Starting phenix.real_space_refine on Wed Aug 5 22:24:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10yd_75525/08_2026/10yd_75525.cif Found real_map, /net/cci-nas-00/data/ceres_data/10yd_75525/08_2026/10yd_75525.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/10yd_75525/08_2026/10yd_75525.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10yd_75525/08_2026/10yd_75525.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10yd_75525/08_2026/10yd_75525.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10yd_75525/08_2026/10yd_75525.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 6601 2.51 5 N 2240 2.21 5 O 2814 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: 11959 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: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} 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: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} 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: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} 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: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 310 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "K" Number of atoms: 2722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2722 Classifications: {'DNA': 132} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 131} Time building chain proxies: 1.86, per 1000 atoms: 0.16 Number of scatterers: 11959 At special positions: 0 Unit cell: (74.328, 123.88, 118.664, 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 2814 8.00 N 2240 7.00 C 6601 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: 0.69 Conformation dependent library (CDL) restraints added in 179.5 milliseconds 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 74.1% alpha, 2.7% beta 147 base pairs and 258 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 50 through 55 removed outlier: 3.544A pdb=" N TYR A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.982A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) 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: 3.544A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.775A 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: 4.365A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.654A 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 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.511A 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 103 through 123 removed outlier: 3.509A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 57 removed outlier: 4.173A pdb=" N VAL E 46 " --> pdb=" O ARG E 42 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA E 47 " --> pdb=" O PRO E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.082A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (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 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.658A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.547A 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: 4.318A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 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 103 through 124 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.151A 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: 6.599A 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: 7.340A 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: 6.925A 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: 7.293A 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 78 399 hydrogen bonds defined for protein. 1179 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 376 hydrogen bonds 752 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 258 stacking parallelities Total time for adding SS restraints: 1.84 Time building geometry restraints manager: 0.92 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: 2117 1.33 - 1.45: 4288 1.45 - 1.57: 5760 1.57 - 1.69: 586 1.69 - 1.81: 20 Bond restraints: 12771 Sorted by residual: bond pdb=" C3' DG K 52 " pdb=" C2' DG K 52 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.50e+00 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 9.26e+00 bond pdb=" C3' DG I 94 " pdb=" C2' DG I 94 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.76e+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 8.69e+00 bond pdb=" C3' DC I 95 " pdb=" C2' DC I 95 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.46e+00 ... (remaining 12766 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 17436 1.68 - 3.36: 1021 3.36 - 5.04: 35 5.04 - 6.72: 9 6.72 - 8.39: 8 Bond angle restraints: 18509 Sorted by residual: angle pdb=" N GLN G 24 " pdb=" CA GLN G 24 " pdb=" C GLN G 24 " ideal model delta sigma weight residual 113.88 108.19 5.69 1.23e+00 6.61e-01 2.14e+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 angle pdb=" N3 DT K 50 " pdb=" C4 DT K 50 " pdb=" O4 DT K 50 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT I 32 " pdb=" C4 DT I 32 " pdb=" O4 DT I 32 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT I 112 " pdb=" C4 DT I 112 " pdb=" O4 DT I 112 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 ... (remaining 18504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.57: 5033 28.57 - 57.14: 1729 57.14 - 85.71: 151 85.71 - 114.28: 1 114.28 - 142.86: 2 Dihedral angle restraints: 6916 sinusoidal: 4750 harmonic: 2166 Sorted by residual: dihedral pdb=" CD ARG H 33 " pdb=" NE ARG H 33 " pdb=" CZ ARG H 33 " pdb=" NH1 ARG H 33 " ideal model delta sinusoidal sigma weight residual 0.00 -45.11 45.11 1 1.00e+01 1.00e-02 2.83e+01 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 -41.25 41.25 1 1.00e+01 1.00e-02 2.38e+01 dihedral pdb=" CA LEU A 48 " pdb=" C LEU A 48 " pdb=" N ARG A 49 " pdb=" CA ARG A 49 " ideal model delta harmonic sigma weight residual 180.00 160.17 19.83 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 6913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1420 0.041 - 0.082: 509 0.082 - 0.123: 163 0.123 - 0.164: 13 0.164 - 0.205: 3 Chirality restraints: 2108 Sorted by residual: chirality pdb=" CA VAL G 107 " pdb=" N VAL G 107 " pdb=" C VAL G 107 " pdb=" CB VAL G 107 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ASP A 81 " pdb=" N ASP A 81 " pdb=" C ASP A 81 " pdb=" CB ASP A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" C3' DC K 126 " pdb=" C4' DC K 126 " pdb=" O3' DC K 126 " pdb=" C2' DC K 126 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 6.87e-01 ... (remaining 2105 not shown) Planarity restraints: 1322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 33 " 0.775 9.50e-02 1.11e+02 3.47e-01 7.34e+01 pdb=" NE ARG H 33 " -0.046 2.00e-02 2.50e+03 pdb=" CZ ARG H 33 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG H 33 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG H 33 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 40 " 0.732 9.50e-02 1.11e+02 3.28e-01 6.56e+01 pdb=" NE ARG A 40 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG A 40 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 40 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 40 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 58 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.90e+00 pdb=" C THR A 58 " 0.038 2.00e-02 2.50e+03 pdb=" O THR A 58 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU A 59 " -0.013 2.00e-02 2.50e+03 ... (remaining 1319 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.01: 5639 3.01 - 3.48: 11328 3.48 - 3.95: 24553 3.95 - 4.43: 27404 4.43 - 4.90: 35526 Nonbonded interactions: 104450 Sorted by model distance: nonbonded pdb=" O5' DA I 124 " pdb=" O4' DA I 124 " model vdw 2.533 2.432 nonbonded pdb=" N ILE C 79 " pdb=" O ILE C 79 " model vdw 2.590 2.496 nonbonded pdb=" N ILE G 79 " pdb=" O ILE G 79 " model vdw 2.592 2.496 nonbonded pdb=" N1 DG K 120 " pdb=" C4 DG K 120 " model vdw 2.593 2.672 nonbonded pdb=" N1 DG I 40 " pdb=" C4 DG I 40 " model vdw 2.594 2.672 ... (remaining 104445 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' and resid 38 through 133) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 15 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 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: 4.960 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: 0.240 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.700 Find NCS groups from input model: 0.080 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:8.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 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 0.051 12771 Z= 0.536 Angle : 0.789 8.394 18509 Z= 0.691 Chirality : 0.045 0.205 2108 Planarity : 0.014 0.347 1322 Dihedral : 28.326 142.855 5520 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.32 % Allowed : 20.10 % Favored : 79.58 % 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: 1.38 (0.30), residues: 732 helix: 1.48 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.60 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 71 TYR 0.013 0.001 TYR D 40 PHE 0.008 0.002 PHE C 25 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.54 (12771) covalent geometry : angle 0.78857 / 0.69 (18509) hydrogen bonds : bond 0.11085 / 7.39 ( 775) hydrogen bonds : angle 4.15265 / 2.90 ( 1931) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8234 (ttt90) cc_final: 0.7923 (mtp85) REVERT: C 90 ASP cc_start: 0.8599 (t0) cc_final: 0.8017 (t70) REVERT: D 42 TYR cc_start: 0.8226 (t80) cc_final: 0.7966 (m-80) REVERT: G 64 GLU cc_start: 0.8632 (tt0) cc_final: 0.8345 (tp30) REVERT: G 71 ARG cc_start: 0.8598 (ttp80) cc_final: 0.8348 (ttp80) REVERT: G 73 ASN cc_start: 0.8789 (t0) cc_final: 0.8048 (t0) REVERT: G 91 GLU cc_start: 0.8975 (tp30) cc_final: 0.8699 (tp30) REVERT: H 63 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8467 (m-40) outliers start: 2 outliers final: 0 residues processed: 161 average time/residue: 0.7157 time to fit residues: 121.6214 Evaluate side-chains 158 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN F 25 ASN G 104 GLN H 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.099642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.066964 restraints weight = 21585.635| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.51 r_work: 0.2751 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.0478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12771 Z= 0.168 Angle : 0.626 5.969 18509 Z= 0.378 Chirality : 0.045 0.207 2108 Planarity : 0.005 0.070 1322 Dihedral : 30.555 143.080 4045 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.93 % Allowed : 17.85 % Favored : 80.23 % 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: 2.17 (0.30), residues: 732 helix: 2.05 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.44 (0.42), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 71 TYR 0.009 0.001 TYR H 40 PHE 0.010 0.001 PHE A 67 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.17 (12771) covalent geometry : angle 0.62629 / 0.38 (18509) hydrogen bonds : bond 0.05171 / 3.47 ( 775) hydrogen bonds : angle 3.26553 / 2.27 ( 1931) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8202 (ttt90) cc_final: 0.7870 (mtp85) REVERT: G 64 GLU cc_start: 0.8635 (tt0) cc_final: 0.8321 (tp30) REVERT: G 73 ASN cc_start: 0.8743 (t0) cc_final: 0.8002 (t0) REVERT: G 91 GLU cc_start: 0.8731 (tp30) cc_final: 0.8525 (tp30) REVERT: H 63 ASN cc_start: 0.8820 (OUTLIER) cc_final: 0.8513 (m-40) outliers start: 12 outliers final: 4 residues processed: 161 average time/residue: 0.7909 time to fit residues: 134.5456 Evaluate side-chains 161 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 156 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 35 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 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 = 0.3536 r_free = 0.3536 target = 0.099869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.066927 restraints weight = 21674.189| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.52 r_work: 0.2748 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.0546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 12771 Z= 0.159 Angle : 0.623 7.204 18509 Z= 0.374 Chirality : 0.044 0.210 2108 Planarity : 0.004 0.037 1322 Dihedral : 30.599 142.819 4045 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.89 % Allowed : 17.20 % Favored : 79.90 % 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: 2.35 (0.31), residues: 732 helix: 2.19 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.45 (0.43), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 79 TYR 0.010 0.001 TYR D 42 PHE 0.009 0.001 PHE A 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.16 (12771) covalent geometry : angle 0.62254 / 0.37 (18509) hydrogen bonds : bond 0.04817 / 3.23 ( 775) hydrogen bonds : angle 3.16191 / 2.20 ( 1931) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8235 (ttt90) cc_final: 0.7898 (mtp85) REVERT: C 64 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8323 (tt0) REVERT: C 75 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8790 (mttm) REVERT: G 64 GLU cc_start: 0.8674 (tt0) cc_final: 0.8357 (tp30) REVERT: G 73 ASN cc_start: 0.8741 (t0) cc_final: 0.8001 (t0) REVERT: G 91 GLU cc_start: 0.8732 (tp30) cc_final: 0.8526 (tp30) REVERT: H 63 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8568 (m-40) outliers start: 18 outliers final: 8 residues processed: 164 average time/residue: 0.7333 time to fit residues: 127.2222 Evaluate side-chains 167 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.098979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.066047 restraints weight = 21586.057| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.52 r_work: 0.2728 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.0753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12771 Z= 0.201 Angle : 0.627 5.878 18509 Z= 0.371 Chirality : 0.043 0.211 2108 Planarity : 0.004 0.040 1322 Dihedral : 30.813 143.238 4045 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.89 % Allowed : 16.72 % Favored : 80.39 % 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: 2.52 (0.31), residues: 732 helix: 2.33 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -0.47 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 71 TYR 0.012 0.001 TYR H 40 PHE 0.012 0.002 PHE A 67 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.20 (12771) covalent geometry : angle 0.62732 / 0.37 (18509) hydrogen bonds : bond 0.04527 / 3.05 ( 775) hydrogen bonds : angle 2.98161 / 2.08 ( 1931) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.326 Fit side-chains REVERT: A 42 ARG cc_start: 0.8250 (ttt90) cc_final: 0.7927 (mtp85) REVERT: B 77 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8754 (mtpt) REVERT: C 64 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8322 (tt0) REVERT: C 95 LYS cc_start: 0.9227 (ttpp) cc_final: 0.8950 (ttpp) REVERT: E 120 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.7755 (mtt) REVERT: G 91 GLU cc_start: 0.8692 (tp30) cc_final: 0.8468 (tp30) REVERT: H 63 ASN cc_start: 0.8981 (OUTLIER) cc_final: 0.8654 (m-40) outliers start: 18 outliers final: 7 residues processed: 162 average time/residue: 0.7238 time to fit residues: 123.8661 Evaluate side-chains 163 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 39 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 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 = 0.3530 r_free = 0.3530 target = 0.099474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.066653 restraints weight = 21486.105| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.50 r_work: 0.2739 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12771 Z= 0.155 Angle : 0.611 7.908 18509 Z= 0.364 Chirality : 0.043 0.218 2108 Planarity : 0.004 0.041 1322 Dihedral : 30.842 143.620 4045 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.57 % Allowed : 18.65 % Favored : 78.78 % 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: 2.65 (0.31), residues: 732 helix: 2.41 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -0.37 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 71 TYR 0.010 0.001 TYR D 40 PHE 0.011 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (12771) covalent geometry : angle 0.61131 / 0.36 (18509) hydrogen bonds : bond 0.04349 / 2.92 ( 775) hydrogen bonds : angle 2.95659 / 2.06 ( 1931) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.335 Fit side-chains REVERT: A 42 ARG cc_start: 0.8243 (ttt90) cc_final: 0.7924 (mtp85) REVERT: B 77 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8743 (mtpt) REVERT: C 95 LYS cc_start: 0.9187 (ttpp) cc_final: 0.8927 (ttpp) REVERT: G 91 GLU cc_start: 0.8693 (tp30) cc_final: 0.8446 (tp30) REVERT: H 63 ASN cc_start: 0.8937 (OUTLIER) cc_final: 0.8603 (m-40) outliers start: 16 outliers final: 9 residues processed: 159 average time/residue: 0.8093 time to fit residues: 136.1737 Evaluate side-chains 164 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 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 = 0.3489 r_free = 0.3489 target = 0.096890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.063823 restraints weight = 21415.232| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.47 r_work: 0.2686 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12771 Z= 0.251 Angle : 0.683 7.544 18509 Z= 0.385 Chirality : 0.047 0.227 2108 Planarity : 0.005 0.045 1322 Dihedral : 31.379 146.777 4045 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.73 % Allowed : 19.29 % Favored : 77.97 % 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: 2.45 (0.31), residues: 732 helix: 2.33 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.65 (0.42), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 71 TYR 0.015 0.002 TYR H 42 PHE 0.015 0.002 PHE G 25 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.25 (12771) covalent geometry : angle 0.68345 / 0.39 (18509) hydrogen bonds : bond 0.05175 / 3.47 ( 775) hydrogen bonds : angle 2.94008 / 2.05 ( 1931) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.353 Fit side-chains REVERT: A 42 ARG cc_start: 0.8288 (ttt90) cc_final: 0.7980 (mtp85) REVERT: B 77 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8781 (mtpt) REVERT: C 64 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8301 (tt0) REVERT: C 75 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8830 (mttm) REVERT: C 95 LYS cc_start: 0.9192 (ttpp) cc_final: 0.8890 (ttpp) REVERT: E 59 GLU cc_start: 0.8731 (pt0) cc_final: 0.8462 (pm20) REVERT: G 91 GLU cc_start: 0.8676 (tp30) cc_final: 0.8405 (tp30) REVERT: H 63 ASN cc_start: 0.9087 (OUTLIER) cc_final: 0.8754 (m-40) outliers start: 17 outliers final: 8 residues processed: 162 average time/residue: 0.8019 time to fit residues: 136.8743 Evaluate side-chains 165 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 2 optimal weight: 0.2980 chunk 89 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 86 optimal weight: 30.0000 chunk 26 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 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 = 0.3519 r_free = 0.3519 target = 0.098729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.065947 restraints weight = 21401.950| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.49 r_work: 0.2733 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12771 Z= 0.140 Angle : 0.620 6.192 18509 Z= 0.360 Chirality : 0.043 0.259 2108 Planarity : 0.004 0.048 1322 Dihedral : 31.285 145.423 4045 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.09 % Allowed : 20.58 % Favored : 77.33 % 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: 2.73 (0.31), residues: 732 helix: 2.51 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.47 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 71 TYR 0.010 0.001 TYR D 40 PHE 0.009 0.001 PHE A 67 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.14 (12771) covalent geometry : angle 0.62008 / 0.36 (18509) hydrogen bonds : bond 0.03863 / 2.60 ( 775) hydrogen bonds : angle 2.81142 / 1.96 ( 1931) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.311 Fit side-chains REVERT: A 42 ARG cc_start: 0.8276 (ttt90) cc_final: 0.7977 (mtp85) REVERT: B 77 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8774 (mtpt) REVERT: B 79 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8671 (mtmp) REVERT: C 64 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: C 95 LYS cc_start: 0.9205 (ttpp) cc_final: 0.8929 (ttpp) REVERT: E 59 GLU cc_start: 0.8585 (pt0) cc_final: 0.8336 (pm20) REVERT: G 64 GLU cc_start: 0.8685 (tt0) cc_final: 0.8339 (tp30) REVERT: G 91 GLU cc_start: 0.8645 (tp30) cc_final: 0.8371 (tp30) REVERT: H 63 ASN cc_start: 0.8985 (OUTLIER) cc_final: 0.8650 (m-40) REVERT: H 99 ARG cc_start: 0.8983 (mmm-85) cc_final: 0.8716 (mtm-85) outliers start: 13 outliers final: 5 residues processed: 163 average time/residue: 0.7661 time to fit residues: 131.9460 Evaluate side-chains 166 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 157 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 99 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 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 = 0.3495 r_free = 0.3495 target = 0.097156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.064226 restraints weight = 21504.831| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.47 r_work: 0.2702 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12771 Z= 0.221 Angle : 0.650 7.148 18509 Z= 0.371 Chirality : 0.045 0.247 2108 Planarity : 0.004 0.048 1322 Dihedral : 31.333 145.042 4045 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.41 % Allowed : 20.26 % Favored : 77.33 % 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: 2.58 (0.31), residues: 732 helix: 2.42 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.58 (0.43), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 71 TYR 0.013 0.002 TYR H 42 PHE 0.011 0.002 PHE A 67 HIS 0.002 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.22 (12771) covalent geometry : angle 0.65040 / 0.37 (18509) hydrogen bonds : bond 0.04591 / 3.08 ( 775) hydrogen bonds : angle 2.87029 / 2.00 ( 1931) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.192 Fit side-chains REVERT: A 42 ARG cc_start: 0.8267 (ttt90) cc_final: 0.7987 (mtp85) REVERT: B 77 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8783 (mtpt) REVERT: B 79 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8680 (mtmp) REVERT: B 92 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8155 (ttp80) REVERT: C 64 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: C 75 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8837 (mttm) REVERT: C 95 LYS cc_start: 0.9228 (ttpp) cc_final: 0.8923 (ttpp) REVERT: E 59 GLU cc_start: 0.8663 (pt0) cc_final: 0.8412 (pm20) REVERT: G 64 GLU cc_start: 0.8707 (tt0) cc_final: 0.8356 (tp30) REVERT: G 91 GLU cc_start: 0.8660 (tp30) cc_final: 0.8378 (tp30) REVERT: H 63 ASN cc_start: 0.9071 (OUTLIER) cc_final: 0.8764 (m-40) outliers start: 15 outliers final: 6 residues processed: 161 average time/residue: 0.7645 time to fit residues: 129.7505 Evaluate side-chains 165 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 90 optimal weight: 10.0000 chunk 86 optimal weight: 30.0000 chunk 50 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 42 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 70 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 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 = 0.3501 r_free = 0.3501 target = 0.097569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.064610 restraints weight = 21471.951| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.48 r_work: 0.2712 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12771 Z= 0.173 Angle : 0.641 7.378 18509 Z= 0.367 Chirality : 0.044 0.252 2108 Planarity : 0.004 0.048 1322 Dihedral : 31.344 145.276 4045 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.25 % Allowed : 20.26 % Favored : 77.49 % 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: 2.64 (0.31), residues: 732 helix: 2.47 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.58 (0.43), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 71 TYR 0.011 0.001 TYR H 42 PHE 0.011 0.002 PHE A 67 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 (12771) covalent geometry : angle 0.64079 / 0.37 (18509) hydrogen bonds : bond 0.04293 / 2.88 ( 775) hydrogen bonds : angle 2.86972 / 1.99 ( 1931) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 0.208 Fit side-chains REVERT: A 42 ARG cc_start: 0.8255 (ttt90) cc_final: 0.7970 (mtp85) REVERT: B 77 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8787 (mtpt) REVERT: B 79 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8675 (mtmp) REVERT: C 64 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8263 (tt0) REVERT: C 75 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8836 (mttm) REVERT: C 95 LYS cc_start: 0.9222 (ttpp) cc_final: 0.8940 (ttpp) REVERT: E 59 GLU cc_start: 0.8652 (pt0) cc_final: 0.8401 (pm20) REVERT: G 64 GLU cc_start: 0.8704 (tt0) cc_final: 0.8357 (tp30) REVERT: G 91 GLU cc_start: 0.8650 (tp30) cc_final: 0.8364 (tp30) REVERT: H 63 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8727 (m-40) outliers start: 14 outliers final: 6 residues processed: 160 average time/residue: 0.7407 time to fit residues: 125.1598 Evaluate side-chains 165 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 20.0000 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 18 optimal weight: 0.0170 chunk 7 optimal weight: 5.9990 chunk 95 optimal weight: 10.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 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 = 0.3507 r_free = 0.3507 target = 0.097938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.064958 restraints weight = 21559.033| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.48 r_work: 0.2722 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12771 Z= 0.151 Angle : 0.637 7.270 18509 Z= 0.366 Chirality : 0.044 0.254 2108 Planarity : 0.004 0.048 1322 Dihedral : 31.335 145.284 4045 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.61 % Allowed : 20.74 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 732 helix: 2.50 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.56 (0.43), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 71 TYR 0.011 0.001 TYR H 42 PHE 0.011 0.002 PHE A 67 HIS 0.002 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (12771) covalent geometry : angle 0.63708 / 0.37 (18509) hydrogen bonds : bond 0.04151 / 2.79 ( 775) hydrogen bonds : angle 2.86215 / 1.99 ( 1931) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.209 Fit side-chains REVERT: A 42 ARG cc_start: 0.8255 (ttt90) cc_final: 0.7967 (mtp85) REVERT: B 77 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8784 (mtpt) REVERT: B 79 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8665 (mtmp) REVERT: C 75 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8828 (mttm) REVERT: C 95 LYS cc_start: 0.9220 (ttpp) cc_final: 0.8938 (ttpp) REVERT: E 59 GLU cc_start: 0.8649 (pt0) cc_final: 0.8397 (pm20) REVERT: G 64 GLU cc_start: 0.8698 (tt0) cc_final: 0.8349 (tp30) REVERT: G 91 GLU cc_start: 0.8653 (tp30) cc_final: 0.8375 (tp30) REVERT: H 63 ASN cc_start: 0.9032 (OUTLIER) cc_final: 0.8719 (m-40) outliers start: 10 outliers final: 6 residues processed: 161 average time/residue: 0.8603 time to fit residues: 146.2197 Evaluate side-chains 166 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 156 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 78 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 26 optimal weight: 0.0770 chunk 6 optimal weight: 2.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 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 = 0.3512 r_free = 0.3512 target = 0.098243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.065327 restraints weight = 21426.319| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.48 r_work: 0.2729 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12771 Z= 0.137 Angle : 0.635 7.603 18509 Z= 0.365 Chirality : 0.043 0.256 2108 Planarity : 0.004 0.048 1322 Dihedral : 31.328 145.258 4045 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.77 % Allowed : 20.26 % Favored : 77.97 % 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: 2.71 (0.31), residues: 732 helix: 2.52 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.55 (0.43), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 71 TYR 0.011 0.001 TYR H 42 PHE 0.011 0.001 PHE A 67 HIS 0.002 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.14 (12771) covalent geometry : angle 0.63548 / 0.36 (18509) hydrogen bonds : bond 0.04025 / 2.70 ( 775) hydrogen bonds : angle 2.85128 / 1.98 ( 1931) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4070.59 seconds wall clock time: 69 minutes 38.94 seconds (4178.94 seconds total)