ASP A 590 " pdb=" N HIS A 591 " pdb=" CA HIS A 591 " ideal model delta harmonic sigma weight residual 180.00 147.74 32.26 0 5.00e+00 4.00e-02 4.16e+01 dihedral pdb=" CB CYS A 575 " pdb=" SG CYS A 575 " pdb=" SG CYS A 613 " pdb=" CB CYS A 613 " ideal model delta sinusoidal sigma weight residual -86.00 -141.31 55.31 1 1.00e+01 1.00e-02 4.14e+01 ... (remaining 7524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1725 0.066 - 0.132: 268 0.132 - 0.198: 19 0.198 - 0.264: 4 0.264 - 0.330: 4 Chirality restraints: 2020 Sorted by residual: chirality pdb=" CG LEU A 84 " pdb=" CB LEU A 84 " pdb=" CD1 LEU A 84 " pdb=" CD2 LEU A 84 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CB ILE A 24 " pdb=" CA ILE A 24 " pdb=" CG1 ILE A 24 " pdb=" CG2 ILE A 24 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C1' G B 30 " pdb=" O4' G B 30 " pdb=" C2' G B 30 " pdb=" N9 G B 30 " both_signs ideal model delta sigma weight residual False 2.46 2.18 0.28 2.00e-01 2.50e+01 1.89e+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: 1.400 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: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 39.150 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 12440 Z= 0.245 Angle : 1.060 35.157 17568 Z= 0.545 Chirality : 0.049 0.330 2020 Planarity : 0.007 0.073 1738 Dihedral : 19.795 166.247 5435 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (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 TRP 0.023 0.002 TRP A 721 HIS 0.004 0.001 HIS A 574 PHE 0.071 0.003 PHE A 363 TYR 0.018 0.003 TYR A 986 ARG 0.011 0.001 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.07234 ( 573) hydrogen bonds : angle 4.77559 ( 1520) SS BOND : bond 0.07162 ( 6) SS BOND : angle 22.79990 ( 12) covalent geometry : bond 0.00481 (12433) covalent geometry : angle 0.87697 (17556) Misc. bond : bond 0.00085 ( 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 : 1.029 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: 2.4379 time to fit residues: 302.0482 Evaluate side-chains 103 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 2.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.160238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.122523 restraints weight = 10037.188| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.15 r_work: 0.3138 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 12440 Z= 0.232 Angle : 0.860 28.640 17568 Z= 0.432 Chirality : 0.040 0.222 2020 Planarity : 0.005 0.049 1738 Dihedral : 20.892 159.951 3346 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.08 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.25), residues: 1097 helix: 1.20 (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 TRP 0.016 0.002 TRP A 161 HIS 0.006 0.001 HIS A 138 PHE 0.024 0.002 PHE A 282 TYR 0.021 0.002 TYR A 986 ARG 0.004 0.001 ARG A 923 Details of bonding type rmsd hydrogen bonds : bond 0.06361 ( 573) hydrogen bonds : angle 4.17855 ( 1520) SS BOND : bond 0.08392 ( 6) SS BOND : angle 22.14106 ( 12) covalent geometry : bond 0.00453 (12433) covalent geometry : angle 0.63620 (17556) Misc. bond : bond 0.00011 ( 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 115 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7145 (pm20) cc_final: 0.6838 (pp20) REVERT: A 230 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7670 (mpt-90) REVERT: A 724 ILE cc_start: 0.7823 (mm) cc_final: 0.7558 (mp) REVERT: A 864 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7717 (mp0) outliers start: 12 outliers final: 3 residues processed: 111 average time/residue: 2.0561 time to fit residues: 241.1148 Evaluate side-chains 98 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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 23 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 28 optimal weight: 0.0270 chunk 104 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.159205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.120776 restraints weight = 10225.892| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.18 r_work: 0.3123 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 12440 Z= 0.264 Angle : 0.880 32.271 17568 Z= 0.441 Chirality : 0.041 0.223 2020 Planarity : 0.005 0.036 1738 Dihedral : 20.885 158.461 3346 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.31 % Allowed : 7.87 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.25), residues: 1097 helix: 1.43 (0.22), residues: 546 sheet: -0.09 (0.58), residues: 81 loop : -0.02 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 161 HIS 0.007 0.001 HIS A 138 PHE 0.026 0.002 PHE A 282 TYR 0.022 0.002 TYR A 986 ARG 0.004 0.001 ARG A 137 Details of bonding type rmsd hydrogen bonds : bond 0.06557 ( 573) hydrogen bonds : angle 4.20130 ( 1520) SS BOND : bond 0.08425 ( 6) SS BOND : angle 22.19342 ( 12) covalent geometry : bond 0.00532 (12433) covalent geometry : angle 0.66148 (17556) Misc. bond : bond 0.00004 ( 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 109 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 1.106 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7180 (pm20) cc_final: 0.6757 (pp20) REVERT: A 230 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7684 (mpt-90) REVERT: A 724 ILE cc_start: 0.7847 (mm) cc_final: 0.7571 (mp) outliers start: 12 outliers final: 6 residues processed: 105 average time/residue: 1.9575 time to fit residues: 217.9685 Evaluate side-chains 102 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 41 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.159899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.121874 restraints weight = 10085.373| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.21 r_work: 0.3131 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 12440 Z= 0.232 Angle : 0.854 31.821 17568 Z= 0.427 Chirality : 0.040 0.220 2020 Planarity : 0.005 0.042 1738 Dihedral : 20.839 158.565 3346 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.42 % Allowed : 8.09 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.25), residues: 1097 helix: 1.56 (0.22), residues: 546 sheet: -0.11 (0.57), residues: 81 loop : 0.04 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 161 HIS 0.006 0.001 HIS A 138 PHE 0.023 0.002 PHE A 282 TYR 0.020 0.002 TYR A 986 ARG 0.007 0.001 ARG A 631 Details of bonding type rmsd hydrogen bonds : bond 0.06203 ( 573) hydrogen bonds : angle 4.11253 ( 1520) SS BOND : bond 0.08165 ( 6) SS BOND : angle 22.34826 ( 12) covalent geometry : bond 0.00460 (12433) covalent geometry : angle 0.62323 (17556) Misc. bond : bond 0.00003 ( 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 109 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 1.125 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7183 (pm20) cc_final: 0.6785 (pp20) REVERT: A 137 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.6384 (mtt180) REVERT: A 149 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8372 (ttmt) REVERT: A 230 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7720 (mpt-90) REVERT: A 365 GLU cc_start: 0.8124 (tt0) cc_final: 0.7474 (pt0) REVERT: A 372 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6834 (tt0) REVERT: A 724 ILE cc_start: 0.7816 (mm) cc_final: 0.7531 (mp) REVERT: A 864 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7700 (mp0) outliers start: 13 outliers final: 5 residues processed: 103 average time/residue: 1.9765 time to fit residues: 215.6916 Evaluate side-chains 105 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 53 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 104 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.159743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.121680 restraints weight = 10153.225| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.16 r_work: 0.3139 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 12440 Z= 0.226 Angle : 0.843 31.431 17568 Z= 0.422 Chirality : 0.039 0.219 2020 Planarity : 0.005 0.034 1738 Dihedral : 20.817 158.553 3346 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.31 % Allowed : 9.51 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.25), residues: 1097 helix: 1.64 (0.22), residues: 546 sheet: -0.12 (0.57), residues: 81 loop : 0.05 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 161 HIS 0.006 0.001 HIS A 138 PHE 0.022 0.002 PHE A 282 TYR 0.020 0.002 TYR A 986 ARG 0.006 0.000 ARG A 631 Details of bonding type rmsd hydrogen bonds : bond 0.06146 ( 573) hydrogen bonds : angle 4.08695 ( 1520) SS BOND : bond 0.08560 ( 6) SS BOND : angle 22.12034 ( 12) covalent geometry : bond 0.00441 (12433) covalent geometry : angle 0.61439 (17556) Misc. bond : bond 0.00003 ( 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 111 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7260 (pm20) cc_final: 0.6824 (pp20) REVERT: A 121 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7270 (mp0) REVERT: A 137 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.6384 (mtt180) REVERT: A 149 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8352 (ttmt) REVERT: A 230 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7711 (mpt-90) REVERT: A 365 GLU cc_start: 0.8117 (tt0) cc_final: 0.7448 (pt0) REVERT: A 372 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6823 (tt0) REVERT: A 724 ILE cc_start: 0.7829 (mm) cc_final: 0.7540 (mp) REVERT: A 864 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7660 (mp0) outliers start: 12 outliers final: 7 residues processed: 108 average time/residue: 1.8402 time to fit residues: 210.9842 Evaluate side-chains 109 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.159265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.121239 restraints weight = 10239.743| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.24 r_work: 0.3117 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 12440 Z= 0.251 Angle : 0.872 31.938 17568 Z= 0.437 Chirality : 0.041 0.220 2020 Planarity : 0.005 0.034 1738 Dihedral : 20.840 158.194 3346 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.53 % Allowed : 9.29 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.25), residues: 1097 helix: 1.59 (0.22), residues: 547 sheet: -0.11 (0.58), residues: 81 loop : 0.05 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 161 HIS 0.006 0.001 HIS A 138 PHE 0.024 0.002 PHE A 282 TYR 0.021 0.002 TYR A 986 ARG 0.004 0.001 ARG A 631 Details of bonding type rmsd hydrogen bonds : bond 0.06420 ( 573) hydrogen bonds : angle 4.15481 ( 1520) SS BOND : bond 0.08049 ( 6) SS BOND : angle 22.53928 ( 12) covalent geometry : bond 0.00505 (12433) covalent geometry : angle 0.64329 (17556) Misc. bond : bond 0.00014 ( 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 112 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7284 (pm20) cc_final: 0.6825 (pp20) REVERT: A 137 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.6354 (mtt180) REVERT: A 149 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8355 (ttmt) REVERT: A 230 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7735 (mpt-90) REVERT: A 365 GLU cc_start: 0.8122 (tt0) cc_final: 0.7440 (pt0) REVERT: A 372 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6821 (tt0) REVERT: A 724 ILE cc_start: 0.7867 (mm) cc_final: 0.7571 (mp) REVERT: A 864 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7671 (mp0) outliers start: 14 outliers final: 7 residues processed: 107 average time/residue: 1.9300 time to fit residues: 219.8061 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 : 1.322 ------------------------------------------------------------------------------- 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 97 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 115 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.159635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.121136 restraints weight = 10131.099| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.17 r_work: 0.3136 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 12440 Z= 0.240 Angle : 0.856 31.694 17568 Z= 0.429 Chirality : 0.040 0.221 2020 Planarity : 0.005 0.034 1738 Dihedral : 20.814 158.413 3346 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.42 % Allowed : 10.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.25), residues: 1097 helix: 1.64 (0.22), residues: 547 sheet: -0.11 (0.57), residues: 81 loop : 0.07 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 161 HIS 0.006 0.001 HIS A 138 PHE 0.023 0.002 PHE A 282 TYR 0.020 0.002 TYR A 986 ARG 0.004 0.001 ARG A 125 Details of bonding type rmsd hydrogen bonds : bond 0.06227 ( 573) hydrogen bonds : angle 4.11546 ( 1520) SS BOND : bond 0.08325 ( 6) SS BOND : angle 22.32678 ( 12) covalent geometry : bond 0.00475 (12433) covalent geometry : angle 0.62630 (17556) Misc. bond : bond 0.00012 ( 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 115 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 1.215 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7220 (pm20) cc_final: 0.6900 (pp20) REVERT: A 137 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.6368 (mtt180) REVERT: A 149 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8348 (ttmt) REVERT: A 230 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7719 (mpt-90) REVERT: A 365 GLU cc_start: 0.8085 (tt0) cc_final: 0.7425 (pt0) REVERT: A 372 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6815 (tt0) REVERT: A 724 ILE cc_start: 0.7880 (mm) cc_final: 0.7585 (mp) REVERT: A 864 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7640 (mp0) outliers start: 13 outliers final: 8 residues processed: 111 average time/residue: 2.9096 time to fit residues: 343.0103 Evaluate side-chains 112 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 2.082 ------------------------------------------------------------------------------- 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 11 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 chunk 118 optimal weight: 10.0000 chunk 50 optimal weight: 0.0470 chunk 93 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.162567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.125281 restraints weight = 10246.070| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.14 r_work: 0.3184 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 12440 Z= 0.171 Angle : 0.798 30.726 17568 Z= 0.399 Chirality : 0.037 0.225 2020 Planarity : 0.004 0.034 1738 Dihedral : 20.748 159.443 3346 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.98 % Allowed : 10.71 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.25), residues: 1097 helix: 1.86 (0.22), residues: 546 sheet: -0.11 (0.58), residues: 81 loop : 0.12 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 161 HIS 0.004 0.001 HIS A 138 PHE 0.017 0.001 PHE A 282 TYR 0.017 0.001 TYR A 986 ARG 0.004 0.000 ARG A 631 Details of bonding type rmsd hydrogen bonds : bond 0.05501 ( 573) hydrogen bonds : angle 3.94249 ( 1520) SS BOND : bond 0.08409 ( 6) SS BOND : angle 22.08384 ( 12) covalent geometry : bond 0.00304 (12433) covalent geometry : angle 0.55108 (17556) Misc. bond : bond 0.00005 ( 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 108 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 1.156 Fit side-chains revert: symmetry clash REVERT: A 137 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.6443 (mtt180) REVERT: A 230 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7706 (mpt-90) REVERT: A 365 GLU cc_start: 0.8033 (tt0) cc_final: 0.7399 (pt0) REVERT: A 724 ILE cc_start: 0.7814 (mm) cc_final: 0.7518 (mp) REVERT: A 864 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7591 (mp0) outliers start: 9 outliers final: 4 residues processed: 106 average time/residue: 2.0806 time to fit residues: 234.3063 Evaluate side-chains 101 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ARG 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 87 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.160635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.123075 restraints weight = 10177.870| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.18 r_work: 0.3132 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 12440 Z= 0.209 Angle : 0.828 31.314 17568 Z= 0.414 Chirality : 0.038 0.217 2020 Planarity : 0.004 0.035 1738 Dihedral : 20.774 158.900 3346 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.98 % Allowed : 11.04 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.25), residues: 1097 helix: 1.81 (0.22), residues: 547 sheet: -0.07 (0.58), residues: 81 loop : 0.08 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 387 HIS 0.005 0.001 HIS A 138 PHE 0.021 0.002 PHE A 282 TYR 0.020 0.002 TYR A 986 ARG 0.004 0.000 ARG A 631 Details of bonding type rmsd hydrogen bonds : bond 0.05926 ( 573) hydrogen bonds : angle 4.00941 ( 1520) SS BOND : bond 0.08420 ( 6) SS BOND : angle 22.13768 ( 12) covalent geometry : bond 0.00401 (12433) covalent geometry : angle 0.59210 (17556) Misc. bond : bond 0.00007 ( 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 105 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 1.141 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6798 (pp20) REVERT: A 137 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.6456 (mtt180) REVERT: A 230 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7720 (mpt-90) REVERT: A 365 GLU cc_start: 0.8088 (tt0) cc_final: 0.7472 (pt0) REVERT: A 724 ILE cc_start: 0.7888 (mm) cc_final: 0.7598 (mp) REVERT: A 864 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7604 (mp0) outliers start: 9 outliers final: 6 residues processed: 103 average time/residue: 2.7571 time to fit residues: 301.9529 Evaluate side-chains 105 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 137 ARG 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 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 10 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 chunk 109 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.160743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.122965 restraints weight = 10175.887| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.19 r_work: 0.3152 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 12440 Z= 0.207 Angle : 0.827 31.306 17568 Z= 0.413 Chirality : 0.038 0.219 2020 Planarity : 0.004 0.035 1738 Dihedral : 20.781 159.011 3346 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.09 % Allowed : 10.82 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.25), residues: 1097 helix: 1.79 (0.22), residues: 546 sheet: -0.06 (0.58), residues: 81 loop : 0.09 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 387 HIS 0.005 0.001 HIS A 138 PHE 0.021 0.002 PHE A 282 TYR 0.020 0.002 TYR A 986 ARG 0.003 0.000 ARG A 631 Details of bonding type rmsd hydrogen bonds : bond 0.05877 ( 573) hydrogen bonds : angle 4.01982 ( 1520) SS BOND : bond 0.08453 ( 6) SS BOND : angle 22.13101 ( 12) covalent geometry : bond 0.00395 (12433) covalent geometry : angle 0.59064 (17556) Misc. bond : bond 0.00009 ( 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 108 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6819 (pp20) REVERT: A 137 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.6468 (mtt180) REVERT: A 230 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7718 (mpt-90) REVERT: A 365 GLU cc_start: 0.8086 (tt0) cc_final: 0.7456 (pt0) REVERT: A 724 ILE cc_start: 0.7895 (mm) cc_final: 0.7607 (mp) REVERT: A 866 GLU cc_start: 0.7598 (mp0) cc_final: 0.6986 (mp0) outliers start: 10 outliers final: 7 residues processed: 105 average time/residue: 1.8370 time to fit residues: 205.8225 Evaluate side-chains 108 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 137 ARG 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 47 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 15 optimal weight: 0.1980 chunk 93 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 51 optimal weight: 0.2980 chunk 80 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 72 optimal weight: 0.0670 overall best weight: 3.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.159319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.121065 restraints weight = 10055.912| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.18 r_work: 0.3123 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1487 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= 0.257 Angle : 0.867 31.862 17568 Z= 0.434 Chirality : 0.041 0.219 2020 Planarity : 0.005 0.035 1738 Dihedral : 20.839 158.471 3346 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.20 % Allowed : 10.82 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.25), residues: 1097 helix: 1.68 (0.22), residues: 547 sheet: -0.08 (0.58), residues: 81 loop : 0.05 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 387 HIS 0.006 0.001 HIS A 138 PHE 0.025 0.002 PHE A 282 TYR 0.021 0.002 TYR A 986 ARG 0.004 0.001 ARG A 830 Details of bonding type rmsd hydrogen bonds : bond 0.06382 ( 573) hydrogen bonds : angle 4.13775 ( 1520) SS BOND : bond 0.08389 ( 6) SS BOND : angle 22.23636 ( 12) covalent geometry : bond 0.00514 (12433) covalent geometry : angle 0.64329 (17556) Misc. bond : bond 0.00025 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11961.97 seconds wall clock time: 211 minutes 9.74 seconds (12669.74 seconds total)