Starting phenix.real_space_refine on Fri Jul 3 04:22:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10yd_75525/07_2026/10yd_75525.cif Found real_map, /net/cci-nas-00/data/ceres_data/10yd_75525/07_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_75525/07_2026/10yd_75525.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10yd_75525/07_2026/10yd_75525.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10yd_75525/07_2026/10yd_75525.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10yd_75525/07_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-dev-6108/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: 2.37, per 1000 atoms: 0.20 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: 0.94 Conformation dependent library (CDL) restraints added in 224.0 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: 1.73 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: 2.29 Time building geometry restraints manager: 1.28 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: 17449 1.68 - 3.36: 1008 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: 4.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.160 Find NCS groups from input model: 0.110 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:7.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.440 ------------------------------------------------------------------------------- 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 : 0.781 8.394 18509 Z= 0.684 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 0.78106 / 0.68 (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 : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8234 (ttt90) cc_final: 0.7924 (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: 0.8352 time to fit residues: 141.7876 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 : 0.268 ------------------------------------------------------------------------------- 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: 0.0770 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: 0.9744 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.099568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.066807 restraints weight = 21541.610| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.50 r_work: 0.2752 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.0474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12771 Z= 0.163 Angle : 0.608 5.870 18509 Z= 0.373 Chirality : 0.044 0.185 2108 Planarity : 0.004 0.053 1322 Dihedral : 30.589 143.233 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 : 1.77 % Allowed : 18.17 % Favored : 80.06 % 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: 2.04 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.42 (0.42), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 40 TYR 0.009 0.001 TYR H 40 PHE 0.008 0.001 PHE A 67 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.16 (12771) covalent geometry : angle 0.60835 / 0.37 (18509) hydrogen bonds : bond 0.05178 / 3.47 ( 775) hydrogen bonds : angle 3.25446 / 2.26 ( 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 170 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8236 (ttt90) cc_final: 0.7911 (mtp85) REVERT: G 64 GLU cc_start: 0.8652 (tt0) cc_final: 0.8350 (tp30) REVERT: G 73 ASN cc_start: 0.8764 (t0) cc_final: 0.8022 (t0) REVERT: H 63 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8522 (m-40) outliers start: 11 outliers final: 4 residues processed: 162 average time/residue: 0.7573 time to fit residues: 129.6920 Evaluate side-chains 162 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 157 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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: 10.0000 chunk 51 optimal weight: 0.0570 chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 chunk 65 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 74 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.100292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.067450 restraints weight = 21740.890| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.52 r_work: 0.2756 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.0555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 12771 Z= 0.150 Angle : 0.598 6.982 18509 Z= 0.367 Chirality : 0.043 0.192 2108 Planarity : 0.004 0.037 1322 Dihedral : 30.646 143.180 4045 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.73 % Allowed : 17.85 % Favored : 79.42 % 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: 2.38 (0.31), residues: 732 helix: 2.21 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.42 (0.43), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 79 TYR 0.009 0.001 TYR H 40 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 0.00238 / 0.15 (12771) covalent geometry : angle 0.59756 / 0.37 (18509) hydrogen bonds : bond 0.04738 / 3.17 ( 775) hydrogen bonds : angle 3.15568 / 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: 17 poor density : 158 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8238 (ttt90) cc_final: 0.7916 (mtp85) REVERT: B 77 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8772 (mtpt) REVERT: C 64 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8325 (tt0) REVERT: C 75 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8801 (mttm) REVERT: G 64 GLU cc_start: 0.8664 (tt0) cc_final: 0.8349 (tp30) REVERT: G 73 ASN cc_start: 0.8737 (t0) cc_final: 0.7996 (t0) REVERT: H 63 ASN cc_start: 0.8858 (OUTLIER) cc_final: 0.8532 (m-40) outliers start: 17 outliers final: 9 residues processed: 163 average time/residue: 0.7039 time to fit residues: 121.3877 Evaluate side-chains 168 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 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 C residue 114 VAL Chi-restraints excluded: chain D residue 106 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 chunk 91 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.098095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.065154 restraints weight = 21326.833| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.49 r_work: 0.2717 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12771 Z= 0.211 Angle : 0.623 5.806 18509 Z= 0.367 Chirality : 0.044 0.202 2108 Planarity : 0.004 0.044 1322 Dihedral : 31.110 145.428 4045 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.73 % Allowed : 17.52 % Favored : 79.74 % 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: 732 helix: 2.33 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -0.52 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 79 TYR 0.011 0.002 TYR D 40 PHE 0.012 0.002 PHE G 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.21 (12771) covalent geometry : angle 0.62286 / 0.37 (18509) hydrogen bonds : bond 0.04723 / 3.17 ( 775) hydrogen bonds : angle 2.92680 / 2.04 ( 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: 17 poor density : 158 time to evaluate : 0.267 Fit side-chains REVERT: A 42 ARG cc_start: 0.8253 (ttt90) cc_final: 0.7936 (mtp85) REVERT: B 77 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8771 (mtpt) REVERT: C 64 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8288 (tt0) REVERT: C 75 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8808 (mttm) REVERT: E 59 GLU cc_start: 0.8549 (pt0) cc_final: 0.8107 (pm20) REVERT: H 63 ASN cc_start: 0.9007 (OUTLIER) cc_final: 0.8679 (m-40) outliers start: 17 outliers final: 5 residues processed: 165 average time/residue: 0.7656 time to fit residues: 133.4406 Evaluate side-chains 165 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 C residue 64 GLU Chi-restraints excluded: chain C residue 75 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 39 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 0.0670 chunk 51 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.099115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.066326 restraints weight = 21484.753| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.50 r_work: 0.2732 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12771 Z= 0.140 Angle : 0.605 6.822 18509 Z= 0.360 Chirality : 0.043 0.215 2108 Planarity : 0.004 0.041 1322 Dihedral : 31.131 145.621 4045 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.91 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: 2.69 (0.31), residues: 732 helix: 2.46 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -0.41 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 71 TYR 0.019 0.001 TYR D 42 PHE 0.009 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.14 (12771) covalent geometry : angle 0.60475 / 0.36 (18509) hydrogen bonds : bond 0.04168 / 2.80 ( 775) hydrogen bonds : angle 2.90917 / 2.02 ( 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 172 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8225 (ttt90) cc_final: 0.7897 (mtp85) REVERT: B 77 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8764 (mtpt) REVERT: C 64 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8266 (tt0) REVERT: C 75 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8733 (mmtm) REVERT: C 95 LYS cc_start: 0.9195 (ttpp) cc_final: 0.8939 (ttpp) REVERT: H 63 ASN cc_start: 0.8970 (OUTLIER) cc_final: 0.8620 (m-40) outliers start: 16 outliers final: 6 residues processed: 162 average time/residue: 0.7993 time to fit residues: 136.5784 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 : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU 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 C residue 64 GLU Chi-restraints excluded: chain C residue 75 LYS 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: 10.9990 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.097394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.064390 restraints weight = 21476.502| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.49 r_work: 0.2697 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12771 Z= 0.229 Angle : 0.639 6.770 18509 Z= 0.370 Chirality : 0.045 0.219 2108 Planarity : 0.004 0.046 1322 Dihedral : 31.379 145.966 4045 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.25 % Allowed : 19.94 % Favored : 77.81 % 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: 2.57 (0.31), residues: 732 helix: 2.41 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.57 (0.43), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 79 TYR 0.013 0.002 TYR H 42 PHE 0.011 0.002 PHE A 67 HIS 0.003 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.23 (12771) covalent geometry : angle 0.63853 / 0.37 (18509) hydrogen bonds : bond 0.04766 / 3.21 ( 775) hydrogen bonds : angle 2.89725 / 2.01 ( 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 170 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.307 Fit side-chains REVERT: A 42 ARG cc_start: 0.8270 (ttt90) cc_final: 0.7939 (mtp85) REVERT: B 77 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8789 (mtpt) REVERT: C 64 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8282 (tt0) REVERT: C 75 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8827 (mttm) REVERT: C 95 LYS cc_start: 0.9205 (ttpp) cc_final: 0.8910 (ttpp) REVERT: E 59 GLU cc_start: 0.8675 (pt0) cc_final: 0.8416 (pm20) REVERT: H 63 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8762 (m-40) outliers start: 14 outliers final: 7 residues processed: 161 average time/residue: 0.8279 time to fit residues: 140.4162 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 : 0.379 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 89 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 86 optimal weight: 30.0000 chunk 26 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.098462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.065723 restraints weight = 21411.398| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.48 r_work: 0.2733 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12771 Z= 0.143 Angle : 0.609 6.600 18509 Z= 0.358 Chirality : 0.043 0.236 2108 Planarity : 0.004 0.045 1322 Dihedral : 31.367 145.966 4045 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.25 % Allowed : 20.10 % 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: 2.70 (0.31), residues: 732 helix: 2.50 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.49 (0.43), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 71 TYR 0.012 0.001 TYR D 42 PHE 0.009 0.001 PHE A 67 HIS 0.002 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 (12771) covalent geometry : angle 0.60918 / 0.36 (18509) hydrogen bonds : bond 0.04002 / 2.69 ( 775) hydrogen bonds : angle 2.85494 / 1.98 ( 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 170 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.294 Fit side-chains REVERT: A 42 ARG cc_start: 0.8298 (ttt90) cc_final: 0.7982 (mtp85) REVERT: B 77 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8797 (mtpt) REVERT: C 64 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8265 (tt0) REVERT: C 75 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8748 (mmtm) REVERT: C 95 LYS cc_start: 0.9227 (ttpp) cc_final: 0.8955 (ttpp) REVERT: E 59 GLU cc_start: 0.8602 (pt0) cc_final: 0.8349 (pm20) REVERT: G 64 GLU cc_start: 0.8708 (tt0) cc_final: 0.8356 (tp30) REVERT: H 63 ASN cc_start: 0.9038 (OUTLIER) cc_final: 0.8715 (m-40) outliers start: 14 outliers final: 6 residues processed: 160 average time/residue: 0.8016 time to fit residues: 135.3483 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 : 0.309 ------------------------------------------------------------------------------- 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 84 MET 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 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: 0.5980 chunk 99 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.097134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.064113 restraints weight = 21468.866| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.48 r_work: 0.2700 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 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 : 0.005 0.040 12771 Z= 0.223 Angle : 0.638 6.874 18509 Z= 0.369 Chirality : 0.044 0.233 2108 Planarity : 0.004 0.046 1322 Dihedral : 31.428 145.672 4045 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.61 % Allowed : 20.90 % 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: 2.55 (0.31), residues: 732 helix: 2.42 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.68 (0.42), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 71 TYR 0.014 0.002 TYR H 42 PHE 0.012 0.002 PHE A 67 HIS 0.003 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.22 (12771) covalent geometry : angle 0.63810 / 0.37 (18509) hydrogen bonds : bond 0.04610 / 3.10 ( 775) hydrogen bonds : angle 2.88852 / 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 165 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 0.303 Fit side-chains REVERT: A 42 ARG cc_start: 0.8256 (ttt90) cc_final: 0.7945 (mtp85) REVERT: B 77 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8796 (mtpt) REVERT: C 64 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8282 (tt0) REVERT: C 95 LYS cc_start: 0.9228 (ttpp) cc_final: 0.8945 (ttpp) REVERT: E 59 GLU cc_start: 0.8697 (pt0) cc_final: 0.8426 (pm20) REVERT: H 63 ASN cc_start: 0.9073 (OUTLIER) cc_final: 0.8765 (m-40) outliers start: 10 outliers final: 5 residues processed: 159 average time/residue: 0.8112 time to fit residues: 136.0301 Evaluate side-chains 159 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 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=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: 1.9990 chunk 32 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 42 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 74 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.097748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.064813 restraints weight = 21460.849| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.47 r_work: 0.2718 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12771 Z= 0.157 Angle : 0.625 7.101 18509 Z= 0.362 Chirality : 0.043 0.238 2108 Planarity : 0.004 0.045 1322 Dihedral : 31.441 145.862 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 : 1.45 % Allowed : 21.06 % 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: 2.68 (0.31), residues: 732 helix: 2.51 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.62 (0.43), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 71 TYR 0.013 0.001 TYR H 42 PHE 0.011 0.002 PHE A 67 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.16 (12771) covalent geometry : angle 0.62487 / 0.36 (18509) hydrogen bonds : bond 0.04268 / 2.87 ( 775) hydrogen bonds : angle 2.88650 / 2.00 ( 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 163 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 0.296 Fit side-chains REVERT: A 42 ARG cc_start: 0.8254 (ttt90) cc_final: 0.7940 (mtp85) REVERT: B 77 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8799 (mtpt) REVERT: C 95 LYS cc_start: 0.9222 (ttpp) cc_final: 0.8938 (ttpp) REVERT: E 59 GLU cc_start: 0.8683 (pt0) cc_final: 0.8411 (pm20) REVERT: G 64 GLU cc_start: 0.8702 (tt0) cc_final: 0.8352 (tp30) REVERT: H 63 ASN cc_start: 0.9042 (OUTLIER) cc_final: 0.8729 (m-40) outliers start: 9 outliers final: 6 residues processed: 157 average time/residue: 0.7641 time to fit residues: 126.8550 Evaluate side-chains 161 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 153 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 81 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 18 optimal weight: 0.0670 chunk 7 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 overall best weight: 1.2922 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.097794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.064853 restraints weight = 21563.923| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.47 r_work: 0.2719 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12771 Z= 0.167 Angle : 0.622 7.175 18509 Z= 0.361 Chirality : 0.043 0.242 2108 Planarity : 0.004 0.047 1322 Dihedral : 31.430 145.808 4045 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.29 % Allowed : 21.22 % 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: 2.48 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.64 (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 0.010 0.002 PHE A 67 HIS 0.002 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.17 (12771) covalent geometry : angle 0.62233 / 0.36 (18509) hydrogen bonds : bond 0.04182 / 2.81 ( 775) hydrogen bonds : angle 2.86962 / 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 158 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 150 time to evaluate : 0.331 Fit side-chains REVERT: A 42 ARG cc_start: 0.8250 (ttt90) cc_final: 0.7934 (mtp85) REVERT: B 77 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8797 (mtpt) REVERT: C 95 LYS cc_start: 0.9224 (ttpp) cc_final: 0.8939 (ttpp) REVERT: E 59 GLU cc_start: 0.8676 (pt0) cc_final: 0.8405 (pm20) REVERT: G 64 GLU cc_start: 0.8697 (tt0) cc_final: 0.8348 (tp30) REVERT: H 63 ASN cc_start: 0.9048 (OUTLIER) cc_final: 0.8737 (m-40) outliers start: 8 outliers final: 6 residues processed: 153 average time/residue: 0.7564 time to fit residues: 122.2333 Evaluate side-chains 158 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 150 time to evaluate : 0.180 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 41 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 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 = 0.3511 r_free = 0.3511 target = 0.098190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.065110 restraints weight = 21410.570| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.47 r_work: 0.2727 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12771 Z= 0.138 Angle : 0.617 6.981 18509 Z= 0.359 Chirality : 0.043 0.242 2108 Planarity : 0.004 0.046 1322 Dihedral : 31.427 145.859 4045 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.45 % Allowed : 20.74 % Favored : 77.81 % 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: 2.72 (0.31), residues: 732 helix: 2.54 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.59 (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 0.00226 / 0.14 (12771) covalent geometry : angle 0.61717 / 0.36 (18509) hydrogen bonds : bond 0.04062 / 2.73 ( 775) hydrogen bonds : angle 2.86848 / 1.99 ( 1931) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4017.33 seconds wall clock time: 68 minutes 54.17 seconds (4134.17 seconds total)