Starting phenix.real_space_refine on Wed Aug 5 22:16:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10yb_75523/08_2026/10yb_75523.cif Found real_map, /net/cci-nas-00/data/ceres_data/10yb_75523/08_2026/10yb_75523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10yb_75523/08_2026/10yb_75523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10yb_75523/08_2026/10yb_75523.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10yb_75523/08_2026/10yb_75523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10yb_75523/08_2026/10yb_75523.map" } resolution = 2.8 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= 0.005 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 294 5.49 5 S 10 5.16 5 C 6568 2.51 5 N 2225 2.21 5 O 2807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11904 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 789 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 789 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 793 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1155 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain: "K" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1877 Classifications: {'DNA': 91} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 90} Time building chain proxies: 2.75, per 1000 atoms: 0.23 Number of scatterers: 11904 At special positions: 0 Unit cell: (74.328, 123.88, 117.36, 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 10 16.00 P 294 15.00 O 2807 8.00 N 2225 7.00 C 6568 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: 1.00 Conformation dependent library (CDL) restraints added in 191.3 milliseconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1384 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 74.5% alpha, 2.7% beta 147 base pairs and 262 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 50 through 57 removed outlier: 3.772A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.626A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.383A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.543A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.514A pdb=" N LYS D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 57 removed outlier: 4.209A pdb=" N VAL E 46 " --> pdb=" O ARG E 42 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA E 47 " --> pdb=" O PRO E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.527A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.793A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.525A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.351A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.511A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.300A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.667A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.341A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.036A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.291A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 397 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 376 hydrogen bonds 752 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 262 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2053 1.33 - 1.45: 4259 1.45 - 1.57: 5798 1.57 - 1.68: 586 1.68 - 1.80: 20 Bond restraints: 12716 Sorted by residual: bond pdb=" C3' DA I 52 " pdb=" C2' DA I 52 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.18e+00 bond pdb=" C3' DT J 15 " pdb=" C2' DT J 15 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.90e+00 bond pdb=" C3' DG K 137 " pdb=" C2' DG K 137 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.68e+00 bond pdb=" C3' DC I 12 " pdb=" C2' DC I 12 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.58e+00 bond pdb=" C3' DG J 52 " pdb=" C2' DG J 52 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.45e+00 ... (remaining 12711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 17168 1.60 - 3.20: 1190 3.20 - 4.79: 56 4.79 - 6.39: 16 6.39 - 7.99: 7 Bond angle restraints: 18437 Sorted by residual: angle pdb=" N VAL A 117 " pdb=" CA VAL A 117 " pdb=" C VAL A 117 " ideal model delta sigma weight residual 112.96 108.39 4.57 1.00e+00 1.00e+00 2.09e+01 angle pdb=" N LEU H 106 " pdb=" CA LEU H 106 " pdb=" C LEU H 106 " ideal model delta sigma weight residual 111.33 105.87 5.46 1.21e+00 6.83e-01 2.04e+01 angle pdb=" N3 DT J 50 " pdb=" C4 DT J 50 " pdb=" O4 DT J 50 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT I 32 " pdb=" C4 DT I 32 " pdb=" O4 DT I 32 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 ... (remaining 18432 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.56: 5022 28.56 - 57.12: 1700 57.12 - 85.68: 152 85.68 - 114.24: 1 114.24 - 142.81: 3 Dihedral angle restraints: 6878 sinusoidal: 4730 harmonic: 2148 Sorted by residual: dihedral pdb=" CD ARG A 40 " pdb=" NE ARG A 40 " pdb=" CZ ARG A 40 " pdb=" NH1 ARG A 40 " ideal model delta sinusoidal sigma weight residual 0.00 -49.68 49.68 1 1.00e+01 1.00e-02 3.39e+01 dihedral pdb=" CA GLU A 50 " pdb=" C GLU A 50 " pdb=" N ILE A 51 " pdb=" CA ILE A 51 " ideal model delta harmonic sigma weight residual 180.00 160.58 19.42 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" C4' DG K 82 " pdb=" C3' DG K 82 " pdb=" O3' DG K 82 " pdb=" P DT K 83 " ideal model delta sinusoidal sigma weight residual 220.00 77.19 142.81 1 3.50e+01 8.16e-04 1.41e+01 ... (remaining 6875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1452 0.043 - 0.087: 479 0.087 - 0.130: 156 0.130 - 0.174: 9 0.174 - 0.217: 4 Chirality restraints: 2100 Sorted by residual: chirality pdb=" CA GLN E 76 " pdb=" N GLN E 76 " pdb=" C GLN E 76 " pdb=" CB GLN E 76 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB THR H 119 " pdb=" CA THR H 119 " pdb=" OG1 THR H 119 " pdb=" CG2 THR H 119 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA PRO H 103 " pdb=" N PRO H 103 " pdb=" C PRO H 103 " pdb=" CB PRO H 103 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.16e-01 ... (remaining 2097 not shown) Planarity restraints: 1313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 40 " -0.848 9.50e-02 1.11e+02 3.80e-01 8.78e+01 pdb=" NE ARG A 40 " 0.049 2.00e-02 2.50e+03 pdb=" CZ ARG A 40 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A 40 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 40 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 24 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.24e+00 pdb=" C ASP B 24 " -0.047 2.00e-02 2.50e+03 pdb=" O ASP B 24 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN B 25 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 63 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C GLU F 63 " 0.036 2.00e-02 2.50e+03 pdb=" O GLU F 63 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN F 64 " -0.012 2.00e-02 2.50e+03 ... (remaining 1310 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 5773 3.01 - 3.48: 11374 3.48 - 3.96: 24290 3.96 - 4.43: 27157 4.43 - 4.90: 35310 Nonbonded interactions: 103904 Sorted by model distance: nonbonded pdb=" O ASP B 24 " pdb=" OD1 ASP B 24 " model vdw 2.540 3.040 nonbonded pdb=" O5' DA I 124 " pdb=" O4' DA I 124 " model vdw 2.542 2.432 nonbonded pdb=" N ILE G 79 " pdb=" O ILE G 79 " model vdw 2.580 2.496 nonbonded pdb=" N ILE C 79 " pdb=" O ILE C 79 " model vdw 2.589 2.496 nonbonded pdb=" N1 DG K 120 " pdb=" C4 DG K 120 " model vdw 2.592 2.672 ... (remaining 103899 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 24 through 101) } ncs_group { reference = (chain 'C' and resid 15 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 34 through 124) selection = chain 'H' } 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: 6.230 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.450 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:9.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 12716 Z= 0.550 Angle : 0.811 7.991 18437 Z= 0.703 Chirality : 0.047 0.217 2100 Planarity : 0.012 0.380 1313 Dihedral : 28.466 142.806 5494 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.49 % Allowed : 19.32 % Favored : 80.19 % 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 are not related in a simple way. whole: 1.37 (0.30), residues: 726 helix: 1.52 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.77 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 33 TYR 0.015 0.002 TYR H 40 PHE 0.009 0.001 PHE C 25 HIS 0.005 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00645 / 0.55 (12716) covalent geometry : angle 0.81072 / 0.70 (18437) hydrogen bonds : bond 0.10596 / 6.76 ( 773) hydrogen bonds : angle 4.31198 / 3.00 ( 1925) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 147 time to evaluate : 0.209 Fit side-chains REVERT: A 59 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8171 (mt-10) REVERT: B 78 ARG cc_start: 0.9145 (mtm-85) cc_final: 0.8809 (mtm-85) REVERT: C 15 LYS cc_start: 0.8401 (ptpp) cc_final: 0.8132 (ptmm) REVERT: C 73 ASN cc_start: 0.9060 (t0) cc_final: 0.8520 (t0) REVERT: E 59 GLU cc_start: 0.8542 (pt0) cc_final: 0.8196 (pm20) REVERT: E 79 LYS cc_start: 0.8882 (tttt) cc_final: 0.8616 (tttp) REVERT: G 73 ASN cc_start: 0.8932 (t0) cc_final: 0.8707 (t160) outliers start: 3 outliers final: 0 residues processed: 148 average time/residue: 0.9151 time to fit residues: 142.4599 Evaluate side-chains 144 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.0010 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 109 HIS E 39 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.097473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.062303 restraints weight = 23134.763| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.53 r_work: 0.2706 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.0531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12716 Z= 0.176 Angle : 0.645 6.330 18437 Z= 0.381 Chirality : 0.046 0.216 2100 Planarity : 0.004 0.056 1313 Dihedral : 30.753 144.752 4034 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.95 % Allowed : 16.56 % Favored : 81.49 % 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 are not related in a simple way. whole: 2.23 (0.31), residues: 726 helix: 2.13 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.62 (0.42), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 79 TYR 0.010 0.001 TYR H 40 PHE 0.008 0.001 PHE A 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.18 (12716) covalent geometry : angle 0.64496 / 0.38 (18437) hydrogen bonds : bond 0.05053 / 3.42 ( 773) hydrogen bonds : angle 3.30949 / 2.30 ( 1925) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.223 Fit side-chains REVERT: A 59 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8105 (mt-10) REVERT: B 78 ARG cc_start: 0.9123 (mtm-85) cc_final: 0.8720 (mtm-85) REVERT: C 15 LYS cc_start: 0.8415 (ptpp) cc_final: 0.8149 (ptmm) REVERT: C 73 ASN cc_start: 0.9030 (t0) cc_final: 0.8486 (t0) REVERT: E 59 GLU cc_start: 0.8484 (pt0) cc_final: 0.8076 (pm20) REVERT: E 79 LYS cc_start: 0.8567 (tttt) cc_final: 0.8328 (tttp) REVERT: G 64 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8199 (tp30) REVERT: G 73 ASN cc_start: 0.8870 (t0) cc_final: 0.8647 (t160) outliers start: 12 outliers final: 4 residues processed: 150 average time/residue: 0.9374 time to fit residues: 147.8675 Evaluate side-chains 147 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 142 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 29 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 109 HIS G 104 GLN G 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.097735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.062511 restraints weight = 23409.892| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.55 r_work: 0.2712 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.0582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12716 Z= 0.153 Angle : 0.626 6.665 18437 Z= 0.374 Chirality : 0.045 0.219 2100 Planarity : 0.004 0.036 1313 Dihedral : 30.779 144.478 4034 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.79 % Allowed : 17.21 % Favored : 81.01 % 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 are not related in a simple way. whole: 2.50 (0.31), residues: 726 helix: 2.35 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.59 (0.42), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 71 TYR 0.010 0.001 TYR C 57 PHE 0.010 0.001 PHE A 67 HIS 0.010 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.15 (12716) covalent geometry : angle 0.62553 / 0.37 (18437) hydrogen bonds : bond 0.04634 / 3.14 ( 773) hydrogen bonds : angle 3.19979 / 2.22 ( 1925) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.307 Fit side-chains REVERT: A 59 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8122 (mt-10) REVERT: B 78 ARG cc_start: 0.9104 (mtm-85) cc_final: 0.8654 (mtm-85) REVERT: C 15 LYS cc_start: 0.8387 (ptpp) cc_final: 0.8116 (ptmm) REVERT: C 73 ASN cc_start: 0.9039 (t0) cc_final: 0.8506 (t0) REVERT: E 59 GLU cc_start: 0.8473 (pt0) cc_final: 0.8067 (pm20) REVERT: E 79 LYS cc_start: 0.8485 (tttt) cc_final: 0.8271 (tttp) REVERT: G 73 ASN cc_start: 0.8857 (t0) cc_final: 0.8623 (t160) outliers start: 11 outliers final: 6 residues processed: 145 average time/residue: 0.8845 time to fit residues: 134.9991 Evaluate side-chains 148 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 142 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 94 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 30.0000 chunk 11 optimal weight: 0.0470 chunk 57 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN G 104 GLN G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.097049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.061779 restraints weight = 23233.042| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.54 r_work: 0.2742 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.0700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12716 Z= 0.202 Angle : 0.629 5.835 18437 Z= 0.372 Chirality : 0.044 0.261 2100 Planarity : 0.004 0.038 1313 Dihedral : 30.882 145.055 4034 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.27 % Allowed : 15.75 % Favored : 81.98 % 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 are not related in a simple way. whole: 2.68 (0.31), residues: 726 helix: 2.50 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.58 (0.42), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 71 TYR 0.011 0.001 TYR C 57 PHE 0.012 0.001 PHE A 67 HIS 0.010 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.20 (12716) covalent geometry : angle 0.62889 / 0.37 (18437) hydrogen bonds : bond 0.04495 / 3.07 ( 773) hydrogen bonds : angle 3.10563 / 2.15 ( 1925) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.342 Fit side-chains REVERT: B 77 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.9001 (mtmp) REVERT: C 15 LYS cc_start: 0.8429 (ptpp) cc_final: 0.8152 (ptmm) REVERT: C 73 ASN cc_start: 0.9026 (t0) cc_final: 0.8471 (t0) REVERT: E 59 GLU cc_start: 0.8314 (pt0) cc_final: 0.7945 (pm20) REVERT: E 122 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8656 (ptpt) REVERT: G 64 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8031 (tp30) REVERT: G 73 ASN cc_start: 0.8838 (t0) cc_final: 0.8618 (t160) REVERT: H 105 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8453 (tp30) outliers start: 14 outliers final: 7 residues processed: 146 average time/residue: 0.9114 time to fit residues: 139.8820 Evaluate side-chains 150 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 45 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 chunk 85 optimal weight: 30.0000 chunk 83 optimal weight: 30.0000 chunk 74 optimal weight: 9.9990 chunk 82 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 104 GLN D 109 HIS G 104 GLN G 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.093979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.058295 restraints weight = 23292.335| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 1.53 r_work: 0.2665 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 12716 Z= 0.353 Angle : 0.747 6.915 18437 Z= 0.412 Chirality : 0.051 0.253 2100 Planarity : 0.005 0.045 1313 Dihedral : 31.692 146.846 4034 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.76 % Allowed : 17.05 % Favored : 80.19 % 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 are not related in a simple way. whole: 2.28 (0.31), residues: 726 helix: 2.28 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.99 (0.40), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 71 TYR 0.016 0.002 TYR D 42 PHE 0.016 0.003 PHE C 25 HIS 0.009 0.002 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00767 / 0.35 (12716) covalent geometry : angle 0.74655 / 0.41 (18437) hydrogen bonds : bond 0.05929 / 4.02 ( 773) hydrogen bonds : angle 3.13872 / 2.18 ( 1925) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.264 Fit side-chains REVERT: A 97 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8442 (mt-10) REVERT: A 120 MET cc_start: 0.8779 (mtt) cc_final: 0.8447 (mtt) REVERT: C 15 LYS cc_start: 0.8582 (ptpp) cc_final: 0.8285 (ptmm) REVERT: C 73 ASN cc_start: 0.9066 (t0) cc_final: 0.8523 (t0) REVERT: E 59 GLU cc_start: 0.8610 (pt0) cc_final: 0.8239 (pm20) REVERT: G 64 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8328 (tt0) REVERT: G 73 ASN cc_start: 0.9089 (t0) cc_final: 0.8865 (t160) outliers start: 17 outliers final: 7 residues processed: 142 average time/residue: 0.9490 time to fit residues: 141.6063 Evaluate side-chains 144 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 46 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 71 optimal weight: 30.0000 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN A 113 HIS C 104 GLN G 104 GLN G 110 ASN H 63 ASN H 109 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.096440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.060843 restraints weight = 23165.343| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.52 r_work: 0.2726 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12716 Z= 0.143 Angle : 0.633 6.469 18437 Z= 0.365 Chirality : 0.045 0.294 2100 Planarity : 0.004 0.042 1313 Dihedral : 31.544 145.600 4034 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.11 % Allowed : 19.16 % Favored : 78.73 % 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 are not related in a simple way. whole: 2.76 (0.31), residues: 726 helix: 2.55 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.54 (0.43), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 79 TYR 0.014 0.001 TYR H 40 PHE 0.006 0.001 PHE A 67 HIS 0.005 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.14 (12716) covalent geometry : angle 0.63336 / 0.37 (18437) hydrogen bonds : bond 0.03893 / 2.63 ( 773) hydrogen bonds : angle 2.90054 / 2.02 ( 1925) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.231 Fit side-chains REVERT: A 87 SER cc_start: 0.9039 (OUTLIER) cc_final: 0.8777 (p) REVERT: A 120 MET cc_start: 0.8674 (mtt) cc_final: 0.8331 (mtt) REVERT: C 15 LYS cc_start: 0.8591 (ptpp) cc_final: 0.8284 (ptmm) REVERT: C 73 ASN cc_start: 0.9053 (t0) cc_final: 0.8522 (t0) REVERT: E 59 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8142 (pm20) REVERT: E 120 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8227 (mtt) REVERT: E 122 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8658 (pttt) REVERT: G 64 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8227 (tp30) outliers start: 13 outliers final: 4 residues processed: 150 average time/residue: 0.8682 time to fit residues: 137.3616 Evaluate side-chains 150 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 85 optimal weight: 30.0000 chunk 57 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 90 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 84 optimal weight: 30.0000 chunk 92 optimal weight: 9.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN G 104 GLN G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.095668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.060254 restraints weight = 23134.429| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 1.51 r_work: 0.2711 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12716 Z= 0.205 Angle : 0.647 6.401 18437 Z= 0.371 Chirality : 0.045 0.294 2100 Planarity : 0.004 0.042 1313 Dihedral : 31.534 145.737 4034 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.95 % Allowed : 19.48 % Favored : 78.57 % 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 are not related in a simple way. whole: 2.77 (0.32), residues: 726 helix: 2.58 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.62 (0.43), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 71 TYR 0.011 0.002 TYR C 57 PHE 0.012 0.002 PHE A 67 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.21 (12716) covalent geometry : angle 0.64688 / 0.37 (18437) hydrogen bonds : bond 0.04353 / 2.96 ( 773) hydrogen bonds : angle 2.90428 / 2.03 ( 1925) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.359 Fit side-chains REVERT: A 87 SER cc_start: 0.9027 (OUTLIER) cc_final: 0.8756 (p) REVERT: A 120 MET cc_start: 0.8685 (mtt) cc_final: 0.8354 (mtt) REVERT: C 15 LYS cc_start: 0.8607 (ptpp) cc_final: 0.8291 (ptmm) REVERT: C 56 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8563 (tt0) REVERT: C 73 ASN cc_start: 0.9057 (t0) cc_final: 0.8606 (t0) REVERT: C 75 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8547 (mtpp) REVERT: E 59 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8168 (pm20) outliers start: 12 outliers final: 4 residues processed: 145 average time/residue: 0.8198 time to fit residues: 125.1950 Evaluate side-chains 146 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 18 optimal weight: 0.1980 chunk 28 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 19 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 58 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN G 104 GLN G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.096713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.061450 restraints weight = 22873.615| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.49 r_work: 0.2740 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 12716 Z= 0.133 Angle : 0.622 6.698 18437 Z= 0.363 Chirality : 0.045 0.303 2100 Planarity : 0.004 0.042 1313 Dihedral : 31.498 145.347 4034 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.27 % Allowed : 19.64 % Favored : 78.08 % 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 are not related in a simple way. whole: 2.87 (0.31), residues: 726 helix: 2.63 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.47 (0.43), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 71 TYR 0.013 0.001 TYR H 40 PHE 0.008 0.001 PHE A 67 HIS 0.010 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.13 (12716) covalent geometry : angle 0.62228 / 0.36 (18437) hydrogen bonds : bond 0.03836 / 2.61 ( 773) hydrogen bonds : angle 2.85746 / 2.01 ( 1925) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.422 Fit side-chains REVERT: A 59 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8039 (pm20) REVERT: A 87 SER cc_start: 0.9027 (OUTLIER) cc_final: 0.8765 (p) REVERT: A 120 MET cc_start: 0.8594 (mtt) cc_final: 0.8244 (mtt) REVERT: B 78 ARG cc_start: 0.9150 (mtm-85) cc_final: 0.8532 (mtm-85) REVERT: C 15 LYS cc_start: 0.8593 (ptpp) cc_final: 0.8268 (ptmm) REVERT: C 56 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8514 (tt0) REVERT: C 73 ASN cc_start: 0.9037 (t0) cc_final: 0.8573 (t0) REVERT: C 75 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8515 (mtpp) REVERT: E 59 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8124 (pm20) REVERT: G 92 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8521 (mt-10) outliers start: 14 outliers final: 3 residues processed: 152 average time/residue: 0.9355 time to fit residues: 149.6447 Evaluate side-chains 151 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 59 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 18 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 84 optimal weight: 30.0000 chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 96 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN G 104 GLN G 110 ASN H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.097163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.062004 restraints weight = 22953.300| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.49 r_work: 0.2744 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12716 Z= 0.138 Angle : 0.611 9.904 18437 Z= 0.358 Chirality : 0.043 0.309 2100 Planarity : 0.004 0.042 1313 Dihedral : 31.380 145.205 4034 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.95 % Allowed : 19.48 % Favored : 78.57 % 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 are not related in a simple way. whole: 3.07 (0.32), residues: 726 helix: 2.78 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.42 (0.44), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 71 TYR 0.013 0.001 TYR H 40 PHE 0.010 0.001 PHE A 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.14 (12716) covalent geometry : angle 0.61089 / 0.36 (18437) hydrogen bonds : bond 0.03666 / 2.50 ( 773) hydrogen bonds : angle 2.79221 / 1.95 ( 1925) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.352 Fit side-chains REVERT: A 59 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7830 (pm20) REVERT: A 87 SER cc_start: 0.9027 (OUTLIER) cc_final: 0.8779 (p) REVERT: B 78 ARG cc_start: 0.9140 (mtm-85) cc_final: 0.8550 (mtm-85) REVERT: C 15 LYS cc_start: 0.8609 (ptpp) cc_final: 0.8340 (ptmm) REVERT: C 56 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8522 (tt0) REVERT: C 73 ASN cc_start: 0.9053 (t0) cc_final: 0.8608 (t0) REVERT: C 75 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8492 (mtpp) REVERT: E 59 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8110 (pm20) REVERT: G 74 LYS cc_start: 0.9299 (mtpp) cc_final: 0.8982 (mtmt) outliers start: 12 outliers final: 4 residues processed: 151 average time/residue: 0.9391 time to fit residues: 149.2041 Evaluate side-chains 151 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 59 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 1 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.0010 chunk 5 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 19 optimal weight: 0.0570 chunk 26 optimal weight: 2.9990 overall best weight: 0.7706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.097725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.062503 restraints weight = 23213.138| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.51 r_work: 0.2762 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12716 Z= 0.138 Angle : 0.609 11.119 18437 Z= 0.356 Chirality : 0.042 0.312 2100 Planarity : 0.004 0.040 1313 Dihedral : 31.300 144.947 4034 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.46 % Allowed : 20.29 % Favored : 78.25 % 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 are not related in a simple way. whole: 3.18 (0.32), residues: 726 helix: 2.85 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.36 (0.44), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 71 TYR 0.012 0.001 TYR H 40 PHE 0.010 0.001 PHE A 67 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.14 (12716) covalent geometry : angle 0.60912 / 0.36 (18437) hydrogen bonds : bond 0.03591 / 2.44 ( 773) hydrogen bonds : angle 2.74636 / 1.94 ( 1925) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 0.322 Fit side-chains REVERT: A 42 ARG cc_start: 0.8787 (mmm-85) cc_final: 0.8488 (mmm-85) REVERT: A 59 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7916 (pm20) REVERT: A 87 SER cc_start: 0.9049 (OUTLIER) cc_final: 0.8812 (p) REVERT: B 78 ARG cc_start: 0.9127 (mtm-85) cc_final: 0.8552 (mtm-85) REVERT: C 15 LYS cc_start: 0.8674 (ptpp) cc_final: 0.8244 (ptmm) REVERT: C 56 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8557 (tt0) REVERT: C 73 ASN cc_start: 0.9062 (t0) cc_final: 0.8644 (t0) REVERT: C 75 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8462 (mtpp) REVERT: C 76 THR cc_start: 0.9036 (p) cc_final: 0.8761 (t) REVERT: E 59 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8144 (pm20) REVERT: G 74 LYS cc_start: 0.9320 (mtpp) cc_final: 0.9060 (mtmt) outliers start: 9 outliers final: 3 residues processed: 153 average time/residue: 0.9526 time to fit residues: 153.2806 Evaluate side-chains 153 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 59 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 77 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 0.0030 chunk 69 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN G 104 GLN G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.097719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.062716 restraints weight = 23089.703| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.49 r_work: 0.2771 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12716 Z= 0.136 Angle : 0.611 10.107 18437 Z= 0.357 Chirality : 0.042 0.315 2100 Planarity : 0.004 0.052 1313 Dihedral : 31.284 144.856 4034 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.46 % Allowed : 20.78 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.21 (0.32), residues: 726 helix: 2.87 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.36 (0.44), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 71 TYR 0.012 0.001 TYR H 40 PHE 0.010 0.001 PHE A 67 HIS 0.005 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.14 (12716) covalent geometry : angle 0.61147 / 0.36 (18437) hydrogen bonds : bond 0.03570 / 2.43 ( 773) hydrogen bonds : angle 2.71434 / 1.91 ( 1925) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4560.05 seconds wall clock time: 78 minutes 12.76 seconds (4692.76 seconds total)