Starting phenix.real_space_refine on Mon Dec 30 07:10:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d2k_27141/12_2024/8d2k_27141.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2k_27141/12_2024/8d2k_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_27141/12_2024/8d2k_27141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2k_27141/12_2024/8d2k_27141.map" model { file = "/net/cci-nas-00/data/ceres_data/8d2k_27141/12_2024/8d2k_27141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2k_27141/12_2024/8d2k_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-5532/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: 7.95, per 1000 atoms: 0.65 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: 3.21 Conformation dependent library (CDL) restraints added in 1.1 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: 5.21 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: 7.61 Time building geometry restraints manager: 3.72 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: 2.050 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 36.690 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.970 ------------------------------------------------------------------------------- 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 12555 Z= 0.391 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 *********************** 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 : 1.185 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: 2.0088 time to fit residues: 247.0198 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 : 1.042 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 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 12555 Z= 0.341 Angle : 0.678 8.857 17747 Z= 0.355 Chirality : 0.043 0.286 2045 Planarity : 0.006 0.085 1743 Dihedral : 21.590 177.523 3432 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 7.29 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 *********************** 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 : 1.148 Fit side-chains REVERT: A 311 ASN cc_start: 0.7650 (m-40) cc_final: 0.7228 (m-40) REVERT: A 548 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.5532 (mp0) REVERT: A 602 ARG cc_start: 0.7593 (mtp85) cc_final: 0.7230 (mtm-85) REVERT: A 650 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7622 (ptm) REVERT: A 720 ARG cc_start: 0.7021 (ttp-170) cc_final: 0.6433 (ttp-170) REVERT: A 724 ILE cc_start: 0.7348 (mm) cc_final: 0.7018 (mt) outliers start: 12 outliers final: 4 residues processed: 97 average time/residue: 1.9271 time to fit residues: 199.1458 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 : 1.121 ------------------------------------------------------------------------------- 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 62 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 12555 Z= 0.381 Angle : 0.693 9.337 17747 Z= 0.362 Chirality : 0.045 0.257 2045 Planarity : 0.006 0.065 1743 Dihedral : 21.589 176.753 3432 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.08 % Allowed : 7.76 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.67 (0.24), residues: 1097 helix: 1.06 (0.22), residues: 543 sheet: -0.61 (0.55), residues: 82 loop : 0.06 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 161 HIS 0.008 0.001 HIS A 603 PHE 0.023 0.002 PHE A 282 TYR 0.023 0.002 TYR A 986 ARG 0.008 0.001 ARG A 775 *********************** 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 108 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 1.024 Fit side-chains REVERT: A 311 ASN cc_start: 0.7551 (m-40) cc_final: 0.7137 (m-40) REVERT: A 548 GLU cc_start: 0.6468 (OUTLIER) cc_final: 0.5093 (mp0) REVERT: A 602 ARG cc_start: 0.7668 (mtp85) cc_final: 0.7300 (mtm-85) REVERT: A 662 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7298 (mtpt) REVERT: A 701 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6948 (mttt) REVERT: A 720 ARG cc_start: 0.7048 (ttp-170) cc_final: 0.6475 (ttp-170) REVERT: A 747 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7381 (mtp85) REVERT: A 1028 MET cc_start: 0.6954 (ttp) cc_final: 0.6500 (tpt) outliers start: 19 outliers final: 5 residues processed: 101 average time/residue: 1.9635 time to fit residues: 210.6067 Evaluate side-chains 93 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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 701 LYS Chi-restraints excluded: chain A residue 706 GLN 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 111 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12555 Z= 0.256 Angle : 0.606 9.261 17747 Z= 0.317 Chirality : 0.040 0.233 2045 Planarity : 0.005 0.055 1743 Dihedral : 21.466 171.724 3432 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: 1.00 (0.25), residues: 1097 helix: 1.38 (0.22), residues: 544 sheet: -0.50 (0.57), residues: 76 loop : 0.15 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 161 HIS 0.004 0.001 HIS A 749 PHE 0.020 0.002 PHE A 282 TYR 0.018 0.002 TYR A 986 ARG 0.005 0.000 ARG A 659 *********************** 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 107 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 1.151 Fit side-chains REVERT: A 191 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7809 (ttt-90) REVERT: A 311 ASN cc_start: 0.7510 (m-40) cc_final: 0.7040 (m-40) REVERT: A 548 GLU cc_start: 0.6374 (OUTLIER) cc_final: 0.5040 (mp0) REVERT: A 602 ARG cc_start: 0.7616 (mtp85) cc_final: 0.7372 (mtt-85) REVERT: A 662 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7289 (mtpt) REVERT: A 720 ARG cc_start: 0.7003 (ttp-170) cc_final: 0.6470 (ttp-170) REVERT: A 747 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7356 (mtp85) outliers start: 17 outliers final: 6 residues processed: 101 average time/residue: 2.0663 time to fit residues: 221.4274 Evaluate side-chains 97 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12555 Z= 0.304 Angle : 0.633 9.197 17747 Z= 0.330 Chirality : 0.041 0.231 2045 Planarity : 0.005 0.056 1743 Dihedral : 21.478 170.249 3432 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.19 % Allowed : 9.40 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.00 (0.25), residues: 1097 helix: 1.37 (0.22), residues: 545 sheet: -0.52 (0.57), residues: 76 loop : 0.17 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 161 HIS 0.005 0.001 HIS A1100 PHE 0.021 0.002 PHE A 282 TYR 0.021 0.002 TYR A 986 ARG 0.006 0.001 ARG A 165 *********************** 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 107 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 1.181 Fit side-chains revert: symmetry clash REVERT: A 137 ARG cc_start: 0.9196 (OUTLIER) cc_final: 0.6433 (mtt180) REVERT: A 191 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7833 (ttt-90) REVERT: A 311 ASN cc_start: 0.7527 (m-40) cc_final: 0.7018 (m-40) REVERT: A 602 ARG cc_start: 0.7678 (mtp85) cc_final: 0.7317 (mtt-85) REVERT: A 662 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7286 (mtpt) REVERT: A 720 ARG cc_start: 0.7001 (ttp-170) cc_final: 0.6458 (ttp-170) REVERT: A 747 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7140 (mtp85) REVERT: A 847 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7566 (mm-30) outliers start: 20 outliers final: 8 residues processed: 103 average time/residue: 2.0635 time to fit residues: 225.3352 Evaluate side-chains 97 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 191 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 55 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12555 Z= 0.320 Angle : 0.645 9.298 17747 Z= 0.336 Chirality : 0.042 0.231 2045 Planarity : 0.005 0.064 1743 Dihedral : 21.500 168.411 3432 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.75 % Allowed : 10.49 % Favored : 87.76 % 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: 1.00 (0.25), residues: 1097 helix: 1.35 (0.22), residues: 545 sheet: -0.55 (0.56), residues: 76 loop : 0.20 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 161 HIS 0.005 0.001 HIS A1100 PHE 0.021 0.002 PHE A 282 TYR 0.021 0.002 TYR A 986 ARG 0.006 0.001 ARG A 165 *********************** 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: 16 poor density : 85 time to evaluate : 1.135 Fit side-chains REVERT: A 137 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.6431 (mtt180) REVERT: A 191 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7845 (ttt-90) REVERT: A 311 ASN cc_start: 0.7545 (m-40) cc_final: 0.7028 (m-40) REVERT: A 548 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.5138 (mp0) REVERT: A 602 ARG cc_start: 0.7679 (mtp85) cc_final: 0.7301 (mtt-85) REVERT: A 662 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7290 (mtpt) REVERT: A 720 ARG cc_start: 0.7031 (ttp-170) cc_final: 0.6494 (ttp-170) REVERT: A 747 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7139 (mtp85) REVERT: A 847 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7552 (mm-30) outliers start: 16 outliers final: 6 residues processed: 99 average time/residue: 2.0106 time to fit residues: 211.4903 Evaluate side-chains 96 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 191 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 115 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 87 optimal weight: 0.0270 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 72 optimal weight: 0.0870 chunk 55 optimal weight: 9.9990 overall best weight: 1.6222 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12555 Z= 0.217 Angle : 0.576 9.145 17747 Z= 0.300 Chirality : 0.039 0.233 2045 Planarity : 0.004 0.050 1743 Dihedral : 21.395 165.113 3432 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.31 % Allowed : 11.37 % Favored : 87.32 % 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: 1.60 (0.22), residues: 545 sheet: -0.52 (0.56), residues: 76 loop : 0.28 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 161 HIS 0.005 0.001 HIS A 749 PHE 0.018 0.002 PHE A 282 TYR 0.016 0.002 TYR A 986 ARG 0.006 0.000 ARG A 659 *********************** 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 99 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 137 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.6403 (mtt180) REVERT: A 311 ASN cc_start: 0.7543 (m-40) cc_final: 0.7061 (m-40) REVERT: A 602 ARG cc_start: 0.7588 (mtp85) cc_final: 0.7348 (mtt-85) REVERT: A 662 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7269 (mtpt) REVERT: A 747 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7084 (mtp85) REVERT: A 880 ARG cc_start: 0.6514 (ptt90) cc_final: 0.6204 (ptt90) REVERT: A 1028 MET cc_start: 0.6647 (ttp) cc_final: 0.6291 (tpt) outliers start: 12 outliers final: 5 residues processed: 96 average time/residue: 2.0294 time to fit residues: 206.8360 Evaluate side-chains 93 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 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 73 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 12555 Z= 0.439 Angle : 0.725 9.276 17747 Z= 0.376 Chirality : 0.046 0.235 2045 Planarity : 0.006 0.059 1743 Dihedral : 21.552 169.358 3432 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.53 % Allowed : 11.91 % Favored : 86.56 % 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: 0.88 (0.25), residues: 1097 helix: 1.25 (0.22), residues: 544 sheet: -0.67 (0.53), residues: 82 loop : 0.18 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 13 HIS 0.006 0.001 HIS A1100 PHE 0.023 0.003 PHE A 282 TYR 0.024 0.003 TYR A 986 ARG 0.008 0.001 ARG A 165 *********************** 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 94 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 1.102 Fit side-chains REVERT: A 137 ARG cc_start: 0.9230 (OUTLIER) cc_final: 0.6484 (mtt180) REVERT: A 191 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7927 (ttt-90) REVERT: A 311 ASN cc_start: 0.7555 (m-40) cc_final: 0.7069 (m-40) REVERT: A 377 ASN cc_start: 0.6034 (m-40) cc_final: 0.5723 (m110) REVERT: A 548 GLU cc_start: 0.6592 (OUTLIER) cc_final: 0.5387 (mp0) REVERT: A 602 ARG cc_start: 0.7722 (mtp85) cc_final: 0.7384 (mtt-85) REVERT: A 662 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7290 (mtpt) REVERT: A 747 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7175 (mtp85) outliers start: 14 outliers final: 6 residues processed: 93 average time/residue: 2.0298 time to fit residues: 200.0643 Evaluate side-chains 90 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 191 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 7.9990 chunk 104 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 0.0470 chunk 34 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12555 Z= 0.199 Angle : 0.575 9.329 17747 Z= 0.300 Chirality : 0.038 0.230 2045 Planarity : 0.004 0.050 1743 Dihedral : 21.424 163.719 3432 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.87 % Allowed : 12.90 % Favored : 86.23 % 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: 1.24 (0.25), residues: 1097 helix: 1.59 (0.22), residues: 544 sheet: -0.50 (0.56), residues: 76 loop : 0.28 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 161 HIS 0.005 0.001 HIS A 749 PHE 0.017 0.001 PHE A 282 TYR 0.016 0.002 TYR A 986 ARG 0.005 0.000 ARG A 659 *********************** 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: 8 poor density : 90 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 137 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.6385 (mtt180) REVERT: A 191 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7814 (ttt-90) REVERT: A 311 ASN cc_start: 0.7542 (m-40) cc_final: 0.7086 (m-40) REVERT: A 602 ARG cc_start: 0.7599 (mtp85) cc_final: 0.7297 (mtt-85) REVERT: A 662 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7267 (mtpt) REVERT: A 747 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7088 (mtp85) REVERT: A 880 ARG cc_start: 0.6518 (ptt90) cc_final: 0.6262 (ptt90) REVERT: A 1028 MET cc_start: 0.6650 (ttp) cc_final: 0.6309 (tpt) outliers start: 8 outliers final: 3 residues processed: 97 average time/residue: 1.9856 time to fit residues: 204.4089 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 : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 191 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 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 117 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 12555 Z= 0.377 Angle : 0.681 9.267 17747 Z= 0.354 Chirality : 0.044 0.234 2045 Planarity : 0.006 0.054 1743 Dihedral : 21.511 167.401 3432 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.87 % Allowed : 13.11 % Favored : 86.01 % 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: 1.01 (0.25), residues: 1097 helix: 1.35 (0.22), residues: 545 sheet: -0.46 (0.56), residues: 76 loop : 0.21 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1128 HIS 0.005 0.001 HIS A1100 PHE 0.021 0.002 PHE A 282 TYR 0.023 0.002 TYR A 986 ARG 0.008 0.001 ARG A 165 ********************** 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 90 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 1.084 Fit side-chains REVERT: A 137 ARG cc_start: 0.9227 (OUTLIER) cc_final: 0.6521 (mtt180) REVERT: A 191 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7905 (ttt-90) REVERT: A 311 ASN cc_start: 0.7535 (m-40) cc_final: 0.7041 (m-40) REVERT: A 548 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.5135 (mp0) REVERT: A 602 ARG cc_start: 0.7708 (mtp85) cc_final: 0.7367 (mtt-85) REVERT: A 747 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7165 (mtp85) REVERT: A 1028 MET cc_start: 0.6621 (ttp) cc_final: 0.6297 (tpt) outliers start: 8 outliers final: 2 residues processed: 89 average time/residue: 1.9724 time to fit residues: 186.3678 Evaluate side-chains 86 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 191 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 104 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 101 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.169714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.130104 restraints weight = 11076.324| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.28 r_work: 0.3195 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12555 Z= 0.177 Angle : 0.562 9.251 17747 Z= 0.293 Chirality : 0.037 0.229 2045 Planarity : 0.004 0.056 1743 Dihedral : 21.363 162.661 3432 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.55 % Allowed : 13.55 % Favored : 85.90 % 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: 1.33 (0.25), residues: 1097 helix: 1.66 (0.22), residues: 544 sheet: -0.43 (0.57), residues: 76 loop : 0.31 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 161 HIS 0.005 0.001 HIS A 749 PHE 0.016 0.001 PHE A 282 TYR 0.016 0.002 TYR A 986 ARG 0.008 0.000 ARG A1048 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3973.74 seconds wall clock time: 72 minutes 9.94 seconds (4329.94 seconds total)