Starting phenix.real_space_refine on Sun Jun 8 02:42:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hnv_34919/06_2025/8hnv_34919.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hnv_34919/06_2025/8hnv_34919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hnv_34919/06_2025/8hnv_34919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hnv_34919/06_2025/8hnv_34919.map" model { file = "/net/cci-nas-00/data/ceres_data/8hnv_34919/06_2025/8hnv_34919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hnv_34919/06_2025/8hnv_34919.cif" } resolution = 3.1 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= 0.009 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: 5 Type Number sf(0) Gaussians P 127 5.49 5 S 20 5.16 5 C 5381 2.51 5 N 1623 2.21 5 O 2045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9196 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5821 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 25, 'TRANS': 719} Chain breaks: 9 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 128 Chain: "B" Number of atoms: 2046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 2046 Classifications: {'RNA': 97} Modifications used: {'rna2p_pyr': 6, 'rna3p_pur': 45, 'rna3p_pyr': 46} Link IDs: {'rna2p': 5, 'rna3p': 91} Chain breaks: 3 Chain: "C" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 370 Classifications: {'DNA': 18} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 17} Chain: "D" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 267 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "E" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 692 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Time building chain proxies: 6.74, per 1000 atoms: 0.73 Number of scatterers: 9196 At special positions: 0 Unit cell: (119.6, 106.08, 108.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 127 15.00 O 2045 8.00 N 1623 7.00 C 5381 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=0, symmetry=0 Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 809.2 milliseconds 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 8 sheets defined 51.3% alpha, 10.6% beta 48 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain 'A' and resid 54 through 86 removed outlier: 4.032A pdb=" N SER A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 109 removed outlier: 3.693A pdb=" N LEU A 108 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASP A 109 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 127 Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 174 through 179 removed outlier: 3.949A pdb=" N GLU A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 192 removed outlier: 3.944A pdb=" N HIS A 191 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 212 Processing helix chain 'A' and resid 218 through 231 Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.572A pdb=" N LYS A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 295 removed outlier: 3.986A pdb=" N LEU A 294 " --> pdb=" O ARG A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 removed outlier: 3.597A pdb=" N LYS A 301 " --> pdb=" O GLN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 removed outlier: 3.638A pdb=" N GLN A 308 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A 309 " --> pdb=" O TYR A 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 305 through 309' Processing helix chain 'A' and resid 343 through 356 removed outlier: 3.989A pdb=" N ASN A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 368 removed outlier: 3.768A pdb=" N TRP A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 382 removed outlier: 3.985A pdb=" N LEU A 372 " --> pdb=" O ASN A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 392 Processing helix chain 'A' and resid 397 through 405 Processing helix chain 'A' and resid 417 through 430 Proline residue: A 426 - end of helix Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 467 through 489 Processing helix chain 'A' and resid 666 through 678 Processing helix chain 'A' and resid 692 through 703 removed outlier: 3.947A pdb=" N THR A 696 " --> pdb=" O ASN A 692 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP A 703 " --> pdb=" O LEU A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 715 through 722 removed outlier: 4.089A pdb=" N ASP A 719 " --> pdb=" O HIS A 715 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 720 " --> pdb=" O HIS A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 725 No H-bonds generated for 'chain 'A' and resid 723 through 725' Processing helix chain 'A' and resid 771 through 779 Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 829 through 832 removed outlier: 3.574A pdb=" N GLU A 832 " --> pdb=" O ARG A 829 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 829 through 832' Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 845 through 851 Processing helix chain 'A' and resid 858 through 872 removed outlier: 4.136A pdb=" N TYR A 862 " --> pdb=" O GLU A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 880 Processing helix chain 'A' and resid 938 through 944 Processing helix chain 'A' and resid 956 through 960 removed outlier: 3.989A pdb=" N TRP A 960 " --> pdb=" O GLU A 957 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 12 removed outlier: 3.667A pdb=" N ILE E 11 " --> pdb=" O ASN E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 20 Processing helix chain 'E' and resid 21 through 23 No H-bonds generated for 'chain 'E' and resid 21 through 23' Processing helix chain 'E' and resid 24 through 44 Proline residue: E 30 - end of helix removed outlier: 3.523A pdb=" N SER E 44 " --> pdb=" O GLU E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 50 Processing helix chain 'E' and resid 55 through 84 removed outlier: 4.188A pdb=" N ALA E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 9 removed outlier: 3.744A pdb=" N ALA A 13 " --> pdb=" O GLY A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 8 through 9 removed outlier: 3.894A pdb=" N ASP A 37 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLU A 25 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU A 35 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 494 through 496 removed outlier: 6.697A pdb=" N ILE A 494 " --> pdb=" O PHE A 689 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 825 through 826 Processing sheet with id=AA5, first strand: chain 'A' and resid 834 through 840 Processing sheet with id=AA6, first strand: chain 'A' and resid 884 through 885 removed outlier: 4.392A pdb=" N PHE A 884 " --> pdb=" O VAL A 892 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 930 through 937 removed outlier: 3.750A pdb=" N PHE A 971 " --> pdb=" O VAL A 924 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR A 926 " --> pdb=" O PHE A 969 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N PHE A 969 " --> pdb=" O THR A 926 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1018 through 1022 removed outlier: 3.623A pdb=" N ILE A1004 " --> pdb=" O PHE A1019 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY A1021 " --> pdb=" O ILE A1002 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ILE A1002 " --> pdb=" O GLY A1021 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 978 " --> pdb=" O TYR A1033 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER A1029 " --> pdb=" O VAL A 982 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN A1034 " --> pdb=" O ARG A1043 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG A1043 " --> pdb=" O GLN A1034 " (cutoff:3.500A) 285 hydrogen bonds defined for protein. 825 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 113 hydrogen bonds 214 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 4.64 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2297 1.34 - 1.45: 2342 1.45 - 1.57: 4690 1.57 - 1.69: 249 1.69 - 1.81: 35 Bond restraints: 9613 Sorted by residual: bond pdb=" C3' U B 76 " pdb=" O3' U B 76 " ideal model delta sigma weight residual 1.427 1.449 -0.022 1.50e-02 4.44e+03 2.08e+00 bond pdb=" C3' DC C 7 " pdb=" O3' DC C 7 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.66e+00 bond pdb=" O3' U B 76 " pdb=" P U B 77 " ideal model delta sigma weight residual 1.607 1.625 -0.018 1.50e-02 4.44e+03 1.48e+00 bond pdb=" CA ASP A 959 " pdb=" CB ASP A 959 " ideal model delta sigma weight residual 1.531 1.563 -0.033 3.28e-02 9.30e+02 9.91e-01 bond pdb=" N TYR A 254 " pdb=" CA TYR A 254 " ideal model delta sigma weight residual 1.458 1.470 -0.012 1.42e-02 4.96e+03 6.86e-01 ... (remaining 9608 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 13164 1.44 - 2.89: 308 2.89 - 4.33: 58 4.33 - 5.77: 14 5.77 - 7.22: 6 Bond angle restraints: 13550 Sorted by residual: angle pdb=" C3' U B 76 " pdb=" O3' U B 76 " pdb=" P U B 77 " ideal model delta sigma weight residual 120.20 126.20 -6.00 1.50e+00 4.44e-01 1.60e+01 angle pdb=" CA TYR A 254 " pdb=" CB TYR A 254 " pdb=" CG TYR A 254 " ideal model delta sigma weight residual 113.90 120.96 -7.06 1.80e+00 3.09e-01 1.54e+01 angle pdb=" C GLU A 253 " pdb=" N TYR A 254 " pdb=" CA TYR A 254 " ideal model delta sigma weight residual 122.32 128.42 -6.10 1.76e+00 3.23e-01 1.20e+01 angle pdb=" C ASP A 109 " pdb=" N HIS A 110 " pdb=" CA HIS A 110 " ideal model delta sigma weight residual 121.54 126.37 -4.83 1.91e+00 2.74e-01 6.39e+00 angle pdb=" C CYS A 248 " pdb=" N THR A 249 " pdb=" CA THR A 249 " ideal model delta sigma weight residual 121.54 126.35 -4.81 1.91e+00 2.74e-01 6.35e+00 ... (remaining 13545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 5431 35.63 - 71.26: 389 71.26 - 106.88: 25 106.88 - 142.51: 2 142.51 - 178.14: 6 Dihedral angle restraints: 5853 sinusoidal: 3438 harmonic: 2415 Sorted by residual: dihedral pdb=" O4' U B 77 " pdb=" C1' U B 77 " pdb=" N1 U B 77 " pdb=" C2 U B 77 " ideal model delta sinusoidal sigma weight residual -160.00 18.14 -178.14 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U B 125 " pdb=" C1' U B 125 " pdb=" N1 U B 125 " pdb=" C2 U B 125 " ideal model delta sinusoidal sigma weight residual -128.00 30.10 -158.10 1 1.70e+01 3.46e-03 6.40e+01 dihedral pdb=" C4' DC C 7 " pdb=" C3' DC C 7 " pdb=" O3' DC C 7 " pdb=" P DA C 8 " ideal model delta sinusoidal sigma weight residual 220.00 46.94 173.06 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 5850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1236 0.036 - 0.072: 295 0.072 - 0.107: 68 0.107 - 0.143: 20 0.143 - 0.179: 5 Chirality restraints: 1624 Sorted by residual: chirality pdb=" C3' G B 87 " pdb=" C4' G B 87 " pdb=" O3' G B 87 " pdb=" C2' G B 87 " both_signs ideal model delta sigma weight residual False -2.48 -2.30 -0.18 2.00e-01 2.50e+01 8.01e-01 chirality pdb=" C3' G B 92 " pdb=" C4' G B 92 " pdb=" O3' G B 92 " pdb=" C2' G B 92 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" C3' C B 94 " pdb=" C4' C B 94 " pdb=" O3' C B 94 " pdb=" C2' C B 94 " both_signs ideal model delta sigma weight residual False -2.48 -2.32 -0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 1621 not shown) Planarity restraints: 1264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 253 " -0.011 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" C GLU A 253 " 0.040 2.00e-02 2.50e+03 pdb=" O GLU A 253 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR A 254 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 166 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO A 167 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 167 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 167 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 974 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.92e+00 pdb=" N PRO A 975 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 975 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 975 " -0.024 5.00e-02 4.00e+02 ... (remaining 1261 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 216 2.66 - 3.22: 8279 3.22 - 3.78: 15958 3.78 - 4.34: 21788 4.34 - 4.90: 32021 Nonbonded interactions: 78262 Sorted by model distance: nonbonded pdb=" O ILE A 891 " pdb=" O2' U B 56 " model vdw 2.103 3.040 nonbonded pdb=" O HIS A 98 " pdb=" O2' U B 59 " model vdw 2.134 3.040 nonbonded pdb=" O2' G B 69 " pdb=" O ASN E 26 " model vdw 2.158 3.040 nonbonded pdb=" OP1 U B 124 " pdb=" NZ LYS E 32 " model vdw 2.159 3.120 nonbonded pdb=" O2' G B 92 " pdb=" OP1 U B 93 " model vdw 2.162 3.040 ... (remaining 78257 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=1.00 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: 0.010 Normalize map: mean=0, sd=1: 0.560 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.880 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 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 : 0.002 0.039 9613 Z= 0.118 Angle : 0.572 7.216 13550 Z= 0.303 Chirality : 0.035 0.179 1624 Planarity : 0.004 0.054 1264 Dihedral : 20.855 178.138 4277 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.35 (0.30), residues: 810 helix: 0.77 (0.29), residues: 339 sheet: -0.99 (0.63), residues: 72 loop : -0.93 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 117 HIS 0.003 0.001 HIS A 191 PHE 0.017 0.001 PHE A 266 TYR 0.012 0.001 TYR A 164 ARG 0.005 0.001 ARG A 114 Details of bonding type rmsd hydrogen bonds : bond 0.15737 ( 396) hydrogen bonds : angle 6.43192 ( 1039) covalent geometry : bond 0.00240 ( 9613) covalent geometry : angle 0.57158 (13550) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.813 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2524 time to fit residues: 37.3452 Evaluate side-chains 82 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 47 optimal weight: 0.0010 chunk 37 optimal weight: 0.0040 chunk 72 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 overall best weight: 3.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 348 GLN A 901 GLN A1034 GLN E 51 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.185335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.155522 restraints weight = 10915.208| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.36 r_work: 0.3574 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9613 Z= 0.246 Angle : 0.690 7.932 13550 Z= 0.359 Chirality : 0.043 0.252 1624 Planarity : 0.005 0.060 1264 Dihedral : 22.072 179.233 2683 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 1.18 % Allowed : 10.88 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.72 (0.29), residues: 810 helix: 0.42 (0.28), residues: 368 sheet: -0.62 (0.69), residues: 65 loop : -1.34 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 231 HIS 0.005 0.001 HIS A 123 PHE 0.013 0.002 PHE A 971 TYR 0.014 0.002 TYR A 254 ARG 0.005 0.001 ARG A 128 Details of bonding type rmsd hydrogen bonds : bond 0.05523 ( 396) hydrogen bonds : angle 4.95967 ( 1039) covalent geometry : bond 0.00542 ( 9613) covalent geometry : angle 0.69043 (13550) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 464 GLU cc_start: 0.6073 (tm-30) cc_final: 0.5831 (tm-30) REVERT: A 873 ASN cc_start: 0.5730 (t0) cc_final: 0.5386 (p0) outliers start: 8 outliers final: 6 residues processed: 86 average time/residue: 0.2362 time to fit residues: 28.9499 Evaluate side-chains 79 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 21 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 20 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 803 GLN E 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.191823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.170886 restraints weight = 11008.322| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 0.90 r_work: 0.3721 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9613 Z= 0.148 Angle : 0.571 5.697 13550 Z= 0.300 Chirality : 0.038 0.228 1624 Planarity : 0.004 0.056 1264 Dihedral : 21.977 179.333 2683 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.91 % Allowed : 13.09 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.42 (0.30), residues: 810 helix: 0.73 (0.28), residues: 370 sheet: -0.74 (0.65), residues: 73 loop : -1.21 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 231 HIS 0.003 0.001 HIS A 679 PHE 0.010 0.001 PHE A 971 TYR 0.013 0.001 TYR A 254 ARG 0.004 0.000 ARG A 114 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 396) hydrogen bonds : angle 4.52950 ( 1039) covalent geometry : bond 0.00321 ( 9613) covalent geometry : angle 0.57108 (13550) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.903 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 86 average time/residue: 0.2106 time to fit residues: 26.0153 Evaluate side-chains 77 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain E residue 6 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 8 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 ASN A 873 ASN E 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.189017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.168362 restraints weight = 10917.770| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 0.82 r_work: 0.3711 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9613 Z= 0.199 Angle : 0.628 9.964 13550 Z= 0.325 Chirality : 0.040 0.249 1624 Planarity : 0.004 0.057 1264 Dihedral : 22.007 178.798 2683 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.21 % Allowed : 16.03 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.50 (0.30), residues: 810 helix: 0.67 (0.27), residues: 372 sheet: -0.77 (0.69), residues: 65 loop : -1.26 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 231 HIS 0.004 0.001 HIS A 679 PHE 0.018 0.002 PHE A 216 TYR 0.013 0.002 TYR A 254 ARG 0.005 0.001 ARG A 829 Details of bonding type rmsd hydrogen bonds : bond 0.04804 ( 396) hydrogen bonds : angle 4.55724 ( 1039) covalent geometry : bond 0.00438 ( 9613) covalent geometry : angle 0.62754 (13550) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.773 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 13 residues processed: 87 average time/residue: 0.2088 time to fit residues: 25.7928 Evaluate side-chains 83 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain E residue 1 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 chunk 88 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 43 optimal weight: 0.0970 chunk 80 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 873 ASN E 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.193582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.173229 restraints weight = 11022.341| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 0.87 r_work: 0.3768 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9613 Z= 0.129 Angle : 0.552 7.787 13550 Z= 0.289 Chirality : 0.037 0.223 1624 Planarity : 0.004 0.056 1264 Dihedral : 21.932 178.921 2683 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.35 % Allowed : 16.32 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.26 (0.30), residues: 810 helix: 0.93 (0.28), residues: 372 sheet: -0.83 (0.66), residues: 73 loop : -1.18 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 231 HIS 0.003 0.001 HIS A 191 PHE 0.017 0.001 PHE A 216 TYR 0.014 0.001 TYR A 254 ARG 0.003 0.000 ARG A 829 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 396) hydrogen bonds : angle 4.25994 ( 1039) covalent geometry : bond 0.00274 ( 9613) covalent geometry : angle 0.55181 (13550) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.779 Fit side-chains REVERT: A 35 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7807 (pp) REVERT: A 299 TYR cc_start: 0.4670 (OUTLIER) cc_final: 0.4436 (m-10) outliers start: 16 outliers final: 12 residues processed: 89 average time/residue: 0.2085 time to fit residues: 26.4970 Evaluate side-chains 80 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 299 TYR Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain E residue 6 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 27 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 873 ASN E 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.185031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.164983 restraints weight = 10973.882| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 0.86 r_work: 0.3652 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 9613 Z= 0.316 Angle : 0.773 9.724 13550 Z= 0.394 Chirality : 0.047 0.277 1624 Planarity : 0.005 0.060 1264 Dihedral : 22.171 174.783 2683 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 2.79 % Allowed : 18.53 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.90 (0.29), residues: 810 helix: 0.30 (0.27), residues: 371 sheet: -1.02 (0.66), residues: 65 loop : -1.41 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 231 HIS 0.006 0.002 HIS A 123 PHE 0.024 0.003 PHE A 216 TYR 0.017 0.002 TYR A 254 ARG 0.006 0.001 ARG A 128 Details of bonding type rmsd hydrogen bonds : bond 0.06102 ( 396) hydrogen bonds : angle 4.84602 ( 1039) covalent geometry : bond 0.00697 ( 9613) covalent geometry : angle 0.77264 (13550) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.771 Fit side-chains REVERT: A 35 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7954 (pp) outliers start: 19 outliers final: 15 residues processed: 79 average time/residue: 0.1962 time to fit residues: 22.6315 Evaluate side-chains 76 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 13 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 70 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN A1001 ASN E 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.188363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.167281 restraints weight = 11023.038| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 0.90 r_work: 0.3682 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9613 Z= 0.201 Angle : 0.646 7.469 13550 Z= 0.334 Chirality : 0.041 0.255 1624 Planarity : 0.004 0.059 1264 Dihedral : 22.085 176.803 2683 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.68 % Allowed : 18.24 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.70 (0.29), residues: 810 helix: 0.55 (0.28), residues: 362 sheet: -1.04 (0.67), residues: 65 loop : -1.34 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 231 HIS 0.004 0.001 HIS A 679 PHE 0.021 0.002 PHE A 216 TYR 0.013 0.002 TYR A 254 ARG 0.003 0.001 ARG A 128 Details of bonding type rmsd hydrogen bonds : bond 0.04901 ( 396) hydrogen bonds : angle 4.61250 ( 1039) covalent geometry : bond 0.00443 ( 9613) covalent geometry : angle 0.64570 (13550) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 0.841 Fit side-chains REVERT: A 35 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7917 (pp) REVERT: A 962 VAL cc_start: 0.7602 (OUTLIER) cc_final: 0.7402 (t) outliers start: 25 outliers final: 15 residues processed: 86 average time/residue: 0.1928 time to fit residues: 24.5270 Evaluate side-chains 79 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain A residue 1049 LYS Chi-restraints excluded: chain E residue 6 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 16 optimal weight: 7.9990 chunk 53 optimal weight: 0.0020 chunk 64 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 63 optimal weight: 0.0050 chunk 72 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 overall best weight: 0.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.195383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.174920 restraints weight = 11184.771| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 0.76 r_work: 0.3807 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9613 Z= 0.113 Angle : 0.543 5.773 13550 Z= 0.284 Chirality : 0.037 0.210 1624 Planarity : 0.004 0.059 1264 Dihedral : 21.938 178.504 2683 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.35 % Allowed : 18.97 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.23 (0.30), residues: 810 helix: 1.01 (0.28), residues: 371 sheet: -0.87 (0.65), residues: 75 loop : -1.21 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 231 HIS 0.003 0.001 HIS A 191 PHE 0.016 0.001 PHE A 216 TYR 0.015 0.001 TYR A 254 ARG 0.004 0.000 ARG A 114 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 396) hydrogen bonds : angle 4.12483 ( 1039) covalent geometry : bond 0.00236 ( 9613) covalent geometry : angle 0.54253 (13550) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 35 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7739 (pp) REVERT: A 86 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6714 (mt-10) REVERT: A 1034 GLN cc_start: 0.6793 (OUTLIER) cc_final: 0.6487 (tp40) outliers start: 16 outliers final: 11 residues processed: 94 average time/residue: 0.2110 time to fit residues: 28.6188 Evaluate side-chains 84 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain E residue 6 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 31 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 32 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.192299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.173996 restraints weight = 10924.567| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 0.74 r_work: 0.3697 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9613 Z= 0.141 Angle : 0.568 7.891 13550 Z= 0.295 Chirality : 0.038 0.219 1624 Planarity : 0.004 0.058 1264 Dihedral : 21.872 179.240 2683 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.35 % Allowed : 19.56 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.24 (0.30), residues: 810 helix: 1.00 (0.28), residues: 370 sheet: -0.92 (0.68), residues: 66 loop : -1.19 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 231 HIS 0.002 0.001 HIS A 495 PHE 0.014 0.001 PHE A 266 TYR 0.013 0.001 TYR A 254 ARG 0.004 0.000 ARG A 114 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 396) hydrogen bonds : angle 4.22478 ( 1039) covalent geometry : bond 0.00306 ( 9613) covalent geometry : angle 0.56764 (13550) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.832 Fit side-chains REVERT: A 35 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7721 (pp) outliers start: 16 outliers final: 15 residues processed: 86 average time/residue: 0.2073 time to fit residues: 25.6414 Evaluate side-chains 83 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 50 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 28 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.189073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.167936 restraints weight = 11073.435| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 0.88 r_work: 0.3695 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9613 Z= 0.206 Angle : 0.651 9.623 13550 Z= 0.334 Chirality : 0.042 0.286 1624 Planarity : 0.004 0.058 1264 Dihedral : 21.969 177.965 2683 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.94 % Allowed : 19.41 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.54 (0.29), residues: 810 helix: 0.70 (0.27), residues: 369 sheet: -0.93 (0.69), residues: 60 loop : -1.31 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 231 HIS 0.004 0.001 HIS A 679 PHE 0.023 0.002 PHE A 216 TYR 0.012 0.002 TYR A 254 ARG 0.004 0.001 ARG A 114 Details of bonding type rmsd hydrogen bonds : bond 0.04832 ( 396) hydrogen bonds : angle 4.48637 ( 1039) covalent geometry : bond 0.00455 ( 9613) covalent geometry : angle 0.65079 (13550) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.967 Fit side-chains REVERT: A 35 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7837 (pp) outliers start: 20 outliers final: 17 residues processed: 82 average time/residue: 0.2265 time to fit residues: 26.3453 Evaluate side-chains 81 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 254 TYR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 478 ARG Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 1034 GLN Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 50 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 45 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 65 optimal weight: 0.0060 chunk 89 optimal weight: 1.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1001 ASN E 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.193661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.172295 restraints weight = 11048.903| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 0.79 r_work: 0.3755 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9613 Z= 0.120 Angle : 0.562 7.942 13550 Z= 0.291 Chirality : 0.037 0.215 1624 Planarity : 0.004 0.057 1264 Dihedral : 21.873 178.713 2683 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.50 % Allowed : 20.15 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.26 (0.30), residues: 810 helix: 0.93 (0.28), residues: 373 sheet: -0.96 (0.69), residues: 66 loop : -1.15 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 231 HIS 0.003 0.001 HIS A 820 PHE 0.018 0.001 PHE A 216 TYR 0.015 0.001 TYR A 254 ARG 0.003 0.000 ARG A 114 Details of bonding type rmsd hydrogen bonds : bond 0.03699 ( 396) hydrogen bonds : angle 4.14036 ( 1039) covalent geometry : bond 0.00256 ( 9613) covalent geometry : angle 0.56215 (13550) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5137.95 seconds wall clock time: 91 minutes 54.48 seconds (5514.48 seconds total)