Starting phenix.real_space_refine on Wed Jul 30 15:31:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d2k_27141/07_2025/8d2k_27141.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2k_27141/07_2025/8d2k_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d2k_27141/07_2025/8d2k_27141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2k_27141/07_2025/8d2k_27141.map" model { file = "/net/cci-nas-00/data/ceres_data/8d2k_27141/07_2025/8d2k_27141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2k_27141/07_2025/8d2k_27141.cif" } resolution = 2.43 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= 0.007 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'RNA': 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: 8.30, per 1000 atoms: 0.68 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: 3.33 Conformation dependent library (CDL) restraints added in 1.2 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 9 sheets defined 50.6% alpha, 9.8% beta 55 base pairs and 101 stacking pairs defined. Time for finding SS restraints: 5.15 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: 6.91 Time building geometry restraints manager: 3.94 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' G B 97 " pdb=" O3' G B 97 " ideal model delta sigma weight residual 1.427 1.480 -0.053 1.50e-02 4.44e+03 1.25e+01 bond pdb=" C3' DA D 29 " pdb=" O3' DA D 29 " ideal model delta sigma weight residual 1.422 1.517 -0.095 3.00e-02 1.11e+03 1.01e+01 bond pdb=" O3' G B 97 " pdb=" P A B 98 " ideal model delta sigma weight residual 1.607 1.650 -0.043 1.50e-02 4.44e+03 8.35e+00 bond pdb=" C3' DA X 1 " pdb=" O3' DA X 1 " ideal model delta sigma weight residual 1.422 1.502 -0.080 3.00e-02 1.11e+03 7.18e+00 bond pdb=" CB TRP A1128 " pdb=" CG TRP A1128 " ideal model delta sigma weight residual 1.498 1.428 0.070 3.10e-02 1.04e+03 5.16e+00 ... (remaining 12550 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 17324 2.49 - 4.99: 365 4.99 - 7.48: 43 7.48 - 9.97: 13 9.97 - 12.47: 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 120.20 132.67 -12.47 1.50e+00 4.44e-01 6.91e+01 angle pdb=" C3' DA D 29 " pdb=" O3' DA D 29 " pdb=" P DT D 30 " ideal model delta sigma weight residual 120.20 127.99 -7.79 1.50e+00 4.44e-01 2.70e+01 angle pdb=" N GLU A 548 " pdb=" CA GLU A 548 " pdb=" CB GLU A 548 " ideal model delta sigma weight residual 110.28 118.15 -7.87 1.55e+00 4.16e-01 2.58e+01 angle pdb=" C3' C B 96 " pdb=" O3' C B 96 " pdb=" P G B 97 " ideal model delta sigma weight residual 120.20 127.44 -7.24 1.50e+00 4.44e-01 2.33e+01 angle pdb=" O3' G B 97 " pdb=" C3' G B 97 " pdb=" C2' G B 97 " ideal model delta sigma weight residual 109.50 116.42 -6.92 1.50e+00 4.44e-01 2.13e+01 ... (remaining 17742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.86: 7052 34.86 - 69.71: 493 69.71 - 104.57: 46 104.57 - 139.42: 2 139.42 - 174.28: 2 Dihedral angle restraints: 7595 sinusoidal: 4399 harmonic: 3196 Sorted by residual: dihedral pdb=" O4' A B 98 " pdb=" C2' A B 98 " pdb=" C1' A B 98 " pdb=" C3' A B 98 " ideal model delta sinusoidal sigma weight residual 25.00 -13.57 38.57 1 8.00e+00 1.56e-02 3.27e+01 dihedral pdb=" C4' A B 98 " pdb=" O4' A B 98 " pdb=" C1' A B 98 " pdb=" C2' A B 98 " ideal model delta sinusoidal sigma weight residual 3.00 -30.59 33.59 1 8.00e+00 1.56e-02 2.50e+01 dihedral pdb=" C8 GTP B 1 " pdb=" C1' GTP B 1 " pdb=" N9 GTP B 1 " pdb=" O4' GTP B 1 " ideal model delta sinusoidal sigma weight residual 104.59 18.39 86.20 1 2.00e+01 2.50e-03 2.24e+01 ... (remaining 7592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1960 0.112 - 0.225: 77 0.225 - 0.337: 7 0.337 - 0.449: 0 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=" CG LEU A 399 " pdb=" CB LEU A 399 " pdb=" CD1 LEU A 399 " pdb=" CD2 LEU A 399 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CB ILE A 681 " pdb=" CA ILE A 681 " pdb=" CG1 ILE A 681 " pdb=" CG2 ILE A 681 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.28e+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: 2.640 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 37.610 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 12556 Z= 0.288 Angle : 0.908 12.468 17747 Z= 0.481 Chirality : 0.054 0.562 2045 Planarity : 0.008 0.081 1743 Dihedral : 20.179 174.276 5521 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 (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: -0.18 (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 TRP 0.085 0.003 TRP A1128 HIS 0.007 0.002 HIS A 946 PHE 0.072 0.004 PHE A 363 TYR 0.019 0.003 TYR A 986 ARG 0.017 0.001 ARG A 801 Details of bonding type rmsd hydrogen bonds : bond 0.06600 ( 575) hydrogen bonds : angle 4.95389 ( 1535) covalent geometry : bond 0.00625 (12555) covalent geometry : angle 0.90822 (17747) 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 116 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.328 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: 1.9487 time to fit residues: 239.9011 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 : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 0.1980 chunk 63 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3890 r_free = 0.3890 target = 0.168110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.132400 restraints weight = 11187.067| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.34 r_work: 0.3178 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12556 Z= 0.255 Angle : 0.678 8.857 17747 Z= 0.355 Chirality : 0.043 0.286 2045 Planarity : 0.006 0.085 1743 Dihedral : 21.590 177.525 3432 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.31 % Allowed : 6.78 % Favored : 91.91 % 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: 0.56 (0.24), residues: 1097 helix: 0.92 (0.22), residues: 542 sheet: -0.39 (0.54), residues: 87 loop : 0.03 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1128 HIS 0.007 0.001 HIS A 603 PHE 0.023 0.002 PHE A 282 TYR 0.022 0.002 TYR A 986 ARG 0.011 0.001 ARG A 775 Details of bonding type rmsd hydrogen bonds : bond 0.05648 ( 575) hydrogen bonds : angle 4.32332 ( 1535) covalent geometry : bond 0.00542 (12555) covalent geometry : angle 0.67841 (17747) Misc. bond : bond 0.00053 ( 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 102 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 1.073 Fit side-chains REVERT: A 311 ASN cc_start: 0.7751 (m-40) cc_final: 0.7182 (m-40) REVERT: A 358 SER cc_start: 0.7723 (m) cc_final: 0.7488 (m) REVERT: A 548 GLU cc_start: 0.6470 (OUTLIER) cc_final: 0.5415 (mp0) REVERT: A 602 ARG cc_start: 0.7627 (mtp85) cc_final: 0.7082 (mtm-85) REVERT: A 650 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7565 (ptm) REVERT: A 720 ARG cc_start: 0.7247 (ttp-170) cc_final: 0.6515 (ttp-170) REVERT: A 724 ILE cc_start: 0.7251 (mm) cc_final: 0.6927 (mt) REVERT: A 1084 GLN cc_start: 0.6840 (pt0) cc_final: 0.6391 (mp10) outliers start: 12 outliers final: 4 residues processed: 97 average time/residue: 1.8762 time to fit residues: 193.7999 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 : 1.041 ------------------------------------------------------------------------------- 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 650 MET Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 731 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 106 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 45 optimal weight: 0.0010 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 377 ASN A1100 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.168709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.130278 restraints weight = 11072.584| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.23 r_work: 0.3170 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12556 Z= 0.163 Angle : 0.578 9.100 17747 Z= 0.303 Chirality : 0.039 0.241 2045 Planarity : 0.005 0.051 1743 Dihedral : 21.400 173.204 3432 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % 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: 0.99 (0.25), residues: 1097 helix: 1.37 (0.22), residues: 544 sheet: -0.34 (0.59), residues: 76 loop : 0.13 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 161 HIS 0.007 0.001 HIS A 603 PHE 0.019 0.002 PHE A 282 TYR 0.016 0.002 TYR A 986 ARG 0.006 0.000 ARG A 775 Details of bonding type rmsd hydrogen bonds : bond 0.04746 ( 575) hydrogen bonds : angle 4.05507 ( 1535) covalent geometry : bond 0.00343 (12555) covalent geometry : angle 0.57827 (17747) Misc. bond : bond 0.00045 ( 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 103 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 311 ASN cc_start: 0.7627 (m-40) cc_final: 0.6962 (m-40) REVERT: A 358 SER cc_start: 0.7753 (m) cc_final: 0.7504 (m) REVERT: A 602 ARG cc_start: 0.7645 (mtp85) cc_final: 0.7357 (mtt-85) REVERT: A 662 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.7205 (mtpt) REVERT: A 720 ARG cc_start: 0.7197 (ttp-170) cc_final: 0.6440 (ttp-170) REVERT: A 723 ASP cc_start: 0.6334 (m-30) cc_final: 0.5832 (m-30) REVERT: A 747 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7115 (mtp85) outliers start: 13 outliers final: 5 residues processed: 97 average time/residue: 1.9953 time to fit residues: 205.3535 Evaluate side-chains 91 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 342 ASP 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 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 28 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 377 ASN A1084 GLN A1100 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.166880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.128481 restraints weight = 10976.189| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.31 r_work: 0.3131 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12556 Z= 0.213 Angle : 0.620 9.058 17747 Z= 0.324 Chirality : 0.041 0.229 2045 Planarity : 0.005 0.053 1743 Dihedral : 21.434 170.970 3432 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.86 % Allowed : 8.63 % Favored : 89.51 % 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: 1.04 (0.25), residues: 1097 helix: 1.41 (0.22), residues: 546 sheet: -0.44 (0.57), residues: 76 loop : 0.16 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 161 HIS 0.005 0.001 HIS A 603 PHE 0.021 0.002 PHE A 282 TYR 0.020 0.002 TYR A 986 ARG 0.007 0.001 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.05175 ( 575) hydrogen bonds : angle 4.11255 ( 1535) covalent geometry : bond 0.00453 (12555) covalent geometry : angle 0.62025 (17747) Misc. bond : bond 0.00033 ( 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 105 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 1.383 Fit side-chains REVERT: A 217 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7718 (mp0) REVERT: A 311 ASN cc_start: 0.7599 (m-40) cc_final: 0.6921 (m-40) REVERT: A 358 SER cc_start: 0.7829 (m) cc_final: 0.7604 (m) REVERT: A 548 GLU cc_start: 0.6225 (OUTLIER) cc_final: 0.5084 (mp0) REVERT: A 602 ARG cc_start: 0.7610 (mtp85) cc_final: 0.7239 (mtt-85) REVERT: A 662 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.7246 (mtpt) REVERT: A 720 ARG cc_start: 0.7219 (ttp-170) cc_final: 0.6471 (ttp-170) REVERT: A 747 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7307 (mtp85) REVERT: A 1025 ASP cc_start: 0.6460 (t0) cc_final: 0.6183 (t70) outliers start: 17 outliers final: 4 residues processed: 101 average time/residue: 2.8720 time to fit residues: 309.7896 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 : 1.280 ------------------------------------------------------------------------------- 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 662 LYS 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 67 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 377 ASN A1084 GLN ** A1100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.164975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.126510 restraints weight = 10971.814| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.22 r_work: 0.3113 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12556 Z= 0.292 Angle : 0.697 9.343 17747 Z= 0.363 Chirality : 0.045 0.236 2045 Planarity : 0.006 0.063 1743 Dihedral : 21.538 171.319 3432 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % 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 (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: 0.84 (0.25), residues: 1097 helix: 1.21 (0.22), residues: 546 sheet: -0.71 (0.54), residues: 82 loop : 0.17 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 13 HIS 0.005 0.001 HIS A 749 PHE 0.023 0.002 PHE A 282 TYR 0.023 0.002 TYR A 986 ARG 0.007 0.001 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.05762 ( 575) hydrogen bonds : angle 4.27398 ( 1535) covalent geometry : bond 0.00627 (12555) covalent geometry : angle 0.69732 (17747) Misc. bond : bond 0.00029 ( 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 110 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 311 ASN cc_start: 0.7660 (m-40) cc_final: 0.6964 (m-40) REVERT: A 358 SER cc_start: 0.7857 (m) cc_final: 0.7640 (m) REVERT: A 602 ARG cc_start: 0.7744 (mtp85) cc_final: 0.7355 (mtt-85) REVERT: A 662 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.7242 (mtpt) REVERT: A 720 ARG cc_start: 0.7150 (ttp-170) cc_final: 0.6445 (ttp-170) REVERT: A 747 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7156 (mtp85) REVERT: A 847 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7699 (mm-30) REVERT: A 1025 ASP cc_start: 0.6524 (t0) cc_final: 0.6245 (t70) outliers start: 18 outliers final: 6 residues processed: 106 average time/residue: 1.9567 time to fit residues: 220.0730 Evaluate side-chains 95 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 94 optimal weight: 0.3980 chunk 121 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN A1084 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.167536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.129128 restraints weight = 11160.331| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.34 r_work: 0.3144 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12556 Z= 0.180 Angle : 0.595 9.268 17747 Z= 0.310 Chirality : 0.039 0.231 2045 Planarity : 0.005 0.049 1743 Dihedral : 21.439 167.171 3432 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.86 % Allowed : 9.62 % 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: 1.13 (0.25), residues: 1097 helix: 1.47 (0.22), residues: 547 sheet: -0.54 (0.57), residues: 76 loop : 0.26 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 161 HIS 0.004 0.001 HIS A 749 PHE 0.019 0.002 PHE A 282 TYR 0.017 0.002 TYR A 986 ARG 0.005 0.000 ARG A 659 Details of bonding type rmsd hydrogen bonds : bond 0.04815 ( 575) hydrogen bonds : angle 4.06167 ( 1535) covalent geometry : bond 0.00381 (12555) covalent geometry : angle 0.59471 (17747) Misc. bond : bond 0.00047 ( 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 108 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 1.160 Fit side-chains revert: symmetry clash REVERT: A 137 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.6389 (mtt180) REVERT: A 217 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7720 (mp0) REVERT: A 311 ASN cc_start: 0.7634 (m-40) cc_final: 0.6964 (m-40) REVERT: A 358 SER cc_start: 0.7773 (m) cc_final: 0.7542 (m) REVERT: A 602 ARG cc_start: 0.7646 (mtp85) cc_final: 0.7234 (mtt-85) REVERT: A 662 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.7169 (mtpt) REVERT: A 747 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7070 (mtp85) REVERT: A 839 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8607 (mt-10) REVERT: A 847 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7689 (mm-30) REVERT: A 999 ASP cc_start: 0.7726 (t0) cc_final: 0.7499 (t0) REVERT: A 1011 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8187 (tt0) REVERT: A 1025 ASP cc_start: 0.6448 (t0) cc_final: 0.6235 (t70) outliers start: 17 outliers final: 6 residues processed: 104 average time/residue: 2.1363 time to fit residues: 235.0110 Evaluate side-chains 101 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 1.834 ------------------------------------------------------------------------------- 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 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 839 GLU Chi-restraints excluded: chain A residue 1011 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.0670 chunk 39 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 overall best weight: 5.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN A1084 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.164230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.125420 restraints weight = 11048.311| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.29 r_work: 0.3099 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 12556 Z= 0.346 Angle : 0.745 9.358 17747 Z= 0.386 Chirality : 0.048 0.238 2045 Planarity : 0.007 0.059 1743 Dihedral : 21.572 170.930 3432 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.86 % Allowed : 10.27 % Favored : 87.87 % 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 (0.24), residues: 1097 helix: 1.12 (0.22), residues: 546 sheet: -0.71 (0.53), residues: 82 loop : 0.15 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 13 HIS 0.006 0.001 HIS A 749 PHE 0.023 0.003 PHE A 282 TYR 0.025 0.003 TYR A 986 ARG 0.010 0.001 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.06031 ( 575) hydrogen bonds : angle 4.33916 ( 1535) covalent geometry : bond 0.00746 (12555) covalent geometry : angle 0.74528 (17747) Misc. bond : bond 0.00025 ( 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 101 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 2.163 Fit side-chains REVERT: A 137 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.6512 (mtt180) REVERT: A 311 ASN cc_start: 0.7671 (m-40) cc_final: 0.7033 (m-40) REVERT: A 358 SER cc_start: 0.7857 (m) cc_final: 0.7643 (m) REVERT: A 548 GLU cc_start: 0.6409 (OUTLIER) cc_final: 0.5121 (mp0) REVERT: A 602 ARG cc_start: 0.7770 (mtp85) cc_final: 0.7396 (mtt-85) REVERT: A 662 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7233 (mtpt) REVERT: A 747 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7157 (mtp85) REVERT: A 847 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7769 (mm-30) REVERT: A 1025 ASP cc_start: 0.6461 (t0) cc_final: 0.6198 (t70) outliers start: 17 outliers final: 6 residues processed: 97 average time/residue: 2.6228 time to fit residues: 271.4683 Evaluate side-chains 93 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN A1084 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.170003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.131421 restraints weight = 11147.271| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.24 r_work: 0.3199 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 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 : 0.003 0.039 12556 Z= 0.131 Angle : 0.559 9.109 17747 Z= 0.291 Chirality : 0.037 0.229 2045 Planarity : 0.004 0.050 1743 Dihedral : 21.395 163.946 3432 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.09 % Allowed : 11.48 % Favored : 87.43 % 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: 1.26 (0.25), residues: 1097 helix: 1.59 (0.22), residues: 546 sheet: -0.52 (0.57), residues: 76 loop : 0.31 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 161 HIS 0.004 0.001 HIS A 749 PHE 0.017 0.001 PHE A 282 TYR 0.014 0.002 TYR A 986 ARG 0.006 0.000 ARG A 659 Details of bonding type rmsd hydrogen bonds : bond 0.04317 ( 575) hydrogen bonds : angle 3.96713 ( 1535) covalent geometry : bond 0.00276 (12555) covalent geometry : angle 0.55899 (17747) Misc. bond : bond 0.00063 ( 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 99 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 137 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.6330 (mtt180) REVERT: A 217 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7624 (mp0) REVERT: A 311 ASN cc_start: 0.7631 (m-40) cc_final: 0.6898 (m-40) REVERT: A 358 SER cc_start: 0.7771 (m) cc_final: 0.7550 (m) REVERT: A 377 ASN cc_start: 0.6052 (m-40) cc_final: 0.5726 (m-40) REVERT: A 602 ARG cc_start: 0.7606 (mtp85) cc_final: 0.7248 (mtt-85) REVERT: A 662 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.7163 (mtpt) REVERT: A 720 ARG cc_start: 0.7239 (ttp-170) cc_final: 0.6502 (ttp-170) REVERT: A 747 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7007 (mtp85) REVERT: A 847 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7619 (mm-30) REVERT: A 1025 ASP cc_start: 0.6353 (t0) cc_final: 0.6148 (t70) REVERT: A 1028 MET cc_start: 0.7225 (ttp) cc_final: 0.5913 (tpt) outliers start: 10 outliers final: 2 residues processed: 95 average time/residue: 1.8701 time to fit residues: 189.4961 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 : 1.182 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 10 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 8 optimal weight: 0.0980 chunk 27 optimal weight: 7.9990 chunk 34 optimal weight: 0.0770 chunk 119 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3896 r_free = 0.3896 target = 0.169024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.130214 restraints weight = 11098.549| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.29 r_work: 0.3174 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 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 : 0.003 0.038 12556 Z= 0.152 Angle : 0.564 8.974 17747 Z= 0.294 Chirality : 0.038 0.229 2045 Planarity : 0.004 0.050 1743 Dihedral : 21.331 163.878 3432 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.87 % Allowed : 12.02 % 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 (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: 1.66 (0.22), residues: 547 sheet: -0.42 (0.57), residues: 76 loop : 0.34 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 161 HIS 0.004 0.001 HIS A 749 PHE 0.017 0.002 PHE A 282 TYR 0.017 0.002 TYR A 986 ARG 0.005 0.000 ARG A 659 Details of bonding type rmsd hydrogen bonds : bond 0.04412 ( 575) hydrogen bonds : angle 3.92418 ( 1535) covalent geometry : bond 0.00321 (12555) covalent geometry : angle 0.56373 (17747) Misc. bond : bond 0.00049 ( 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 95 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 137 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.6380 (mtt180) REVERT: A 217 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7610 (mp0) REVERT: A 311 ASN cc_start: 0.7631 (m-40) cc_final: 0.6936 (m-40) REVERT: A 358 SER cc_start: 0.7720 (m) cc_final: 0.7504 (m) REVERT: A 602 ARG cc_start: 0.7621 (mtp85) cc_final: 0.7279 (mtt-85) REVERT: A 720 ARG cc_start: 0.7216 (ttp-170) cc_final: 0.6490 (ttp-170) REVERT: A 747 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7015 (mtp85) REVERT: A 847 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7632 (mm-30) REVERT: A 1025 ASP cc_start: 0.6316 (t0) cc_final: 0.6070 (t70) REVERT: A 1028 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.5846 (tpt) outliers start: 8 outliers final: 2 residues processed: 91 average time/residue: 1.8606 time to fit residues: 180.4337 Evaluate side-chains 92 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 747 ARG Chi-restraints excluded: chain A residue 1028 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 11 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 116 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN A1084 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.166274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.127696 restraints weight = 10919.998| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.23 r_work: 0.3128 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12556 Z= 0.246 Angle : 0.648 9.068 17747 Z= 0.337 Chirality : 0.042 0.229 2045 Planarity : 0.006 0.050 1743 Dihedral : 21.452 166.055 3432 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.77 % Allowed : 12.46 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.46 (0.22), residues: 547 sheet: -0.37 (0.57), residues: 76 loop : 0.29 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1128 HIS 0.004 0.001 HIS A 749 PHE 0.021 0.002 PHE A 282 TYR 0.021 0.002 TYR A 986 ARG 0.006 0.001 ARG A 659 Details of bonding type rmsd hydrogen bonds : bond 0.05199 ( 575) hydrogen bonds : angle 4.11005 ( 1535) covalent geometry : bond 0.00527 (12555) covalent geometry : angle 0.64764 (17747) Misc. bond : bond 0.00035 ( 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 92 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 1.214 Fit side-chains revert: symmetry clash REVERT: A 137 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.6447 (mtt180) REVERT: A 217 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7671 (mp0) REVERT: A 311 ASN cc_start: 0.7607 (m-40) cc_final: 0.6919 (m-40) REVERT: A 358 SER cc_start: 0.7834 (m) cc_final: 0.7617 (m) REVERT: A 602 ARG cc_start: 0.7704 (mtp85) cc_final: 0.7351 (mtt-85) REVERT: A 720 ARG cc_start: 0.7238 (ttp-170) cc_final: 0.6532 (ttp-170) REVERT: A 747 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7123 (mtp85) REVERT: A 847 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7694 (mm-30) REVERT: A 1025 ASP cc_start: 0.6347 (t0) cc_final: 0.6077 (t70) REVERT: A 1028 MET cc_start: 0.7227 (ttp) cc_final: 0.5962 (tpt) outliers start: 7 outliers final: 3 residues processed: 91 average time/residue: 1.9771 time to fit residues: 191.2193 Evaluate side-chains 91 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 731 SER Chi-restraints excluded: chain A residue 747 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 80 optimal weight: 0.4980 chunk 81 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 68 optimal weight: 0.3980 chunk 102 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN A1084 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.168146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.129635 restraints weight = 11078.229| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.21 r_work: 0.3163 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12556 Z= 0.168 Angle : 0.587 9.314 17747 Z= 0.306 Chirality : 0.039 0.231 2045 Planarity : 0.005 0.050 1743 Dihedral : 21.406 163.648 3432 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.66 % Allowed : 12.68 % Favored : 86.67 % 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: 1.25 (0.25), residues: 1097 helix: 1.55 (0.22), residues: 547 sheet: -0.39 (0.57), residues: 76 loop : 0.31 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 161 HIS 0.004 0.001 HIS A 749 PHE 0.019 0.002 PHE A 282 TYR 0.017 0.002 TYR A 986 ARG 0.007 0.000 ARG A 659 Details of bonding type rmsd hydrogen bonds : bond 0.04612 ( 575) hydrogen bonds : angle 4.00510 ( 1535) covalent geometry : bond 0.00358 (12555) covalent geometry : angle 0.58748 (17747) Misc. bond : bond 0.00042 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10598.91 seconds wall clock time: 188 minutes 3.22 seconds (11283.22 seconds total)