Starting phenix.real_space_refine on Sat Sep 12 00:20:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d2k_27141/09_2026/8d2k_27141.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2k_27141/09_2026/8d2k_27141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8d2k_27141/09_2026/8d2k_27141.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d2k_27141/09_2026/8d2k_27141.cif" model { file = "/net/cci-nas-00/data/ceres_data/8d2k_27141/09_2026/8d2k_27141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2k_27141/09_2026/8d2k_27141.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d2k_27141/09_2026/8d2k_27141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2k_27141/09_2026/8d2k_27141.map" } resolution = 2.43 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= 0.007 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 156 5.49 5 Mg 10 5.21 5 S 20 5.16 5 C 6940 2.51 5 N 2220 2.21 5 O 2949 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s 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: 12295 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: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 2189 Unusual residues: {'GTP': 1} Classifications: {'RNAv2': 101, 'undetermined': 1} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 8, 'rna3p_pur': 47, 'rna3p_pyr': 41} Link IDs: {'rna2p': 13, 'rna3p': 87, 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: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Chain: "B" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "X" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "T" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 3.04, per 1000 atoms: 0.25 Number of scatterers: 12295 At special positions: 0 Unit cell: (94.05, 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 156 15.00 Mg 10 11.99 O 2949 8.00 N 2220 7.00 C 6940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.19 Conformation dependent library (CDL) restraints added in 485.1 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 9 sheets defined 50.6% alpha, 9.8% beta 55 base pairs and 101 stacking pairs defined. Time for finding SS restraints: 1.66 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 153 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 406 Processing helix chain 'A' and resid 421 through 431 Processing helix chain 'A' and resid 441 through 456 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 553 Processing helix chain 'A' and resid 558 through 571 Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 602 through 604 No H-bonds generated for 'chain 'A' and resid 602 through 604' Processing helix chain 'A' and resid 611 through 618 Processing helix chain 'A' and resid 621 through 627 Processing helix chain 'A' and resid 633 through 643 Processing helix chain 'A' and resid 653 through 670 removed outlier: 3.653A pdb=" N ARG A 670 " --> pdb=" O ALA A 666 " (cutoff:3.500A) 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: 3.809A pdb=" N LEU A 745 " --> pdb=" O THR A 742 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP A 746 " --> pdb=" O LYS A 743 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ARG A 747 " --> pdb=" O ARG A 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 742 through 747' 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 1025 through 1033 removed outlier: 4.140A pdb=" N TYR A1032 " --> pdb=" O MET A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1071 removed outlier: 3.687A pdb=" N ALA A1061 " --> pdb=" O SER A1057 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A1069 " --> pdb=" O ARG A1065 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP A1070 " --> pdb=" O THR A1066 " (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: 6.914A pdb=" N TRP A 13 " --> pdb=" O SER A 512 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N VAL A 514 " --> pdb=" O TRP A 13 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 15 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N GLU A 516 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL A 17 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE A 24 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL A 43 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU A 26 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA A 41 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ALA A 28 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ILE A 39 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N SER A 30 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 824 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 301 through 304 Processing sheet with id=AA3, first strand: chain 'A' and resid 588 through 591 Processing sheet with id=AA4, first strand: chain 'A' and resid 846 through 849 Processing sheet with id=AA5, first strand: chain 'A' and resid 854 through 855 Processing sheet with id=AA6, first strand: chain 'A' and resid 899 through 900 Processing sheet with id=AA7, first strand: chain 'A' and resid 921 through 924 Processing sheet with id=AA8, first strand: chain 'A' and resid 949 through 956 removed outlier: 3.587A pdb=" N GLY A1004 " --> pdb=" O VAL A 939 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG A 941 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLN A1002 " --> pdb=" O ARG A 941 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1090 through 1093 removed outlier: 6.390A pdb=" N ARG A1048 " --> pdb=" O PHE A1043 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N PHE A1043 " --> pdb=" O ARG A1048 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASN A1050 " --> pdb=" O THR A1041 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU A1011 " --> pdb=" O ILE A1106 " (cutoff:3.500A) 434 hydrogen bonds defined for protein. 1257 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 141 hydrogen bonds 278 hydrogen bond angles 0 basepair planarities 55 basepair parallelities 101 stacking parallelities Total time for adding SS restraints: 3.12 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2214 1.33 - 1.45: 3804 1.45 - 1.57: 6203 1.57 - 1.69: 306 1.69 - 1.81: 28 Bond restraints: 12555 Sorted by residual: bond pdb=" C3' DA D 29 " pdb=" O3' DA D 29 " ideal model delta sigma weight residual 1.435 1.517 -0.082 1.30e-02 5.92e+03 4.00e+01 bond pdb=" C1' DC T 21 " pdb=" N1 DC T 21 " ideal model delta sigma weight residual 1.468 1.551 -0.083 1.40e-02 5.10e+03 3.54e+01 bond pdb=" C3' DA X 1 " pdb=" O3' DA X 1 " ideal model delta sigma weight residual 1.435 1.502 -0.067 1.30e-02 5.92e+03 2.68e+01 bond pdb=" C1' DC T 14 " pdb=" N1 DC T 14 " ideal model delta sigma weight residual 1.468 1.535 -0.067 1.40e-02 5.10e+03 2.29e+01 bond pdb=" N9 DA D 29 " pdb=" C4 DA D 29 " ideal model delta sigma weight residual 1.374 1.397 -0.023 6.00e-03 2.78e+04 1.43e+01 ... (remaining 12550 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 17177 2.59 - 5.19: 506 5.19 - 7.78: 51 7.78 - 10.37: 11 10.37 - 12.97: 2 Bond angle restraints: 17747 Sorted by residual: angle pdb=" C3' G B 97 " pdb=" O3' G B 97 " pdb=" P A B 98 " ideal model delta sigma weight residual 119.70 132.67 -12.97 1.20e+00 6.94e-01 1.17e+02 angle pdb=" O4' DC T 21 " pdb=" C1' DC T 21 " pdb=" N1 DC T 21 " ideal model delta sigma weight residual 108.00 113.24 -5.24 7.00e-01 2.04e+00 5.61e+01 angle pdb=" O4' DG T 17 " pdb=" C1' DG T 17 " pdb=" N9 DG T 17 " ideal model delta sigma weight residual 108.00 112.97 -4.97 7.00e-01 2.04e+00 5.05e+01 angle pdb=" C3' DA D 29 " pdb=" O3' DA D 29 " pdb=" P DT D 30 " ideal model delta sigma weight residual 119.70 127.99 -8.29 1.20e+00 6.94e-01 4.78e+01 angle pdb=" C3' C B 96 " pdb=" O3' C B 96 " pdb=" P G B 97 " ideal model delta sigma weight residual 119.70 127.44 -7.74 1.20e+00 6.94e-01 4.17e+01 ... (remaining 17742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.86: 6888 34.86 - 69.71: 568 69.71 - 104.57: 52 104.57 - 139.42: 1 139.42 - 174.28: 2 Dihedral angle restraints: 7511 sinusoidal: 4315 harmonic: 3196 Sorted by residual: dihedral pdb=" C4' C B 96 " pdb=" C3' C B 96 " pdb=" C2' C B 96 " pdb=" C1' C B 96 " ideal model delta sinusoidal sigma weight residual 36.34 -39.07 75.41 1 3.10e+00 1.04e-01 7.47e+02 dihedral pdb=" C4' G B 97 " pdb=" C3' G B 97 " pdb=" C2' G B 97 " pdb=" C1' G B 97 " ideal model delta sinusoidal sigma weight residual 36.34 -38.09 74.44 1 3.10e+00 1.04e-01 7.31e+02 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 36.35 -38.00 74.34 1 3.10e+00 1.04e-01 7.29e+02 ... (remaining 7508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1824 0.112 - 0.225: 147 0.225 - 0.337: 68 0.337 - 0.449: 5 0.449 - 0.562: 1 Chirality restraints: 2045 Sorted by residual: chirality pdb=" CG LEU A1075 " pdb=" CB LEU A1075 " pdb=" CD1 LEU A1075 " pdb=" CD2 LEU A1075 " both_signs ideal model delta sigma weight residual False -2.59 -2.03 -0.56 2.00e-01 2.50e+01 7.88e+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 -2.57 -0.40 2.00e-01 2.50e+01 4.02e+00 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 -2.55 -0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 2042 not shown) Planarity restraints: 1743 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1128 " -0.021 2.00e-02 2.50e+03 3.62e-02 3.27e+01 pdb=" CG TRP A1128 " 0.085 2.00e-02 2.50e+03 pdb=" CD1 TRP A1128 " -0.067 2.00e-02 2.50e+03 pdb=" CD2 TRP A1128 " 0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP A1128 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP A1128 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A1128 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1128 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1128 " -0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP A1128 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 97 " -0.020 2.00e-02 2.50e+03 3.05e-02 2.78e+01 pdb=" N9 G B 97 " -0.025 2.00e-02 2.50e+03 pdb=" C8 G B 97 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G B 97 " 0.013 2.00e-02 2.50e+03 pdb=" C5 G B 97 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B 97 " 0.056 2.00e-02 2.50e+03 pdb=" O6 G B 97 " -0.054 2.00e-02 2.50e+03 pdb=" N1 G B 97 " -0.013 2.00e-02 2.50e+03 pdb=" C2 G B 97 " 0.041 2.00e-02 2.50e+03 pdb=" N2 G B 97 " -0.034 2.00e-02 2.50e+03 pdb=" N3 G B 97 " 0.006 2.00e-02 2.50e+03 pdb=" C4 G B 97 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 88 " 0.044 2.00e-02 2.50e+03 3.33e-02 2.50e+01 pdb=" N1 C B 88 " -0.072 2.00e-02 2.50e+03 pdb=" C2 C B 88 " 0.035 2.00e-02 2.50e+03 pdb=" O2 C B 88 " -0.011 2.00e-02 2.50e+03 pdb=" N3 C B 88 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C B 88 " -0.028 2.00e-02 2.50e+03 pdb=" N4 C B 88 " 0.025 2.00e-02 2.50e+03 pdb=" C5 C B 88 " 0.012 2.00e-02 2.50e+03 pdb=" C6 C B 88 " -0.001 2.00e-02 2.50e+03 ... (remaining 1740 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 244 2.58 - 3.16: 9289 3.16 - 3.74: 23681 3.74 - 4.32: 32009 4.32 - 4.90: 47097 Nonbonded interactions: 112320 Sorted by model distance: nonbonded pdb=" OD2 ASP A 18 " pdb="MG MG A1203 " model vdw 2.000 2.170 nonbonded pdb=" OP1 U B 78 " pdb="MG MG B 204 " model vdw 2.002 2.170 nonbonded pdb=" OP2 DC T 14 " pdb="MG MG A1201 " model vdw 2.015 2.170 nonbonded pdb=" OP3 DT D 28 " pdb="MG MG A1203 " model vdw 2.025 2.170 nonbonded pdb=" OP2 DT D 28 " pdb="MG MG A1202 " model vdw 2.030 2.170 ... (remaining 112315 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: 2.890 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.020 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:7.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 12556 Z= 0.404 Angle : 1.015 12.968 17747 Z= 0.584 Chirality : 0.081 0.562 2045 Planarity : 0.008 0.081 1743 Dihedral : 21.204 174.276 5437 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: -0.18 (0.23), residues: 1097 helix: 0.16 (0.21), residues: 539 sheet: -0.31 (0.56), residues: 82 loop : -0.24 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 801 TYR 0.019 0.003 TYR A 986 PHE 0.072 0.004 PHE A 363 TRP 0.085 0.003 TRP A1128 HIS 0.007 0.002 HIS A 946 Details of bonding type rmsd/Z covalent geometry : bond 0.00666 / 0.40 (12555) covalent geometry : angle 1.01476 / 0.58 (17747) hydrogen bonds : bond 0.06600 / 4.34 ( 575) hydrogen bonds : angle 4.95389 / 3.63 ( 1535) 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 116 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.412 Fit side-chains REVERT: A 311 ASN cc_start: 0.7667 (m-40) cc_final: 0.7338 (m-40) REVERT: A 358 SER cc_start: 0.7626 (m) cc_final: 0.7420 (m) REVERT: A 720 ARG cc_start: 0.6997 (ttp-170) cc_final: 0.6494 (ttp-170) REVERT: A 723 ASP cc_start: 0.5636 (m-30) cc_final: 0.5329 (m-30) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.9289 time to fit residues: 114.2094 Evaluate side-chains 90 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN A 377 ASN A1084 GLN A1113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.170390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.133918 restraints weight = 11316.702| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.32 r_work: 0.3213 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 12556 Z= 0.254 Angle : 1.108 20.621 17747 Z= 0.481 Chirality : 0.110 1.490 2045 Planarity : 0.006 0.095 1743 Dihedral : 21.791 176.991 3348 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.31 % Allowed : 6.34 % Favored : 92.35 % 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: 0.65 (0.24), residues: 1097 helix: 1.00 (0.22), residues: 542 sheet: -0.25 (0.55), residues: 88 loop : 0.04 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 775 TYR 0.019 0.002 TYR A 986 PHE 0.023 0.002 PHE A 282 TRP 0.021 0.002 TRP A1128 HIS 0.009 0.001 HIS A 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.25 (12555) covalent geometry : angle 1.10753 / 0.48 (17747) hydrogen bonds : bond 0.05314 / 3.47 ( 575) hydrogen bonds : angle 4.30119 / 3.15 ( 1535) Misc. bond : bond 0.00083 / 0.05 ( 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 105 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.393 Fit side-chains REVERT: A 311 ASN cc_start: 0.7728 (m-40) cc_final: 0.7131 (m-40) REVERT: A 357 TYR cc_start: 0.7938 (m-80) cc_final: 0.7695 (m-80) REVERT: A 358 SER cc_start: 0.7701 (m) cc_final: 0.7451 (m) REVERT: A 548 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.5453 (mp0) REVERT: A 602 ARG cc_start: 0.7551 (mtp85) cc_final: 0.7293 (mtt-85) REVERT: A 720 ARG cc_start: 0.7179 (ttp-170) cc_final: 0.6438 (ttp-170) REVERT: A 723 ASP cc_start: 0.5923 (m-30) cc_final: 0.5622 (m-30) REVERT: A 1028 MET cc_start: 0.6915 (OUTLIER) cc_final: 0.6711 (ptp) outliers start: 12 outliers final: 5 residues processed: 100 average time/residue: 0.8781 time to fit residues: 93.3768 Evaluate side-chains 96 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 1028 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 122 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 74 optimal weight: 0.3980 chunk 52 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 119 optimal weight: 8.9990 overall best weight: 3.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN A 377 ASN A1084 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.167131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.128317 restraints weight = 11079.701| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.35 r_work: 0.3136 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 12556 Z= 0.269 Angle : 0.958 17.314 17747 Z= 0.434 Chirality : 0.081 0.995 2045 Planarity : 0.006 0.060 1743 Dihedral : 22.073 170.397 3348 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.42 % Allowed : 8.63 % Favored : 89.95 % 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: 0.78 (0.24), residues: 1097 helix: 1.18 (0.22), residues: 543 sheet: -0.65 (0.54), residues: 82 loop : 0.09 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 775 TYR 0.022 0.002 TYR A 986 PHE 0.024 0.002 PHE A 282 TRP 0.014 0.002 TRP A1128 HIS 0.011 0.002 HIS A 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.27 (12555) covalent geometry : angle 0.95833 / 0.43 (17747) hydrogen bonds : bond 0.05832 / 3.73 ( 575) hydrogen bonds : angle 4.25780 / 3.12 ( 1535) Misc. bond : bond 0.00170 / 0.11 ( 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 101 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.361 Fit side-chains REVERT: A 311 ASN cc_start: 0.7710 (m-40) cc_final: 0.7096 (m-40) REVERT: A 358 SER cc_start: 0.7825 (m) cc_final: 0.7599 (m) REVERT: A 548 GLU cc_start: 0.6351 (OUTLIER) cc_final: 0.5222 (mp0) REVERT: A 602 ARG cc_start: 0.7703 (mtp85) cc_final: 0.7445 (mtt-85) REVERT: A 654 ARG cc_start: 0.7677 (mtt-85) cc_final: 0.7293 (mtp-110) REVERT: A 720 ARG cc_start: 0.7115 (ttp-170) cc_final: 0.6376 (ttp-170) REVERT: A 724 ILE cc_start: 0.7340 (mm) cc_final: 0.7014 (mt) REVERT: A 747 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7448 (mtp85) REVERT: A 1025 ASP cc_start: 0.6477 (t0) cc_final: 0.6178 (t70) outliers start: 13 outliers final: 4 residues processed: 96 average time/residue: 0.8930 time to fit residues: 91.1040 Evaluate side-chains 92 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 747 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 94 optimal weight: 0.0870 chunk 109 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 53 optimal weight: 0.4980 chunk 18 optimal weight: 4.9990 overall best weight: 2.5164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN A 377 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.168387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.129686 restraints weight = 11084.204| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.27 r_work: 0.3168 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12556 Z= 0.218 Angle : 0.865 11.805 17747 Z= 0.395 Chirality : 0.072 0.836 2045 Planarity : 0.005 0.054 1743 Dihedral : 22.097 165.127 3348 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.53 % Allowed : 8.52 % Favored : 89.95 % 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: 0.96 (0.25), residues: 1097 helix: 1.31 (0.22), residues: 546 sheet: -0.51 (0.57), residues: 76 loop : 0.17 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 137 TYR 0.018 0.002 TYR A 986 PHE 0.020 0.002 PHE A 282 TRP 0.013 0.002 TRP A 161 HIS 0.005 0.001 HIS A 603 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.22 (12555) covalent geometry : angle 0.86526 / 0.39 (17747) hydrogen bonds : bond 0.05279 / 3.39 ( 575) hydrogen bonds : angle 4.11542 / 3.01 ( 1535) Misc. bond : bond 0.00089 / 0.06 ( 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 103 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.373 Fit side-chains REVERT: A 311 ASN cc_start: 0.7633 (m-40) cc_final: 0.7040 (m-40) REVERT: A 358 SER cc_start: 0.7818 (m) cc_final: 0.7592 (m) REVERT: A 548 GLU cc_start: 0.6158 (OUTLIER) cc_final: 0.5008 (mp0) REVERT: A 602 ARG cc_start: 0.7630 (mtp85) cc_final: 0.7309 (mtt-85) REVERT: A 654 ARG cc_start: 0.7677 (mtt-85) cc_final: 0.7252 (mtp-110) REVERT: A 720 ARG cc_start: 0.7167 (ttp-170) cc_final: 0.6433 (ttp-170) REVERT: A 724 ILE cc_start: 0.7289 (mm) cc_final: 0.7008 (mt) REVERT: A 747 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7370 (mtp85) REVERT: A 1025 ASP cc_start: 0.6376 (t0) cc_final: 0.6127 (t70) outliers start: 14 outliers final: 3 residues processed: 98 average time/residue: 0.8880 time to fit residues: 92.2882 Evaluate side-chains 90 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 747 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 44 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN A 377 ASN A1084 GLN A1113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.167781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.130681 restraints weight = 11353.696| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.26 r_work: 0.3185 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 12556 Z= 0.316 Angle : 0.950 11.506 17747 Z= 0.437 Chirality : 0.077 1.041 2045 Planarity : 0.006 0.055 1743 Dihedral : 22.197 174.407 3348 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.97 % Allowed : 8.63 % 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: 0.74 (0.24), residues: 1097 helix: 1.15 (0.22), residues: 544 sheet: -0.74 (0.54), residues: 82 loop : 0.09 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 165 TYR 0.024 0.003 TYR A 986 PHE 0.023 0.003 PHE A 282 TRP 0.014 0.002 TRP A 161 HIS 0.006 0.001 HIS A 749 Details of bonding type rmsd/Z covalent geometry : bond 0.00666 / 0.32 (12555) covalent geometry : angle 0.95019 / 0.44 (17747) hydrogen bonds : bond 0.06075 / 3.97 ( 575) hydrogen bonds : angle 4.29803 / 3.15 ( 1535) Misc. bond : bond 0.00101 / 0.06 ( 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 104 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 311 ASN cc_start: 0.7675 (m-40) cc_final: 0.7086 (m-40) REVERT: A 358 SER cc_start: 0.7836 (m) cc_final: 0.7626 (m) REVERT: A 602 ARG cc_start: 0.7695 (mtp85) cc_final: 0.7315 (mtt-85) REVERT: A 654 ARG cc_start: 0.7674 (mtt-85) cc_final: 0.7219 (mtp-110) REVERT: A 720 ARG cc_start: 0.7206 (ttp-170) cc_final: 0.6528 (ttp-170) REVERT: A 747 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7320 (mtp85) REVERT: A 1025 ASP cc_start: 0.6442 (t0) cc_final: 0.6118 (t0) outliers start: 18 outliers final: 8 residues processed: 99 average time/residue: 0.8862 time to fit residues: 92.9490 Evaluate side-chains 94 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 747 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 100 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN A 377 ASN A1084 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.167969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.129200 restraints weight = 11073.263| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.28 r_work: 0.3160 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12556 Z= 0.215 Angle : 0.853 10.959 17747 Z= 0.392 Chirality : 0.070 0.857 2045 Planarity : 0.005 0.052 1743 Dihedral : 22.071 176.853 3348 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.64 % Allowed : 9.40 % Favored : 88.96 % 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: 0.96 (0.25), residues: 1097 helix: 1.34 (0.22), residues: 546 sheet: -0.60 (0.57), residues: 76 loop : 0.16 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 165 TYR 0.019 0.002 TYR A 986 PHE 0.020 0.002 PHE A 282 TRP 0.013 0.002 TRP A 161 HIS 0.005 0.001 HIS A 749 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.22 (12555) covalent geometry : angle 0.85344 / 0.39 (17747) hydrogen bonds : bond 0.05339 / 3.43 ( 575) hydrogen bonds : angle 4.13607 / 3.03 ( 1535) Misc. bond : bond 0.00084 / 0.05 ( 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 101 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 137 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.6455 (mtt180) REVERT: A 311 ASN cc_start: 0.7666 (m-40) cc_final: 0.6961 (m-40) REVERT: A 358 SER cc_start: 0.7811 (m) cc_final: 0.7595 (m) REVERT: A 602 ARG cc_start: 0.7678 (mtp85) cc_final: 0.7358 (mtt-85) REVERT: A 654 ARG cc_start: 0.7664 (mtt-85) cc_final: 0.7208 (mtp-110) REVERT: A 662 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.7265 (mtpt) REVERT: A 720 ARG cc_start: 0.7150 (ttp-170) cc_final: 0.6423 (ttp-170) REVERT: A 747 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7304 (mtp85) REVERT: A 847 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7716 (mm-30) REVERT: A 1025 ASP cc_start: 0.6517 (t0) cc_final: 0.6201 (t70) REVERT: A 1028 MET cc_start: 0.7318 (ttp) cc_final: 0.6210 (tpt) outliers start: 15 outliers final: 7 residues processed: 98 average time/residue: 0.9069 time to fit residues: 94.3103 Evaluate side-chains 94 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 747 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 77 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 25 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN A 377 ASN A1084 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.165969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.128414 restraints weight = 11061.637| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.27 r_work: 0.3121 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 12556 Z= 0.306 Angle : 0.935 11.322 17747 Z= 0.429 Chirality : 0.075 0.977 2045 Planarity : 0.006 0.056 1743 Dihedral : 22.089 173.487 3348 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.08 % Allowed : 9.84 % 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 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: 0.78 (0.25), residues: 1097 helix: 1.17 (0.22), residues: 545 sheet: -0.77 (0.53), residues: 82 loop : 0.13 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 165 TYR 0.024 0.003 TYR A 986 PHE 0.022 0.003 PHE A 282 TRP 0.013 0.002 TRP A 13 HIS 0.006 0.001 HIS A 749 Details of bonding type rmsd/Z covalent geometry : bond 0.00646 / 0.31 (12555) covalent geometry : angle 0.93459 / 0.43 (17747) hydrogen bonds : bond 0.05999 / 3.89 ( 575) hydrogen bonds : angle 4.27342 / 3.13 ( 1535) Misc. bond : bond 0.00018 / 0.01 ( 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 104 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 137 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.6493 (mtt180) REVERT: A 201 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.7162 (pm20) REVERT: A 311 ASN cc_start: 0.7693 (m-40) cc_final: 0.7022 (m-40) REVERT: A 377 ASN cc_start: 0.5915 (m-40) cc_final: 0.5629 (m110) REVERT: A 602 ARG cc_start: 0.7753 (mtp85) cc_final: 0.7335 (mtt-85) REVERT: A 662 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.7285 (mtpt) REVERT: A 720 ARG cc_start: 0.7170 (ttp-170) cc_final: 0.6466 (ttp-170) REVERT: A 747 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7330 (mtp85) REVERT: A 847 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7772 (mm-30) REVERT: A 1028 MET cc_start: 0.7310 (ttp) cc_final: 0.6295 (tpt) REVERT: A 1048 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7717 (mtt90) outliers start: 19 outliers final: 9 residues processed: 101 average time/residue: 0.8539 time to fit residues: 91.5346 Evaluate side-chains 99 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 747 ARG Chi-restraints excluded: chain A residue 1048 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 36 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN A1084 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.166632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.127845 restraints weight = 11028.718| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.27 r_work: 0.3137 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12556 Z= 0.264 Angle : 0.900 11.017 17747 Z= 0.413 Chirality : 0.073 0.914 2045 Planarity : 0.006 0.054 1743 Dihedral : 22.051 171.188 3348 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.08 % Allowed : 10.27 % Favored : 87.65 % 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: 0.86 (0.25), residues: 1097 helix: 1.22 (0.22), residues: 546 sheet: -0.65 (0.56), residues: 76 loop : 0.16 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 659 TYR 0.022 0.002 TYR A 986 PHE 0.021 0.002 PHE A 282 TRP 0.013 0.002 TRP A 161 HIS 0.005 0.001 HIS A 749 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.26 (12555) covalent geometry : angle 0.90024 / 0.41 (17747) hydrogen bonds : bond 0.05715 / 3.67 ( 575) hydrogen bonds : angle 4.21904 / 3.08 ( 1535) Misc. bond : bond 0.00023 / 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 104 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 137 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.6459 (mtt180) REVERT: A 311 ASN cc_start: 0.7671 (m-40) cc_final: 0.7002 (m-40) REVERT: A 602 ARG cc_start: 0.7727 (mtp85) cc_final: 0.7312 (mtt-85) REVERT: A 662 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7275 (mtpt) REVERT: A 720 ARG cc_start: 0.7163 (ttp-170) cc_final: 0.6434 (ttp-170) REVERT: A 747 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7144 (mtp85) REVERT: A 1025 ASP cc_start: 0.6383 (t0) cc_final: 0.6085 (t70) REVERT: A 1028 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.7099 (ptp) REVERT: A 1048 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7645 (mtt90) outliers start: 19 outliers final: 8 residues processed: 99 average time/residue: 0.8973 time to fit residues: 94.3453 Evaluate side-chains 96 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 GLU Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 747 ARG Chi-restraints excluded: chain A residue 1028 MET Chi-restraints excluded: chain A residue 1048 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 32 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN A 377 ASN A1084 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.166634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.128240 restraints weight = 11020.106| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.29 r_work: 0.3135 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 12556 Z= 0.265 Angle : 0.897 10.705 17747 Z= 0.413 Chirality : 0.072 0.873 2045 Planarity : 0.006 0.055 1743 Dihedral : 22.028 168.892 3348 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.75 % Allowed : 11.15 % Favored : 87.10 % 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: 0.87 (0.25), residues: 1097 helix: 1.22 (0.22), residues: 546 sheet: -0.65 (0.56), residues: 76 loop : 0.17 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 659 TYR 0.022 0.002 TYR A 986 PHE 0.021 0.002 PHE A 282 TRP 0.013 0.002 TRP A 161 HIS 0.005 0.001 HIS A 848 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.26 (12555) covalent geometry : angle 0.89714 / 0.41 (17747) hydrogen bonds : bond 0.05747 / 3.69 ( 575) hydrogen bonds : angle 4.22703 / 3.08 ( 1535) Misc. bond : bond 0.00029 / 0.02 ( 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 98 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.467 Fit side-chains REVERT: A 137 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.6478 (mtt180) REVERT: A 311 ASN cc_start: 0.7672 (m-40) cc_final: 0.7003 (m-40) REVERT: A 377 ASN cc_start: 0.6116 (m-40) cc_final: 0.5846 (m110) REVERT: A 548 GLU cc_start: 0.6322 (OUTLIER) cc_final: 0.4876 (mp0) REVERT: A 602 ARG cc_start: 0.7729 (mtp85) cc_final: 0.7307 (mtt-85) REVERT: A 662 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7273 (mtpt) REVERT: A 720 ARG cc_start: 0.7188 (ttp-170) cc_final: 0.6460 (ttp-170) REVERT: A 747 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7144 (mtp85) REVERT: A 1025 ASP cc_start: 0.6437 (t0) cc_final: 0.6139 (t70) REVERT: A 1028 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.7030 (ptp) REVERT: A 1048 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7663 (mtt90) outliers start: 16 outliers final: 6 residues processed: 94 average time/residue: 0.9063 time to fit residues: 90.6236 Evaluate side-chains 93 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 655 ASP Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 747 ARG Chi-restraints excluded: chain A residue 1028 MET Chi-restraints excluded: chain A residue 1048 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 106 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 80 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 94 optimal weight: 0.2980 chunk 92 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.3930 r_free = 0.3930 target = 0.172149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.134447 restraints weight = 11231.266| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.25 r_work: 0.3231 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12556 Z= 0.142 Angle : 0.779 9.875 17747 Z= 0.357 Chirality : 0.063 0.712 2045 Planarity : 0.004 0.052 1743 Dihedral : 21.863 167.426 3348 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.87 % Allowed : 12.24 % Favored : 86.89 % 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: 1.22 (0.25), residues: 1097 helix: 1.56 (0.22), residues: 546 sheet: -0.64 (0.57), residues: 76 loop : 0.32 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 659 TYR 0.015 0.002 TYR A 986 PHE 0.014 0.001 PHE A 282 TRP 0.014 0.001 TRP A 161 HIS 0.004 0.001 HIS A 749 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 (12555) covalent geometry : angle 0.77884 / 0.36 (17747) hydrogen bonds : bond 0.04765 / 2.97 ( 575) hydrogen bonds : angle 3.98346 / 2.91 ( 1535) Misc. bond : bond 0.00069 / 0.04 ( 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 96 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 137 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.6332 (mtt180) REVERT: A 217 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7631 (mp0) REVERT: A 311 ASN cc_start: 0.7673 (m-40) cc_final: 0.7015 (m-40) REVERT: A 602 ARG cc_start: 0.7619 (mtp85) cc_final: 0.7320 (mtt-85) REVERT: A 654 ARG cc_start: 0.7681 (mtt-85) cc_final: 0.7061 (mtp-110) REVERT: A 662 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7289 (mtpt) REVERT: A 747 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7045 (mtp85) REVERT: A 880 ARG cc_start: 0.6705 (ptt90) cc_final: 0.6457 (ptt90) REVERT: A 999 ASP cc_start: 0.7745 (t0) cc_final: 0.7490 (t0) REVERT: A 1028 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6092 (tpt) REVERT: A 1048 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7584 (mtt90) outliers start: 8 outliers final: 2 residues processed: 94 average time/residue: 0.8843 time to fit residues: 88.6025 Evaluate side-chains 90 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 407 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 662 LYS Chi-restraints excluded: chain A residue 747 ARG Chi-restraints excluded: chain A residue 1028 MET Chi-restraints excluded: chain A residue 1048 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 12 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 63 optimal weight: 0.4980 chunk 3 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN A 377 ASN A1084 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.166337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.127239 restraints weight = 10945.294| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.28 r_work: 0.3148 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 12556 Z= 0.310 Angle : 0.927 10.322 17747 Z= 0.426 Chirality : 0.073 0.814 2045 Planarity : 0.006 0.055 1743 Dihedral : 21.990 166.683 3348 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.09 % Allowed : 12.57 % Favored : 86.34 % 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: 0.95 (0.25), residues: 1097 helix: 1.28 (0.22), residues: 546 sheet: -0.56 (0.56), residues: 76 loop : 0.22 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 165 TYR 0.025 0.003 TYR A 986 PHE 0.022 0.003 PHE A 282 TRP 0.013 0.002 TRP A 161 HIS 0.006 0.001 HIS A 749 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.31 (12555) covalent geometry : angle 0.92662 / 0.43 (17747) hydrogen bonds : bond 0.05976 / 3.86 ( 575) hydrogen bonds : angle 4.22950 / 3.09 ( 1535) Misc. bond : bond 0.00042 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4908.08 seconds wall clock time: 84 minutes 22.64 seconds (5062.64 seconds total)