Starting phenix.real_space_refine on Sat Aug 23 02:35:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hnv_34919/08_2025/8hnv_34919.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hnv_34919/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8hnv_34919/08_2025/8hnv_34919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hnv_34919/08_2025/8hnv_34919.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hnv_34919/08_2025/8hnv_34919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hnv_34919/08_2025/8hnv_34919.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 7, 'ASN:plan1': 2, 'TYR:plan': 4, 'GLU:plan': 8, 'PHE:plan': 1, 'ASP:plan': 3, 'GLN:plan1': 3} 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: 1.84, per 1000 atoms: 0.20 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: 0.62 Conformation dependent library (CDL) restraints added in 148.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.02 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: 1.49 Time building geometry restraints manager: 0.79 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: 0.000 Normalize map: mean=0, sd=1: 0.450 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.390 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.260 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG A 114 TYR 0.012 0.001 TYR A 164 PHE 0.017 0.001 PHE A 266 TRP 0.018 0.001 TRP A 117 HIS 0.003 0.001 HIS A 191 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 9613) covalent geometry : angle 0.57158 (13550) hydrogen bonds : bond 0.15737 ( 396) hydrogen bonds : angle 6.43192 ( 1039) *********************** 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 : 0.205 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.0881 time to fit residues: 13.0758 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 : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 901 GLN A1034 GLN E 51 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.184966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.155587 restraints weight = 10973.430| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.32 r_work: 0.3561 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9613 Z= 0.264 Angle : 0.705 8.253 13550 Z= 0.366 Chirality : 0.044 0.252 1624 Planarity : 0.005 0.055 1264 Dihedral : 22.082 178.948 2683 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 1.32 % Allowed : 10.59 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.29), residues: 810 helix: 0.36 (0.28), residues: 368 sheet: -0.63 (0.69), residues: 65 loop : -1.34 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 128 TYR 0.014 0.002 TYR A 254 PHE 0.015 0.002 PHE A 971 TRP 0.018 0.002 TRP A 231 HIS 0.004 0.001 HIS A 123 Details of bonding type rmsd covalent geometry : bond 0.00585 ( 9613) covalent geometry : angle 0.70541 (13550) hydrogen bonds : bond 0.05660 ( 396) hydrogen bonds : angle 5.01975 ( 1039) *********************** 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 88 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.191 Fit side-chains REVERT: A 464 GLU cc_start: 0.6101 (tm-30) cc_final: 0.5820 (tm-30) REVERT: A 873 ASN cc_start: 0.5750 (t0) cc_final: 0.5396 (p0) outliers start: 9 outliers final: 7 residues processed: 85 average time/residue: 0.0693 time to fit residues: 8.5866 Evaluate side-chains 80 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.160 ------------------------------------------------------------------------------- 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 894 SER 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 91 optimal weight: 5.9990 chunk 63 optimal weight: 0.0970 chunk 19 optimal weight: 0.5980 chunk 52 optimal weight: 0.0060 chunk 78 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 803 GLN A 901 GLN E 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.194556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.175215 restraints weight = 10972.404| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 0.82 r_work: 0.3774 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.2006 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= 0.123 Angle : 0.548 5.670 13550 Z= 0.289 Chirality : 0.037 0.224 1624 Planarity : 0.004 0.053 1264 Dihedral : 21.941 178.194 2683 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.76 % Allowed : 12.65 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.30), residues: 810 helix: 0.87 (0.28), residues: 363 sheet: -0.74 (0.65), residues: 73 loop : -1.16 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 114 TYR 0.015 0.001 TYR A 254 PHE 0.008 0.001 PHE A 969 TRP 0.021 0.002 TRP A 231 HIS 0.003 0.001 HIS A 820 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9613) covalent geometry : angle 0.54799 (13550) hydrogen bonds : bond 0.03968 ( 396) hydrogen bonds : angle 4.42146 ( 1039) *********************** 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 94 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.169 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 89 average time/residue: 0.0745 time to fit residues: 9.5066 Evaluate side-chains 73 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 186 GLN Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 357 ASN 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 86 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN A 482 ASN A 873 ASN A 901 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 = 0.4202 r_free = 0.4202 target = 0.185092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.164131 restraints weight = 11177.294| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 0.93 r_work: 0.3649 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 9613 Z= 0.312 Angle : 0.762 9.202 13550 Z= 0.390 Chirality : 0.047 0.272 1624 Planarity : 0.006 0.073 1264 Dihedral : 22.187 175.119 2683 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.65 % Allowed : 16.47 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.29), residues: 810 helix: 0.27 (0.27), residues: 367 sheet: -0.98 (0.67), residues: 65 loop : -1.43 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 829 TYR 0.017 0.002 TYR A 254 PHE 0.022 0.002 PHE A 216 TRP 0.027 0.003 TRP A 231 HIS 0.006 0.002 HIS A 123 Details of bonding type rmsd covalent geometry : bond 0.00689 ( 9613) covalent geometry : angle 0.76220 (13550) hydrogen bonds : bond 0.06043 ( 396) hydrogen bonds : angle 4.90331 ( 1039) *********************** 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: 18 poor density : 72 time to evaluate : 0.220 Fit side-chains REVERT: A 35 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7954 (pp) outliers start: 18 outliers final: 13 residues processed: 86 average time/residue: 0.0709 time to fit residues: 8.8509 Evaluate side-chains 76 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 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 13 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 13 optimal weight: 4.9990 chunk 82 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 chunk 75 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 61 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 873 ASN 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 = 0.4255 r_free = 0.4255 target = 0.190124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.171981 restraints weight = 11031.899| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 0.83 r_work: 0.3742 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9613 Z= 0.159 Angle : 0.594 7.030 13550 Z= 0.311 Chirality : 0.039 0.240 1624 Planarity : 0.004 0.056 1264 Dihedral : 22.041 178.445 2683 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.06 % Allowed : 17.79 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.29), residues: 810 helix: 0.62 (0.27), residues: 371 sheet: -0.94 (0.65), residues: 73 loop : -1.23 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 829 TYR 0.013 0.001 TYR A 254 PHE 0.018 0.001 PHE A 216 TRP 0.028 0.002 TRP A 231 HIS 0.003 0.001 HIS A 679 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9613) covalent geometry : angle 0.59410 (13550) hydrogen bonds : bond 0.04428 ( 396) hydrogen bonds : angle 4.50327 ( 1039) *********************** 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 83 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.165 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 80 average time/residue: 0.0703 time to fit residues: 8.2071 Evaluate side-chains 78 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 E residue 1 MET 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 87 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 0.0170 chunk 81 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- 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 = 0.4243 r_free = 0.4243 target = 0.188919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.171574 restraints weight = 11116.690| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 0.81 r_work: 0.3728 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2665 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= 0.190 Angle : 0.619 6.098 13550 Z= 0.322 Chirality : 0.041 0.247 1624 Planarity : 0.004 0.057 1264 Dihedral : 22.039 177.793 2683 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.24 % Allowed : 17.94 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.29), residues: 810 helix: 0.61 (0.27), residues: 370 sheet: -0.95 (0.67), residues: 65 loop : -1.30 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 71 TYR 0.013 0.002 TYR A 254 PHE 0.019 0.002 PHE A 216 TRP 0.033 0.002 TRP A 231 HIS 0.003 0.001 HIS A 679 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 9613) covalent geometry : angle 0.61923 (13550) hydrogen bonds : bond 0.04739 ( 396) hydrogen bonds : angle 4.51121 ( 1039) *********************** 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 86 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.261 Fit side-chains REVERT: A 35 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7835 (pp) outliers start: 22 outliers final: 16 residues processed: 83 average time/residue: 0.0714 time to fit residues: 8.5185 Evaluate side-chains 80 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.157 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 23 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 = 0.4249 r_free = 0.4249 target = 0.189639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.171470 restraints weight = 11028.188| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 0.82 r_work: 0.3736 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9613 Z= 0.175 Angle : 0.605 6.561 13550 Z= 0.315 Chirality : 0.040 0.241 1624 Planarity : 0.004 0.057 1264 Dihedral : 22.030 178.266 2683 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.09 % Allowed : 18.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.29), residues: 810 helix: 0.75 (0.27), residues: 370 sheet: -0.95 (0.67), residues: 65 loop : -1.33 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1043 TYR 0.013 0.001 TYR A 254 PHE 0.020 0.002 PHE A 216 TRP 0.036 0.002 TRP A 231 HIS 0.003 0.001 HIS A 679 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 9613) covalent geometry : angle 0.60545 (13550) hydrogen bonds : bond 0.04539 ( 396) hydrogen bonds : angle 4.43815 ( 1039) *********************** 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 90 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.168 Fit side-chains REVERT: A 35 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7828 (pp) REVERT: A 1034 GLN cc_start: 0.6949 (OUTLIER) cc_final: 0.6674 (tp40) outliers start: 21 outliers final: 13 residues processed: 87 average time/residue: 0.0682 time to fit residues: 8.4792 Evaluate side-chains 81 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.167 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 17 optimal weight: 0.5980 chunk 84 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.4273 r_free = 0.4273 target = 0.191899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.169229 restraints weight = 10964.749| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 1.06 r_work: 0.3726 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.2606 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 : 0.566 5.992 13550 Z= 0.296 Chirality : 0.038 0.230 1624 Planarity : 0.004 0.057 1264 Dihedral : 21.973 179.498 2683 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.79 % Allowed : 19.41 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.30), residues: 810 helix: 0.90 (0.28), residues: 373 sheet: -0.88 (0.67), residues: 65 loop : -1.29 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1043 TYR 0.014 0.001 TYR A 254 PHE 0.017 0.001 PHE A 216 TRP 0.036 0.002 TRP A 231 HIS 0.003 0.001 HIS A 191 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9613) covalent geometry : angle 0.56638 (13550) hydrogen bonds : bond 0.04062 ( 396) hydrogen bonds : angle 4.25892 ( 1039) *********************** 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 94 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.214 Fit side-chains REVERT: A 497 GLU cc_start: 0.6813 (mp0) cc_final: 0.6552 (mp0) REVERT: A 949 LYS cc_start: 0.7718 (mmtp) cc_final: 0.7493 (mmmt) REVERT: A 1034 GLN cc_start: 0.6840 (OUTLIER) cc_final: 0.6558 (tp40) outliers start: 19 outliers final: 13 residues processed: 91 average time/residue: 0.0728 time to fit residues: 9.4803 Evaluate side-chains 85 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 370 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 860 ASP 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 6 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 70 optimal weight: 0.0570 chunk 73 optimal weight: 0.0870 chunk 61 optimal weight: 0.7980 chunk 76 optimal weight: 20.0000 overall best weight: 1.5278 ------------------------------------------------------------------------------- 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 = 0.4268 r_free = 0.4268 target = 0.191300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.169732 restraints weight = 11045.872| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 0.81 r_work: 0.3717 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.2648 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= 0.143 Angle : 0.569 5.574 13550 Z= 0.297 Chirality : 0.038 0.228 1624 Planarity : 0.004 0.057 1264 Dihedral : 21.912 179.893 2683 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.79 % Allowed : 19.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.30), residues: 810 helix: 0.98 (0.28), residues: 373 sheet: -0.87 (0.67), residues: 65 loop : -1.25 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1043 TYR 0.013 0.001 TYR A 254 PHE 0.018 0.001 PHE A 216 TRP 0.031 0.002 TRP A 231 HIS 0.003 0.001 HIS A 191 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9613) covalent geometry : angle 0.56892 (13550) hydrogen bonds : bond 0.04034 ( 396) hydrogen bonds : angle 4.22194 ( 1039) *********************** 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 96 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.165 Fit side-chains REVERT: A 35 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7722 (pp) REVERT: A 949 LYS cc_start: 0.7703 (mmtp) cc_final: 0.7501 (mmmt) outliers start: 19 outliers final: 15 residues processed: 93 average time/residue: 0.0690 time to fit residues: 9.1427 Evaluate side-chains 87 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 370 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 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 6 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 58 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 70 optimal weight: 0.2980 chunk 60 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 90 optimal weight: 0.0060 chunk 73 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 overall best weight: 2.0400 ------------------------------------------------------------------------------- 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 = 0.4252 r_free = 0.4252 target = 0.189819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.168073 restraints weight = 11053.885| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 0.81 r_work: 0.3707 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9613 Z= 0.164 Angle : 0.599 7.526 13550 Z= 0.311 Chirality : 0.040 0.247 1624 Planarity : 0.004 0.058 1264 Dihedral : 21.909 179.232 2683 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.35 % Allowed : 19.71 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.29), residues: 810 helix: 0.84 (0.27), residues: 372 sheet: -0.80 (0.69), residues: 60 loop : -1.26 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1043 TYR 0.013 0.001 TYR A 254 PHE 0.020 0.001 PHE A 216 TRP 0.032 0.002 TRP A 231 HIS 0.003 0.001 HIS A 495 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9613) covalent geometry : angle 0.59861 (13550) hydrogen bonds : bond 0.04300 ( 396) hydrogen bonds : angle 4.31337 ( 1039) ********************** 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 86 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.173 Fit side-chains REVERT: A 35 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7806 (pp) REVERT: A 949 LYS cc_start: 0.7785 (mmtp) cc_final: 0.7528 (mmmt) outliers start: 16 outliers final: 15 residues processed: 83 average time/residue: 0.0785 time to fit residues: 9.1650 Evaluate side-chains 85 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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 370 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 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 6 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 3 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- 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 = 0.4257 r_free = 0.4257 target = 0.190382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.167426 restraints weight = 10972.344| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 0.82 r_work: 0.3707 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2765 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= 0.142 Angle : 0.588 8.384 13550 Z= 0.305 Chirality : 0.039 0.241 1624 Planarity : 0.004 0.057 1264 Dihedral : 21.913 179.125 2683 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.65 % Allowed : 19.56 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.29), residues: 810 helix: 0.89 (0.27), residues: 372 sheet: -0.77 (0.70), residues: 60 loop : -1.25 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1043 TYR 0.014 0.001 TYR A 254 PHE 0.021 0.001 PHE A 266 TRP 0.029 0.002 TRP A 231 HIS 0.002 0.001 HIS A 191 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9613) covalent geometry : angle 0.58801 (13550) hydrogen bonds : bond 0.04114 ( 396) hydrogen bonds : angle 4.27730 ( 1039) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1723.66 seconds wall clock time: 30 minutes 16.64 seconds (1816.64 seconds total)