Starting phenix.real_space_refine on Thu Jul 2 16:59:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yoz_33991/07_2026/7yoz_33991.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yoz_33991/07_2026/7yoz_33991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yoz_33991/07_2026/7yoz_33991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yoz_33991/07_2026/7yoz_33991.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yoz_33991/07_2026/7yoz_33991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yoz_33991/07_2026/7yoz_33991.map" } resolution = 4.3 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= 1.000 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 242 5.49 5 S 20 5.16 5 C 5365 2.51 5 N 1838 2.21 5 O 2287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 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: 9752 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "B" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 594 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "D" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 568 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "E" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "F" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 565 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "G" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "H" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "I" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2463 Classifications: {'DNA': 121} Link IDs: {'rna3p': 120} Chain: "J" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2498 Classifications: {'DNA': 121} Link IDs: {'rna3p': 120} Time building chain proxies: 1.81, per 1000 atoms: 0.19 Number of scatterers: 9752 At special positions: 0 Unit cell: (122.85, 90.3, 113.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 242 15.00 O 2287 8.00 N 1838 7.00 C 5365 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: 0.74 Conformation dependent library (CDL) restraints added in 162.6 milliseconds 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1124 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 2 sheets defined 79.1% alpha, 0.7% beta 120 base pairs and 215 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 64 through 79 removed outlier: 3.614A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.575A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.537A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.512A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 79 Processing helix chain 'C' and resid 85 through 114 Processing helix chain 'C' and resid 120 through 131 removed outlier: 3.526A pdb=" N ILE C 124 " --> pdb=" O MET C 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 29 Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 49 through 77 Processing helix chain 'D' and resid 82 through 95 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.531A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.563A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) 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: 3.537A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 63 through 79 removed outlier: 3.653A pdb=" N ASP G 77 " --> pdb=" O GLU G 73 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE G 78 " --> pdb=" O ILE G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 114 Processing helix chain 'G' and resid 120 through 132 removed outlier: 3.593A pdb=" N ILE G 124 " --> pdb=" O MET G 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 29 Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 49 through 76 Processing helix chain 'H' and resid 82 through 93 Processing sheet with id=AA1, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'G' and resid 83 through 84 removed outlier: 7.722A pdb=" N ARG G 83 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 350 hydrogen bonds defined for protein. 1023 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 313 hydrogen bonds 626 hydrogen bond angles 0 basepair planarities 120 basepair parallelities 215 stacking parallelities Total time for adding SS restraints: 1.30 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1961 1.34 - 1.45: 3358 1.45 - 1.57: 4570 1.57 - 1.69: 482 1.69 - 1.81: 32 Bond restraints: 10403 Sorted by residual: bond pdb=" C3' DT I 14 " pdb=" C2' DT I 14 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DC I -27 " pdb=" C2' DC I -27 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DC I -8 " pdb=" C2' DC I -8 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DG J -8 " pdb=" C2' DG J -8 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DA I -52 " pdb=" C2' DA I -52 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 ... (remaining 10398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 14297 1.58 - 3.17: 746 3.17 - 4.75: 16 4.75 - 6.33: 6 6.33 - 7.92: 3 Bond angle restraints: 15068 Sorted by residual: angle pdb=" N3 DT I 32 " pdb=" C4 DT I 32 " pdb=" O4 DT I 32 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT J 13 " pdb=" C4 DT J 13 " pdb=" O4 DT J 13 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT J 20 " pdb=" C4 DT J 20 " pdb=" O4 DT J 20 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT I 33 " pdb=" C4 DT I 33 " pdb=" O4 DT I 33 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT I 40 " pdb=" C4 DT I 40 " pdb=" O4 DT I 40 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 ... (remaining 15063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 4528 35.80 - 71.59: 1090 71.59 - 107.39: 15 107.39 - 143.19: 1 143.19 - 178.98: 3 Dihedral angle restraints: 5637 sinusoidal: 3911 harmonic: 1726 Sorted by residual: dihedral pdb=" C4' DT I 14 " pdb=" C3' DT I 14 " pdb=" O3' DT I 14 " pdb=" P DT I 15 " ideal model delta sinusoidal sigma weight residual -140.00 38.98 -178.98 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC I 51 " pdb=" C3' DC I 51 " pdb=" O3' DC I 51 " pdb=" P DA I 52 " ideal model delta sinusoidal sigma weight residual -140.00 36.13 -176.13 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC I -48 " pdb=" C3' DC I -48 " pdb=" O3' DC I -48 " pdb=" P DG I -47 " ideal model delta sinusoidal sigma weight residual 220.00 76.24 143.76 1 3.50e+01 8.16e-04 1.42e+01 ... (remaining 5634 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1338 0.050 - 0.101: 350 0.101 - 0.151: 32 0.151 - 0.201: 1 0.201 - 0.252: 2 Chirality restraints: 1723 Sorted by residual: chirality pdb=" CG LEU A 103 " pdb=" CB LEU A 103 " pdb=" CD1 LEU A 103 " pdb=" CD2 LEU A 103 " both_signs ideal model delta sigma weight residual False -2.59 -2.84 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CG LEU G 103 " pdb=" CB LEU G 103 " pdb=" CD1 LEU G 103 " pdb=" CD2 LEU G 103 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA THR G 107 " pdb=" N THR G 107 " pdb=" C THR G 107 " pdb=" CB THR G 107 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.80e-01 ... (remaining 1720 not shown) Planarity restraints: 1069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP E 77 " 0.024 2.00e-02 2.50e+03 5.00e-02 2.50e+01 pdb=" CG ASP E 77 " -0.086 2.00e-02 2.50e+03 pdb=" OD1 ASP E 77 " 0.031 2.00e-02 2.50e+03 pdb=" OD2 ASP E 77 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 31 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.09e+00 pdb=" N PRO D 32 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 32 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 32 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 92 " 0.031 9.50e-02 1.11e+02 1.84e-02 1.96e+00 pdb=" NE ARG B 92 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 92 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG B 92 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 92 " -0.007 2.00e-02 2.50e+03 ... (remaining 1066 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1872 2.80 - 3.32: 8558 3.32 - 3.85: 18168 3.85 - 4.37: 20847 4.37 - 4.90: 29311 Nonbonded interactions: 78756 Sorted by model distance: nonbonded pdb=" OD2 ASP E 106 " pdb=" NH2 ARG E 131 " model vdw 2.269 3.120 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.270 3.120 nonbonded pdb=" NZ LYS C 115 " pdb=" OP2 DT J 29 " model vdw 2.324 3.120 nonbonded pdb=" NE ARG G 128 " pdb=" OE1 GLU G 133 " model vdw 2.359 3.120 nonbonded pdb=" NZ LYS G 79 " pdb=" OE1 GLU H 74 " model vdw 2.366 3.120 ... (remaining 78751 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 'C' and resid 59 through 134) selection = chain 'E' selection = (chain 'G' and resid 59 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 94) selection = (chain 'D' and resid 25 through 94) selection = (chain 'F' and resid 25 through 94) selection = (chain 'H' and resid 25 through 94) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 8.760 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 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 : 0.005 0.036 10403 Z= 0.489 Angle : 0.718 7.918 15068 Z= 0.635 Chirality : 0.044 0.252 1723 Planarity : 0.004 0.050 1069 Dihedral : 27.407 178.984 4513 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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: 0.64 (0.30), residues: 578 helix: 0.94 (0.21), residues: 450 sheet: None (None), residues: 0 loop : -1.23 (0.43), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG B 92 TYR 0.012 0.001 TYR D 88 PHE 0.014 0.001 PHE G 104 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.49 (10403) covalent geometry : angle 0.71846 / 0.64 (15068) hydrogen bonds : bond 0.17426 / 11.88 ( 663) hydrogen bonds : angle 4.78242 / 3.48 ( 1649) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.8892 (mttm) cc_final: 0.8550 (mtmm) REVERT: A 68 GLN cc_start: 0.8865 (tt0) cc_final: 0.8408 (tp40) REVERT: A 85 GLN cc_start: 0.8636 (tt0) cc_final: 0.8300 (tp40) REVERT: A 93 GLN cc_start: 0.8675 (tt0) cc_final: 0.8038 (tm-30) REVERT: A 119 ILE cc_start: 0.9037 (pt) cc_final: 0.8346 (mt) REVERT: A 120 MET cc_start: 0.8634 (mmm) cc_final: 0.8410 (mmm) REVERT: A 123 ASP cc_start: 0.8834 (m-30) cc_final: 0.8472 (t70) REVERT: A 126 LEU cc_start: 0.9647 (tp) cc_final: 0.9430 (tp) REVERT: A 128 ARG cc_start: 0.8893 (mtp180) cc_final: 0.8314 (mtp180) REVERT: A 130 ILE cc_start: 0.9707 (mt) cc_final: 0.9487 (mm) REVERT: B 51 TYR cc_start: 0.8033 (m-80) cc_final: 0.7735 (m-80) REVERT: C 104 PHE cc_start: 0.9000 (m-80) cc_final: 0.8537 (m-80) REVERT: C 121 PRO cc_start: 0.8850 (Cg_exo) cc_final: 0.8627 (Cg_endo) REVERT: C 123 ASP cc_start: 0.8887 (m-30) cc_final: 0.8366 (m-30) REVERT: C 124 ILE cc_start: 0.9349 (mt) cc_final: 0.9097 (tp) REVERT: C 130 ILE cc_start: 0.8366 (tt) cc_final: 0.8042 (tt) REVERT: D 43 VAL cc_start: 0.8313 (t) cc_final: 0.7889 (t) REVERT: D 52 GLU cc_start: 0.9122 (tt0) cc_final: 0.8831 (pp20) REVERT: D 55 ARG cc_start: 0.8771 (mtt180) cc_final: 0.8372 (mmm-85) REVERT: D 59 LYS cc_start: 0.9150 (tttt) cc_final: 0.8326 (tptt) REVERT: D 66 ILE cc_start: 0.9140 (mm) cc_final: 0.8911 (pt) REVERT: D 71 THR cc_start: 0.8948 (m) cc_final: 0.8443 (m) REVERT: E 60 LEU cc_start: 0.6207 (mt) cc_final: 0.5995 (mp) REVERT: E 70 LEU cc_start: 0.8786 (tp) cc_final: 0.8246 (tt) REVERT: E 87 SER cc_start: 0.8980 (m) cc_final: 0.8511 (p) REVERT: E 104 PHE cc_start: 0.8998 (m-80) cc_final: 0.8464 (m-80) REVERT: E 109 LEU cc_start: 0.9725 (tp) cc_final: 0.9503 (tp) REVERT: E 126 LEU cc_start: 0.9139 (tp) cc_final: 0.8919 (tt) REVERT: F 59 LYS cc_start: 0.9204 (tttt) cc_final: 0.8908 (ttpt) REVERT: F 66 ILE cc_start: 0.9055 (mm) cc_final: 0.8817 (pt) REVERT: G 70 LEU cc_start: 0.9140 (tp) cc_final: 0.8380 (tt) REVERT: G 90 MET cc_start: 0.8385 (ttm) cc_final: 0.8051 (tmm) REVERT: G 97 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7721 (mt-10) REVERT: G 123 ASP cc_start: 0.8589 (m-30) cc_final: 0.8367 (t70) REVERT: H 35 ARG cc_start: 0.8395 (mtp85) cc_final: 0.7964 (ttt180) REVERT: H 43 VAL cc_start: 0.6861 (t) cc_final: 0.5771 (t) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.1370 time to fit residues: 57.1750 Evaluate side-chains 222 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 40.0000 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.086263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.071956 restraints weight = 56021.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.073515 restraints weight = 34625.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.074598 restraints weight = 24351.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.075317 restraints weight = 18905.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.075849 restraints weight = 15737.970| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 10403 Z= 0.278 Angle : 0.819 12.985 15068 Z= 0.464 Chirality : 0.047 0.220 1723 Planarity : 0.008 0.113 1069 Dihedral : 31.640 174.837 3286 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 0.99 % Allowed : 4.56 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 1.30 (0.32), residues: 578 helix: 1.40 (0.23), residues: 465 sheet: None (None), residues: 0 loop : -1.27 (0.48), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 78 TYR 0.024 0.003 TYR D 72 PHE 0.020 0.002 PHE A 104 HIS 0.021 0.005 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.28 (10403) covalent geometry : angle 0.81917 / 0.46 (15068) hydrogen bonds : bond 0.07713 / 5.18 ( 663) hydrogen bonds : angle 3.74502 / 2.64 ( 1649) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 256 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8210 (tt) cc_final: 0.6465 (tt) REVERT: A 64 LYS cc_start: 0.9404 (mttm) cc_final: 0.8911 (mtmm) REVERT: A 68 GLN cc_start: 0.9179 (tt0) cc_final: 0.8534 (tp-100) REVERT: A 69 ARG cc_start: 0.9043 (ptp-110) cc_final: 0.8557 (ptp90) REVERT: A 85 GLN cc_start: 0.9231 (tt0) cc_final: 0.8642 (tp40) REVERT: A 93 GLN cc_start: 0.8921 (tt0) cc_final: 0.8455 (tt0) REVERT: A 96 CYS cc_start: 0.9049 (m) cc_final: 0.8792 (p) REVERT: A 97 GLU cc_start: 0.8389 (tt0) cc_final: 0.7812 (mt-10) REVERT: A 107 THR cc_start: 0.9069 (p) cc_final: 0.8553 (p) REVERT: A 119 ILE cc_start: 0.9306 (pt) cc_final: 0.9042 (mt) REVERT: A 123 ASP cc_start: 0.8943 (m-30) cc_final: 0.8495 (t70) REVERT: B 24 ASP cc_start: 0.8184 (t0) cc_final: 0.7475 (p0) REVERT: B 51 TYR cc_start: 0.8457 (m-80) cc_final: 0.8043 (m-80) REVERT: C 90 MET cc_start: 0.9125 (ppp) cc_final: 0.8664 (ppp) REVERT: C 93 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8779 (tm-30) REVERT: C 94 GLU cc_start: 0.9213 (pt0) cc_final: 0.8807 (pt0) REVERT: C 100 LEU cc_start: 0.9481 (tp) cc_final: 0.9118 (tp) REVERT: C 104 PHE cc_start: 0.9142 (m-80) cc_final: 0.8519 (m-80) REVERT: D 52 GLU cc_start: 0.9207 (tt0) cc_final: 0.8963 (tm-30) REVERT: D 55 ARG cc_start: 0.8865 (mtt180) cc_final: 0.8345 (mmm-85) REVERT: D 59 LYS cc_start: 0.9119 (tttt) cc_final: 0.8414 (tptp) REVERT: D 63 GLU cc_start: 0.8809 (tt0) cc_final: 0.8301 (tm-30) REVERT: D 66 ILE cc_start: 0.9160 (mm) cc_final: 0.8921 (pt) REVERT: E 87 SER cc_start: 0.8783 (m) cc_final: 0.8431 (p) REVERT: E 120 MET cc_start: 0.8351 (mmp) cc_final: 0.8103 (mmm) REVERT: E 123 ASP cc_start: 0.9088 (m-30) cc_final: 0.8871 (m-30) REVERT: F 36 ARG cc_start: 0.8989 (mtm110) cc_final: 0.8701 (mtm180) REVERT: F 59 LYS cc_start: 0.9233 (tttt) cc_final: 0.8836 (ttpt) REVERT: F 66 ILE cc_start: 0.9167 (mm) cc_final: 0.8911 (pt) REVERT: G 61 LEU cc_start: 0.8805 (tt) cc_final: 0.8538 (tt) REVERT: G 65 LEU cc_start: 0.9396 (tp) cc_final: 0.9187 (tp) REVERT: G 90 MET cc_start: 0.8709 (ttm) cc_final: 0.8309 (tmm) REVERT: G 97 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7867 (mt-10) REVERT: G 119 ILE cc_start: 0.9466 (mt) cc_final: 0.9080 (mp) REVERT: G 123 ASP cc_start: 0.8777 (m-30) cc_final: 0.8415 (t70) REVERT: G 128 ARG cc_start: 0.9253 (mtp-110) cc_final: 0.9006 (mtp-110) outliers start: 5 outliers final: 2 residues processed: 257 average time/residue: 0.1115 time to fit residues: 36.4977 Evaluate side-chains 211 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 209 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 40.0000 chunk 44 optimal weight: 5.9990 chunk 78 optimal weight: 40.0000 chunk 28 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 76 optimal weight: 30.0000 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 30.0000 chunk 20 optimal weight: 0.9990 chunk 63 optimal weight: 30.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 27 GLN G 68 GLN ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.080637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.065967 restraints weight = 55768.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.067405 restraints weight = 34197.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.068441 restraints weight = 24391.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.069108 restraints weight = 19157.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.069427 restraints weight = 16150.125| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 10403 Z= 0.229 Angle : 0.742 10.746 15068 Z= 0.427 Chirality : 0.048 0.467 1723 Planarity : 0.009 0.159 1069 Dihedral : 32.191 176.857 3286 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.79 % Allowed : 6.35 % Favored : 92.86 % 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: 1.47 (0.33), residues: 578 helix: 1.57 (0.23), residues: 467 sheet: None (None), residues: 0 loop : -1.57 (0.45), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 134 TYR 0.014 0.003 TYR H 88 PHE 0.023 0.003 PHE E 67 HIS 0.007 0.003 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.23 (10403) covalent geometry : angle 0.74167 / 0.43 (15068) hydrogen bonds : bond 0.06377 / 4.38 ( 663) hydrogen bonds : angle 3.46472 / 2.45 ( 1649) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 256 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8363 (tt) cc_final: 0.8158 (tp) REVERT: A 64 LYS cc_start: 0.9432 (mttm) cc_final: 0.9008 (mtmm) REVERT: A 68 GLN cc_start: 0.9328 (tt0) cc_final: 0.8935 (tp-100) REVERT: A 85 GLN cc_start: 0.9247 (tt0) cc_final: 0.8637 (mm-40) REVERT: A 93 GLN cc_start: 0.9055 (tt0) cc_final: 0.8086 (tm-30) REVERT: A 96 CYS cc_start: 0.8973 (m) cc_final: 0.8661 (m) REVERT: A 119 ILE cc_start: 0.9332 (pt) cc_final: 0.8890 (mt) REVERT: A 120 MET cc_start: 0.8873 (mmm) cc_final: 0.8640 (mmm) REVERT: A 123 ASP cc_start: 0.8962 (m-30) cc_final: 0.8419 (t70) REVERT: B 24 ASP cc_start: 0.8271 (t0) cc_final: 0.7492 (p0) REVERT: B 51 TYR cc_start: 0.8218 (m-80) cc_final: 0.7933 (m-80) REVERT: C 90 MET cc_start: 0.9149 (ppp) cc_final: 0.8563 (ppp) REVERT: C 94 GLU cc_start: 0.9235 (pt0) cc_final: 0.8816 (pt0) REVERT: C 100 LEU cc_start: 0.9537 (tp) cc_final: 0.9265 (tp) REVERT: C 104 PHE cc_start: 0.9003 (m-80) cc_final: 0.8472 (m-80) REVERT: C 129 ARG cc_start: 0.8387 (tpm170) cc_final: 0.7900 (tpm170) REVERT: D 35 ARG cc_start: 0.9111 (mmm-85) cc_final: 0.8760 (ttm110) REVERT: D 53 GLU cc_start: 0.9051 (pp20) cc_final: 0.8795 (pp20) REVERT: D 55 ARG cc_start: 0.9004 (mtt180) cc_final: 0.8469 (mmm-85) REVERT: D 59 LYS cc_start: 0.9250 (tttt) cc_final: 0.8495 (tptp) REVERT: D 63 GLU cc_start: 0.8896 (tt0) cc_final: 0.8413 (tm-30) REVERT: D 66 ILE cc_start: 0.9178 (mm) cc_final: 0.8905 (pt) REVERT: E 76 GLN cc_start: 0.8725 (tt0) cc_final: 0.8274 (tp-100) REVERT: E 90 MET cc_start: 0.8900 (ppp) cc_final: 0.8328 (ppp) REVERT: E 119 ILE cc_start: 0.8228 (pt) cc_final: 0.7691 (pt) REVERT: E 123 ASP cc_start: 0.9024 (m-30) cc_final: 0.8756 (m-30) REVERT: F 36 ARG cc_start: 0.8957 (mtm110) cc_final: 0.8727 (ttp80) REVERT: F 66 ILE cc_start: 0.9162 (mm) cc_final: 0.8911 (pt) REVERT: F 81 VAL cc_start: 0.5982 (t) cc_final: 0.5420 (t) REVERT: F 82 THR cc_start: 0.5703 (p) cc_final: 0.4762 (p) REVERT: F 90 LEU cc_start: 0.8850 (tt) cc_final: 0.8582 (pp) REVERT: G 61 LEU cc_start: 0.8941 (tt) cc_final: 0.8174 (tt) REVERT: G 65 LEU cc_start: 0.9387 (tp) cc_final: 0.9182 (tp) REVERT: G 68 GLN cc_start: 0.9180 (tm130) cc_final: 0.8953 (tm-30) REVERT: G 90 MET cc_start: 0.8664 (ttm) cc_final: 0.8146 (tmm) REVERT: G 96 CYS cc_start: 0.8241 (m) cc_final: 0.7989 (m) REVERT: H 74 GLU cc_start: 0.8992 (tt0) cc_final: 0.8648 (tt0) REVERT: H 84 MET cc_start: 0.8960 (ttm) cc_final: 0.8671 (ttt) outliers start: 4 outliers final: 2 residues processed: 257 average time/residue: 0.1118 time to fit residues: 36.8135 Evaluate side-chains 218 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 216 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 57 optimal weight: 50.0000 chunk 35 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 67 optimal weight: 40.0000 chunk 61 optimal weight: 30.0000 chunk 78 optimal weight: 50.0000 chunk 70 optimal weight: 30.0000 chunk 62 optimal weight: 30.0000 chunk 64 optimal weight: 30.0000 overall best weight: 10.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS E 113 HIS G 68 GLN ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.063859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.048934 restraints weight = 60004.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.050229 restraints weight = 36772.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.051121 restraints weight = 26399.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.051705 restraints weight = 20986.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.052114 restraints weight = 18007.639| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.8204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.115 10403 Z= 0.460 Angle : 1.096 14.743 15068 Z= 0.608 Chirality : 0.060 0.287 1723 Planarity : 0.012 0.213 1069 Dihedral : 33.025 179.228 3286 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 33.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.79 % Allowed : 9.72 % Favored : 89.48 % 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: -0.55 (0.32), residues: 578 helix: 0.15 (0.22), residues: 470 sheet: None (None), residues: 0 loop : -2.22 (0.41), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG A 128 TYR 0.019 0.003 TYR C 99 PHE 0.040 0.006 PHE E 67 HIS 0.017 0.006 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00909 / 0.46 (10403) covalent geometry : angle 1.09630 / 0.61 (15068) hydrogen bonds : bond 0.13717 / 9.30 ( 663) hydrogen bonds : angle 4.81073 / 3.43 ( 1649) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 251 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8951 (mm) cc_final: 0.8159 (mt) REVERT: A 61 LEU cc_start: 0.9314 (tt) cc_final: 0.8634 (tt) REVERT: A 90 MET cc_start: 0.8302 (tmm) cc_final: 0.8014 (tmm) REVERT: A 93 GLN cc_start: 0.9184 (tt0) cc_final: 0.7769 (tm-30) REVERT: A 94 GLU cc_start: 0.9092 (pt0) cc_final: 0.8550 (pt0) REVERT: A 97 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7247 (mt-10) REVERT: A 107 THR cc_start: 0.9702 (p) cc_final: 0.9256 (p) REVERT: A 125 GLN cc_start: 0.9120 (tp40) cc_final: 0.8445 (tm-30) REVERT: B 24 ASP cc_start: 0.8619 (t0) cc_final: 0.8326 (t0) REVERT: B 74 GLU cc_start: 0.8479 (pp20) cc_final: 0.8135 (pp20) REVERT: B 85 ASP cc_start: 0.9336 (m-30) cc_final: 0.9068 (m-30) REVERT: C 78 PHE cc_start: 0.8449 (t80) cc_final: 0.8082 (t80) REVERT: C 90 MET cc_start: 0.9142 (ppp) cc_final: 0.8396 (ppp) REVERT: C 93 GLN cc_start: 0.9265 (tm-30) cc_final: 0.8970 (tm-30) REVERT: C 94 GLU cc_start: 0.9299 (pt0) cc_final: 0.8756 (pt0) REVERT: C 129 ARG cc_start: 0.8634 (tpm170) cc_final: 0.8393 (tpm170) REVERT: D 55 ARG cc_start: 0.9138 (mtt180) cc_final: 0.8620 (mmm-85) REVERT: D 59 LYS cc_start: 0.9494 (tttt) cc_final: 0.8804 (tptp) REVERT: D 63 GLU cc_start: 0.9114 (tt0) cc_final: 0.8730 (tm-30) REVERT: D 64 ASN cc_start: 0.9141 (t0) cc_final: 0.8818 (t0) REVERT: D 72 TYR cc_start: 0.8288 (t80) cc_final: 0.8066 (t80) REVERT: D 78 ARG cc_start: 0.8152 (ptm-80) cc_final: 0.7931 (ptt90) REVERT: E 76 GLN cc_start: 0.8810 (tt0) cc_final: 0.8276 (tp-100) REVERT: E 90 MET cc_start: 0.8844 (ppp) cc_final: 0.8292 (ppp) REVERT: E 119 ILE cc_start: 0.8770 (pt) cc_final: 0.8481 (pt) REVERT: E 123 ASP cc_start: 0.9090 (m-30) cc_final: 0.8513 (m-30) REVERT: F 49 LEU cc_start: 0.9321 (tt) cc_final: 0.9121 (tp) REVERT: F 63 GLU cc_start: 0.9357 (pt0) cc_final: 0.9094 (pp20) REVERT: F 64 ASN cc_start: 0.9122 (t0) cc_final: 0.8694 (t0) REVERT: F 72 TYR cc_start: 0.8183 (t80) cc_final: 0.7740 (t80) REVERT: G 65 LEU cc_start: 0.9509 (tp) cc_final: 0.9309 (tp) REVERT: G 90 MET cc_start: 0.8909 (ttm) cc_final: 0.8394 (tmm) REVERT: G 120 MET cc_start: 0.8959 (mmm) cc_final: 0.8682 (mmm) REVERT: G 123 ASP cc_start: 0.8986 (m-30) cc_final: 0.8730 (m-30) REVERT: G 128 ARG cc_start: 0.9297 (mtp-110) cc_final: 0.8510 (mtp-110) REVERT: H 39 ARG cc_start: 0.8682 (mmt90) cc_final: 0.8410 (mmt90) REVERT: H 63 GLU cc_start: 0.8671 (tt0) cc_final: 0.8264 (tp30) REVERT: H 74 GLU cc_start: 0.9166 (tt0) cc_final: 0.8921 (tt0) REVERT: H 88 TYR cc_start: 0.8700 (m-10) cc_final: 0.8404 (m-10) outliers start: 4 outliers final: 1 residues processed: 252 average time/residue: 0.1035 time to fit residues: 33.9827 Evaluate side-chains 219 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 218 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 77 optimal weight: 40.0000 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 76 optimal weight: 30.0000 chunk 31 optimal weight: 5.9990 chunk 69 optimal weight: 40.0000 chunk 54 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 57 optimal weight: 40.0000 chunk 49 optimal weight: 7.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.067133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.051982 restraints weight = 60152.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.053339 restraints weight = 36216.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.054279 restraints weight = 25837.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.054898 restraints weight = 20458.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.055323 restraints weight = 17448.118| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.8272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 10403 Z= 0.195 Angle : 0.762 7.773 15068 Z= 0.438 Chirality : 0.050 0.269 1723 Planarity : 0.006 0.050 1069 Dihedral : 33.286 176.130 3286 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % 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: 0.62 (0.33), residues: 578 helix: 0.98 (0.23), residues: 470 sheet: None (None), residues: 0 loop : -1.95 (0.43), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 45 TYR 0.014 0.002 TYR H 72 PHE 0.034 0.003 PHE C 104 HIS 0.008 0.002 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.19 (10403) covalent geometry : angle 0.76244 / 0.44 (15068) hydrogen bonds : bond 0.06283 / 4.20 ( 663) hydrogen bonds : angle 3.62181 / 2.57 ( 1649) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9531 (tt0) cc_final: 0.9005 (tp-100) REVERT: A 73 GLU cc_start: 0.9081 (pp20) cc_final: 0.8798 (pp20) REVERT: A 90 MET cc_start: 0.8313 (tmm) cc_final: 0.8029 (tmm) REVERT: A 120 MET cc_start: 0.9282 (mmm) cc_final: 0.8806 (mmm) REVERT: A 125 GLN cc_start: 0.9085 (tp40) cc_final: 0.8376 (tm-30) REVERT: A 128 ARG cc_start: 0.9264 (mtp-110) cc_final: 0.8893 (mmm-85) REVERT: B 24 ASP cc_start: 0.8574 (t0) cc_final: 0.8264 (t0) REVERT: B 35 ARG cc_start: 0.8790 (ttm110) cc_final: 0.8568 (ttt90) REVERT: B 39 ARG cc_start: 0.8371 (mtm-85) cc_final: 0.8129 (mpp80) REVERT: B 85 ASP cc_start: 0.9340 (m-30) cc_final: 0.9112 (m-30) REVERT: C 78 PHE cc_start: 0.8459 (t80) cc_final: 0.8089 (t80) REVERT: C 90 MET cc_start: 0.9049 (ppp) cc_final: 0.8269 (ppp) REVERT: C 93 GLN cc_start: 0.9120 (tm-30) cc_final: 0.8589 (tm-30) REVERT: C 94 GLU cc_start: 0.9294 (pt0) cc_final: 0.8772 (pt0) REVERT: D 55 ARG cc_start: 0.9113 (mtt180) cc_final: 0.8508 (mmm-85) REVERT: D 63 GLU cc_start: 0.9157 (tt0) cc_final: 0.8564 (tm-30) REVERT: D 64 ASN cc_start: 0.9058 (t0) cc_final: 0.8800 (t0) REVERT: D 66 ILE cc_start: 0.9437 (mt) cc_final: 0.9215 (pt) REVERT: E 70 LEU cc_start: 0.9331 (tp) cc_final: 0.8819 (mt) REVERT: E 76 GLN cc_start: 0.8847 (tt0) cc_final: 0.8246 (tp-100) REVERT: E 90 MET cc_start: 0.8774 (ppp) cc_final: 0.8193 (ppp) REVERT: E 123 ASP cc_start: 0.9082 (m-30) cc_final: 0.8867 (m-30) REVERT: F 60 VAL cc_start: 0.9165 (p) cc_final: 0.8505 (p) REVERT: F 63 GLU cc_start: 0.9301 (pt0) cc_final: 0.8957 (pp20) REVERT: F 64 ASN cc_start: 0.9027 (t0) cc_final: 0.8717 (t0) REVERT: F 66 ILE cc_start: 0.9330 (mm) cc_final: 0.9002 (pt) REVERT: F 78 ARG cc_start: 0.7254 (ttt180) cc_final: 0.7035 (ptm160) REVERT: F 90 LEU cc_start: 0.8985 (tt) cc_final: 0.8760 (pp) REVERT: G 65 LEU cc_start: 0.9538 (tp) cc_final: 0.9304 (tp) REVERT: G 73 GLU cc_start: 0.9128 (tm-30) cc_final: 0.8887 (tm-30) REVERT: G 90 MET cc_start: 0.8906 (ttm) cc_final: 0.8289 (tmm) REVERT: G 92 LEU cc_start: 0.9644 (mm) cc_final: 0.9345 (mm) REVERT: G 96 CYS cc_start: 0.8761 (m) cc_final: 0.8501 (m) REVERT: G 106 ASP cc_start: 0.9155 (t70) cc_final: 0.8790 (t70) REVERT: G 107 THR cc_start: 0.9689 (p) cc_final: 0.9217 (p) REVERT: G 110 CYS cc_start: 0.9067 (p) cc_final: 0.7963 (p) REVERT: G 123 ASP cc_start: 0.8899 (m-30) cc_final: 0.8559 (t70) REVERT: G 128 ARG cc_start: 0.9217 (mtp-110) cc_final: 0.8285 (mtp-110) REVERT: H 39 ARG cc_start: 0.8653 (mmt90) cc_final: 0.8370 (mmt90) REVERT: H 63 GLU cc_start: 0.8507 (tt0) cc_final: 0.8010 (tp30) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.1075 time to fit residues: 38.2451 Evaluate side-chains 229 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 33 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 64 optimal weight: 30.0000 chunk 79 optimal weight: 50.0000 chunk 30 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 30.0000 chunk 46 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.067004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.052062 restraints weight = 60080.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.053382 restraints weight = 36481.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.054313 restraints weight = 26042.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.054876 restraints weight = 20639.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.055330 restraints weight = 17823.729| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.8464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10403 Z= 0.183 Angle : 0.740 9.467 15068 Z= 0.423 Chirality : 0.048 0.254 1723 Planarity : 0.006 0.075 1069 Dihedral : 33.061 174.937 3286 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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: 0.76 (0.33), residues: 578 helix: 1.05 (0.23), residues: 469 sheet: None (None), residues: 0 loop : -1.73 (0.45), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 35 TYR 0.015 0.002 TYR D 72 PHE 0.023 0.002 PHE C 104 HIS 0.004 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.18 (10403) covalent geometry : angle 0.73970 / 0.42 (15068) hydrogen bonds : bond 0.05676 / 3.79 ( 663) hydrogen bonds : angle 3.43190 / 2.44 ( 1649) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9498 (tt0) cc_final: 0.9003 (tp-100) REVERT: A 76 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8555 (tp40) REVERT: A 90 MET cc_start: 0.8236 (tmm) cc_final: 0.8028 (tmm) REVERT: A 93 GLN cc_start: 0.9114 (tt0) cc_final: 0.8834 (tt0) REVERT: A 107 THR cc_start: 0.9513 (p) cc_final: 0.8791 (p) REVERT: A 110 CYS cc_start: 0.8425 (p) cc_final: 0.7037 (p) REVERT: A 120 MET cc_start: 0.9168 (mmm) cc_final: 0.8960 (mmm) REVERT: A 123 ASP cc_start: 0.8770 (m-30) cc_final: 0.8294 (t70) REVERT: A 125 GLN cc_start: 0.9070 (tp40) cc_final: 0.8320 (tm-30) REVERT: A 126 LEU cc_start: 0.9691 (tt) cc_final: 0.9475 (tt) REVERT: A 128 ARG cc_start: 0.9289 (mtp-110) cc_final: 0.9045 (mtp-110) REVERT: B 24 ASP cc_start: 0.8502 (t0) cc_final: 0.8122 (t0) REVERT: B 35 ARG cc_start: 0.8761 (ttm110) cc_final: 0.8429 (ttm110) REVERT: B 39 ARG cc_start: 0.8325 (mtm-85) cc_final: 0.8052 (mtm-85) REVERT: C 78 PHE cc_start: 0.8475 (t80) cc_final: 0.8071 (t80) REVERT: C 90 MET cc_start: 0.9038 (ppp) cc_final: 0.8503 (ppp) REVERT: C 106 ASP cc_start: 0.9093 (t0) cc_final: 0.8888 (t70) REVERT: D 55 ARG cc_start: 0.9053 (mtt180) cc_final: 0.8433 (mmm-85) REVERT: D 63 GLU cc_start: 0.9043 (tt0) cc_final: 0.8655 (tm-30) REVERT: D 64 ASN cc_start: 0.9050 (t0) cc_final: 0.8801 (t0) REVERT: D 66 ILE cc_start: 0.9329 (mt) cc_final: 0.9088 (pt) REVERT: E 76 GLN cc_start: 0.8937 (tt0) cc_final: 0.8340 (tp-100) REVERT: E 90 MET cc_start: 0.8715 (ppp) cc_final: 0.8156 (ppp) REVERT: E 94 GLU cc_start: 0.8964 (pt0) cc_final: 0.8260 (pt0) REVERT: E 110 CYS cc_start: 0.8792 (t) cc_final: 0.7711 (t) REVERT: E 123 ASP cc_start: 0.8934 (m-30) cc_final: 0.8304 (m-30) REVERT: F 49 LEU cc_start: 0.9115 (tp) cc_final: 0.8370 (tp) REVERT: F 55 ARG cc_start: 0.9063 (mmt90) cc_final: 0.8365 (mmm-85) REVERT: F 60 VAL cc_start: 0.9197 (p) cc_final: 0.8524 (p) REVERT: F 63 GLU cc_start: 0.9336 (pt0) cc_final: 0.8947 (pp20) REVERT: F 64 ASN cc_start: 0.9008 (t0) cc_final: 0.8728 (t0) REVERT: F 66 ILE cc_start: 0.9336 (mm) cc_final: 0.9026 (pt) REVERT: F 88 TYR cc_start: 0.9197 (m-80) cc_final: 0.8886 (m-80) REVERT: G 61 LEU cc_start: 0.9202 (tp) cc_final: 0.7756 (tp) REVERT: G 64 LYS cc_start: 0.9302 (pttm) cc_final: 0.9082 (pttm) REVERT: G 65 LEU cc_start: 0.9441 (tp) cc_final: 0.9187 (tp) REVERT: G 90 MET cc_start: 0.8860 (ttm) cc_final: 0.8332 (tmm) REVERT: G 93 GLN cc_start: 0.8873 (pt0) cc_final: 0.8353 (pt0) REVERT: G 94 GLU cc_start: 0.8643 (pt0) cc_final: 0.8410 (pt0) REVERT: G 97 GLU cc_start: 0.7818 (mt-10) cc_final: 0.6808 (mt-10) REVERT: G 106 ASP cc_start: 0.9185 (t70) cc_final: 0.8636 (t70) REVERT: G 107 THR cc_start: 0.9618 (p) cc_final: 0.9128 (p) REVERT: G 110 CYS cc_start: 0.9084 (p) cc_final: 0.7837 (p) REVERT: G 123 ASP cc_start: 0.8842 (m-30) cc_final: 0.8465 (t70) REVERT: G 128 ARG cc_start: 0.9140 (mtp-110) cc_final: 0.8872 (mtp-110) REVERT: H 39 ARG cc_start: 0.8601 (mmt90) cc_final: 0.8184 (mmt90) REVERT: H 63 GLU cc_start: 0.8438 (tt0) cc_final: 0.8177 (tt0) REVERT: H 92 ARG cc_start: 0.8017 (ttp80) cc_final: 0.7710 (ttp80) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.0989 time to fit residues: 35.2880 Evaluate side-chains 240 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 55 optimal weight: 0.6980 chunk 29 optimal weight: 8.9990 chunk 68 optimal weight: 50.0000 chunk 15 optimal weight: 9.9990 chunk 12 optimal weight: 0.1980 chunk 70 optimal weight: 30.0000 chunk 53 optimal weight: 0.8980 chunk 58 optimal weight: 30.0000 chunk 59 optimal weight: 30.0000 chunk 20 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.068248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.053967 restraints weight = 57249.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.055349 restraints weight = 33665.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.056336 restraints weight = 23458.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.056980 restraints weight = 18168.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.057428 restraints weight = 15272.940| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.8481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10403 Z= 0.166 Angle : 0.738 12.399 15068 Z= 0.413 Chirality : 0.047 0.266 1723 Planarity : 0.005 0.065 1069 Dihedral : 32.868 174.708 3286 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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: 0.78 (0.33), residues: 578 helix: 1.09 (0.23), residues: 462 sheet: None (None), residues: 0 loop : -1.69 (0.44), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 35 TYR 0.013 0.002 TYR H 72 PHE 0.013 0.002 PHE A 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.17 (10403) covalent geometry : angle 0.73824 / 0.41 (15068) hydrogen bonds : bond 0.04780 / 3.21 ( 663) hydrogen bonds : angle 3.28189 / 2.33 ( 1649) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8882 (mt) cc_final: 0.8448 (mt) REVERT: A 68 GLN cc_start: 0.9501 (tt0) cc_final: 0.9016 (tp-100) REVERT: A 85 GLN cc_start: 0.9060 (tt0) cc_final: 0.8758 (tp40) REVERT: A 94 GLU cc_start: 0.8750 (pt0) cc_final: 0.8377 (pt0) REVERT: A 97 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7513 (mt-10) REVERT: A 107 THR cc_start: 0.9456 (p) cc_final: 0.8752 (p) REVERT: A 110 CYS cc_start: 0.8404 (p) cc_final: 0.7062 (p) REVERT: A 120 MET cc_start: 0.9195 (mmm) cc_final: 0.8977 (mmm) REVERT: A 123 ASP cc_start: 0.8845 (m-30) cc_final: 0.8305 (t70) REVERT: A 125 GLN cc_start: 0.9031 (tp40) cc_final: 0.8326 (tm-30) REVERT: A 126 LEU cc_start: 0.9664 (tt) cc_final: 0.9351 (tt) REVERT: A 128 ARG cc_start: 0.9246 (mtp-110) cc_final: 0.8796 (mmm-85) REVERT: B 24 ASP cc_start: 0.8479 (t0) cc_final: 0.8019 (t0) REVERT: B 35 ARG cc_start: 0.8764 (ttm110) cc_final: 0.8436 (ttm110) REVERT: B 39 ARG cc_start: 0.8291 (mtm-85) cc_final: 0.8022 (mtm-85) REVERT: C 78 PHE cc_start: 0.8406 (t80) cc_final: 0.8044 (t80) REVERT: C 90 MET cc_start: 0.9081 (ppp) cc_final: 0.8568 (ppp) REVERT: C 94 GLU cc_start: 0.9262 (pt0) cc_final: 0.8803 (pt0) REVERT: C 106 ASP cc_start: 0.9081 (t0) cc_final: 0.8716 (t70) REVERT: D 54 THR cc_start: 0.9376 (m) cc_final: 0.9058 (p) REVERT: D 55 ARG cc_start: 0.9054 (mtt180) cc_final: 0.8490 (mmm-85) REVERT: D 63 GLU cc_start: 0.9114 (tt0) cc_final: 0.8684 (tm-30) REVERT: D 64 ASN cc_start: 0.8976 (t0) cc_final: 0.8734 (t0) REVERT: D 66 ILE cc_start: 0.9265 (mt) cc_final: 0.9062 (pt) REVERT: D 78 ARG cc_start: 0.7628 (ptt90) cc_final: 0.7365 (ptt90) REVERT: E 68 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8545 (tp-100) REVERT: E 76 GLN cc_start: 0.8914 (tt0) cc_final: 0.8317 (tp-100) REVERT: E 90 MET cc_start: 0.8674 (ppp) cc_final: 0.8088 (ppp) REVERT: E 94 GLU cc_start: 0.8882 (pt0) cc_final: 0.8107 (pt0) REVERT: E 110 CYS cc_start: 0.8763 (t) cc_final: 0.7878 (t) REVERT: E 123 ASP cc_start: 0.8962 (m-30) cc_final: 0.8732 (m-30) REVERT: F 35 ARG cc_start: 0.8892 (mmm-85) cc_final: 0.8682 (ttm110) REVERT: F 60 VAL cc_start: 0.9189 (p) cc_final: 0.8514 (p) REVERT: F 63 GLU cc_start: 0.9321 (pt0) cc_final: 0.9034 (pp20) REVERT: F 64 ASN cc_start: 0.9174 (t0) cc_final: 0.8715 (t0) REVERT: F 88 TYR cc_start: 0.9156 (m-80) cc_final: 0.8808 (m-80) REVERT: F 90 LEU cc_start: 0.8949 (tt) cc_final: 0.8655 (pp) REVERT: G 60 LEU cc_start: 0.8208 (mm) cc_final: 0.7646 (mm) REVERT: G 64 LYS cc_start: 0.9293 (pttm) cc_final: 0.8972 (pttm) REVERT: G 65 LEU cc_start: 0.9441 (tp) cc_final: 0.9184 (tp) REVERT: G 68 GLN cc_start: 0.9435 (tm-30) cc_final: 0.9216 (tm-30) REVERT: G 90 MET cc_start: 0.8856 (ttm) cc_final: 0.8311 (tmm) REVERT: G 93 GLN cc_start: 0.8655 (pt0) cc_final: 0.7795 (tm-30) REVERT: G 94 GLU cc_start: 0.8511 (pt0) cc_final: 0.8065 (pt0) REVERT: G 97 GLU cc_start: 0.7789 (mt-10) cc_final: 0.5082 (mt-10) REVERT: G 106 ASP cc_start: 0.9081 (t70) cc_final: 0.8716 (t70) REVERT: G 107 THR cc_start: 0.9668 (p) cc_final: 0.9008 (p) REVERT: G 110 CYS cc_start: 0.9009 (p) cc_final: 0.8020 (p) REVERT: G 123 ASP cc_start: 0.8921 (m-30) cc_final: 0.8321 (t70) REVERT: G 128 ARG cc_start: 0.9164 (mtp-110) cc_final: 0.8480 (mtp-110) REVERT: H 39 ARG cc_start: 0.8706 (mmt90) cc_final: 0.8328 (mmt90) REVERT: H 62 LEU cc_start: 0.9092 (mm) cc_final: 0.8886 (mm) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.0949 time to fit residues: 34.4385 Evaluate side-chains 244 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 56 optimal weight: 50.0000 chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 0.0370 chunk 57 optimal weight: 40.0000 chunk 50 optimal weight: 0.9980 chunk 74 optimal weight: 30.0000 chunk 42 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 chunk 29 optimal weight: 5.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.068803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.054014 restraints weight = 58843.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.055356 restraints weight = 35576.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.056316 restraints weight = 25337.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.056977 restraints weight = 19903.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.057444 restraints weight = 16816.677| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.8458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10403 Z= 0.159 Angle : 0.717 9.157 15068 Z= 0.408 Chirality : 0.046 0.262 1723 Planarity : 0.005 0.062 1069 Dihedral : 32.675 174.861 3286 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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: 0.74 (0.33), residues: 578 helix: 1.05 (0.23), residues: 461 sheet: None (None), residues: 0 loop : -1.63 (0.44), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 92 TYR 0.011 0.001 TYR H 72 PHE 0.019 0.002 PHE G 104 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.16 (10403) covalent geometry : angle 0.71699 / 0.41 (15068) hydrogen bonds : bond 0.04575 / 3.08 ( 663) hydrogen bonds : angle 3.22379 / 2.31 ( 1649) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9477 (tt0) cc_final: 0.8947 (tp-100) REVERT: A 73 GLU cc_start: 0.9033 (pp20) cc_final: 0.8587 (pp20) REVERT: A 85 GLN cc_start: 0.9009 (tt0) cc_final: 0.8744 (tp40) REVERT: A 107 THR cc_start: 0.9398 (p) cc_final: 0.8850 (p) REVERT: A 110 CYS cc_start: 0.8362 (p) cc_final: 0.7040 (p) REVERT: A 123 ASP cc_start: 0.8800 (m-30) cc_final: 0.8266 (t70) REVERT: A 125 GLN cc_start: 0.8998 (tp40) cc_final: 0.8326 (tm-30) REVERT: A 126 LEU cc_start: 0.9676 (tt) cc_final: 0.9461 (tt) REVERT: A 128 ARG cc_start: 0.9192 (mtp-110) cc_final: 0.8753 (mmm-85) REVERT: B 24 ASP cc_start: 0.8461 (t0) cc_final: 0.8079 (t0) REVERT: B 35 ARG cc_start: 0.8747 (ttm110) cc_final: 0.8341 (ttm110) REVERT: B 39 ARG cc_start: 0.8282 (mtm-85) cc_final: 0.7914 (mtm-85) REVERT: C 78 PHE cc_start: 0.8428 (t80) cc_final: 0.8073 (t80) REVERT: C 90 MET cc_start: 0.9067 (ppp) cc_final: 0.8374 (ppp) REVERT: C 94 GLU cc_start: 0.9229 (pt0) cc_final: 0.8885 (pt0) REVERT: C 106 ASP cc_start: 0.9058 (t0) cc_final: 0.8681 (t70) REVERT: D 54 THR cc_start: 0.9365 (m) cc_final: 0.8993 (p) REVERT: D 55 ARG cc_start: 0.9042 (mtt180) cc_final: 0.8410 (mmm-85) REVERT: D 63 GLU cc_start: 0.9134 (tt0) cc_final: 0.8669 (tm-30) REVERT: D 64 ASN cc_start: 0.8962 (t0) cc_final: 0.8744 (t0) REVERT: D 66 ILE cc_start: 0.9245 (mt) cc_final: 0.9036 (pt) REVERT: D 78 ARG cc_start: 0.8059 (ptm-80) cc_final: 0.7848 (ptm-80) REVERT: D 84 MET cc_start: 0.9046 (mmm) cc_final: 0.8530 (ppp) REVERT: E 76 GLN cc_start: 0.8925 (tt0) cc_final: 0.8321 (tp-100) REVERT: E 110 CYS cc_start: 0.8605 (t) cc_final: 0.7533 (t) REVERT: E 123 ASP cc_start: 0.8884 (m-30) cc_final: 0.8653 (m-30) REVERT: F 52 GLU cc_start: 0.8599 (pm20) cc_final: 0.8165 (pm20) REVERT: F 55 ARG cc_start: 0.9033 (mmt90) cc_final: 0.8790 (mmt90) REVERT: F 60 VAL cc_start: 0.9199 (p) cc_final: 0.8507 (p) REVERT: F 63 GLU cc_start: 0.9337 (pt0) cc_final: 0.9019 (pp20) REVERT: F 64 ASN cc_start: 0.9183 (t0) cc_final: 0.8757 (t0) REVERT: F 88 TYR cc_start: 0.9105 (m-80) cc_final: 0.8777 (m-80) REVERT: F 90 LEU cc_start: 0.8933 (tt) cc_final: 0.8638 (pp) REVERT: G 61 LEU cc_start: 0.9352 (tp) cc_final: 0.8970 (tp) REVERT: G 64 LYS cc_start: 0.9292 (pttm) cc_final: 0.9063 (pttm) REVERT: G 65 LEU cc_start: 0.9439 (tp) cc_final: 0.9200 (tp) REVERT: G 68 GLN cc_start: 0.9390 (tm-30) cc_final: 0.9186 (tm-30) REVERT: G 90 MET cc_start: 0.8840 (ttm) cc_final: 0.8201 (tmm) REVERT: G 93 GLN cc_start: 0.8615 (pt0) cc_final: 0.8223 (pt0) REVERT: G 94 GLU cc_start: 0.8543 (pt0) cc_final: 0.8311 (pt0) REVERT: G 97 GLU cc_start: 0.7678 (mt-10) cc_final: 0.6627 (mt-10) REVERT: G 106 ASP cc_start: 0.9067 (t70) cc_final: 0.8637 (t70) REVERT: G 107 THR cc_start: 0.9586 (p) cc_final: 0.9163 (p) REVERT: G 110 CYS cc_start: 0.9021 (p) cc_final: 0.7852 (p) REVERT: G 123 ASP cc_start: 0.8866 (m-30) cc_final: 0.8426 (t70) REVERT: G 128 ARG cc_start: 0.9161 (mtp-110) cc_final: 0.8455 (mtp-110) REVERT: H 39 ARG cc_start: 0.8700 (mmt90) cc_final: 0.8410 (mmt90) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.1046 time to fit residues: 36.6905 Evaluate side-chains 245 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 30 optimal weight: 8.9990 chunk 62 optimal weight: 40.0000 chunk 72 optimal weight: 30.0000 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 77 optimal weight: 30.0000 chunk 24 optimal weight: 10.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.064112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.049183 restraints weight = 60975.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.050485 restraints weight = 36936.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.051364 restraints weight = 26492.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.051980 restraints weight = 21078.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.052390 restraints weight = 18005.800| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.9093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 10403 Z= 0.261 Angle : 0.782 7.940 15068 Z= 0.449 Chirality : 0.047 0.262 1723 Planarity : 0.006 0.042 1069 Dihedral : 32.906 176.846 3286 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.32), residues: 578 helix: 0.85 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.65 (0.44), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 92 TYR 0.022 0.002 TYR D 72 PHE 0.018 0.002 PHE E 67 HIS 0.007 0.003 HIS G 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.26 (10403) covalent geometry : angle 0.78244 / 0.45 (15068) hydrogen bonds : bond 0.07496 / 5.05 ( 663) hydrogen bonds : angle 3.61557 / 2.57 ( 1649) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9338 (mtmm) cc_final: 0.9029 (pttm) REVERT: A 65 LEU cc_start: 0.9574 (tp) cc_final: 0.9373 (tp) REVERT: A 68 GLN cc_start: 0.9495 (tt0) cc_final: 0.9187 (tm-30) REVERT: A 73 GLU cc_start: 0.9080 (pp20) cc_final: 0.8837 (pp20) REVERT: A 106 ASP cc_start: 0.9208 (t70) cc_final: 0.8919 (t70) REVERT: A 125 GLN cc_start: 0.9054 (tp40) cc_final: 0.8349 (tm-30) REVERT: A 126 LEU cc_start: 0.9698 (tt) cc_final: 0.9278 (tt) REVERT: A 128 ARG cc_start: 0.9118 (mtp-110) cc_final: 0.8492 (mtp-110) REVERT: B 24 ASP cc_start: 0.8591 (t0) cc_final: 0.8181 (t0) REVERT: B 35 ARG cc_start: 0.8832 (ttm110) cc_final: 0.8305 (ttm110) REVERT: B 39 ARG cc_start: 0.8405 (mtm-85) cc_final: 0.7982 (mtm-85) REVERT: B 74 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8308 (tm-30) REVERT: B 85 ASP cc_start: 0.9274 (m-30) cc_final: 0.9013 (m-30) REVERT: C 78 PHE cc_start: 0.8615 (t80) cc_final: 0.8216 (t80) REVERT: C 90 MET cc_start: 0.9043 (ppp) cc_final: 0.8229 (ppp) REVERT: C 93 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8520 (tm-30) REVERT: C 94 GLU cc_start: 0.9201 (pt0) cc_final: 0.8771 (pt0) REVERT: C 106 ASP cc_start: 0.9119 (t0) cc_final: 0.8895 (t0) REVERT: D 54 THR cc_start: 0.9401 (m) cc_final: 0.9099 (p) REVERT: D 55 ARG cc_start: 0.9121 (mtt180) cc_final: 0.8654 (mtt-85) REVERT: D 63 GLU cc_start: 0.9183 (tt0) cc_final: 0.8709 (tm-30) REVERT: D 64 ASN cc_start: 0.9053 (t0) cc_final: 0.8803 (t0) REVERT: D 66 ILE cc_start: 0.9385 (mt) cc_final: 0.9184 (pt) REVERT: D 78 ARG cc_start: 0.8082 (ptm-80) cc_final: 0.7841 (ptm-80) REVERT: E 76 GLN cc_start: 0.8917 (tt0) cc_final: 0.8286 (tp-100) REVERT: F 60 VAL cc_start: 0.9216 (p) cc_final: 0.8491 (p) REVERT: F 63 GLU cc_start: 0.9405 (pt0) cc_final: 0.9059 (pp20) REVERT: F 64 ASN cc_start: 0.9263 (t0) cc_final: 0.8828 (t0) REVERT: F 66 ILE cc_start: 0.9433 (mt) cc_final: 0.9184 (pt) REVERT: F 88 TYR cc_start: 0.9143 (m-80) cc_final: 0.8756 (m-80) REVERT: G 61 LEU cc_start: 0.9383 (tp) cc_final: 0.8990 (tp) REVERT: G 90 MET cc_start: 0.8947 (ttm) cc_final: 0.8353 (tmm) REVERT: G 93 GLN cc_start: 0.8708 (pt0) cc_final: 0.8333 (pt0) REVERT: G 97 GLU cc_start: 0.7959 (mt-10) cc_final: 0.6879 (mt-10) REVERT: G 107 THR cc_start: 0.9723 (p) cc_final: 0.9209 (p) REVERT: G 110 CYS cc_start: 0.9140 (p) cc_final: 0.7688 (p) REVERT: G 123 ASP cc_start: 0.8945 (m-30) cc_final: 0.8558 (t70) REVERT: G 128 ARG cc_start: 0.9115 (mtp-110) cc_final: 0.8303 (mtp-110) REVERT: H 39 ARG cc_start: 0.8692 (mmt90) cc_final: 0.8360 (mmt90) REVERT: H 63 GLU cc_start: 0.8612 (tt0) cc_final: 0.8289 (tt0) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.0966 time to fit residues: 33.0058 Evaluate side-chains 225 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 75 optimal weight: 30.0000 chunk 78 optimal weight: 50.0000 chunk 1 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.066213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.051293 restraints weight = 59535.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.052627 restraints weight = 36086.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.053571 restraints weight = 25771.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.054170 restraints weight = 20333.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.054601 restraints weight = 17366.226| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.9115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10403 Z= 0.164 Angle : 0.722 8.698 15068 Z= 0.411 Chirality : 0.045 0.286 1723 Planarity : 0.005 0.050 1069 Dihedral : 32.900 175.178 3286 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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: 0.67 (0.32), residues: 578 helix: 1.03 (0.23), residues: 458 sheet: None (None), residues: 0 loop : -1.70 (0.43), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 92 TYR 0.014 0.002 TYR D 72 PHE 0.020 0.002 PHE G 104 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 (10403) covalent geometry : angle 0.72226 / 0.41 (15068) hydrogen bonds : bond 0.04800 / 3.23 ( 663) hydrogen bonds : angle 3.28124 / 2.34 ( 1649) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1156 Ramachandran restraints generated. 578 Oldfield, 0 Emsley, 578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.9002 (mt) cc_final: 0.8528 (mt) REVERT: A 64 LYS cc_start: 0.9480 (mtmm) cc_final: 0.9175 (mtmm) REVERT: A 68 GLN cc_start: 0.9458 (tt0) cc_final: 0.8983 (tp-100) REVERT: A 94 GLU cc_start: 0.8788 (pt0) cc_final: 0.8564 (pt0) REVERT: A 97 GLU cc_start: 0.8501 (mt-10) cc_final: 0.7591 (mt-10) REVERT: A 106 ASP cc_start: 0.9087 (t70) cc_final: 0.8876 (t70) REVERT: A 107 THR cc_start: 0.9513 (p) cc_final: 0.8860 (p) REVERT: A 110 CYS cc_start: 0.8444 (p) cc_final: 0.7087 (p) REVERT: A 123 ASP cc_start: 0.8803 (m-30) cc_final: 0.8200 (t70) REVERT: A 125 GLN cc_start: 0.8992 (tp40) cc_final: 0.8307 (tm-30) REVERT: A 126 LEU cc_start: 0.9718 (tt) cc_final: 0.9318 (tt) REVERT: B 24 ASP cc_start: 0.8560 (t0) cc_final: 0.8167 (t0) REVERT: C 90 MET cc_start: 0.9066 (ppp) cc_final: 0.8263 (ppp) REVERT: C 93 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8459 (tm-30) REVERT: C 94 GLU cc_start: 0.9186 (pt0) cc_final: 0.8727 (pt0) REVERT: D 54 THR cc_start: 0.9396 (m) cc_final: 0.9107 (p) REVERT: D 55 ARG cc_start: 0.9011 (mtt180) cc_final: 0.8449 (mmm-85) REVERT: D 63 GLU cc_start: 0.9145 (tt0) cc_final: 0.8690 (tm-30) REVERT: D 64 ASN cc_start: 0.9055 (t0) cc_final: 0.8834 (t0) REVERT: D 66 ILE cc_start: 0.9379 (mt) cc_final: 0.9176 (pt) REVERT: D 78 ARG cc_start: 0.8066 (ptm-80) cc_final: 0.7799 (ptm-80) REVERT: E 76 GLN cc_start: 0.8931 (tt0) cc_final: 0.8311 (tp-100) REVERT: E 90 MET cc_start: 0.8902 (ptp) cc_final: 0.8330 (ppp) REVERT: E 123 ASP cc_start: 0.8871 (m-30) cc_final: 0.8392 (t70) REVERT: F 60 VAL cc_start: 0.9209 (p) cc_final: 0.8439 (p) REVERT: F 63 GLU cc_start: 0.9364 (pt0) cc_final: 0.9011 (pp20) REVERT: F 64 ASN cc_start: 0.9225 (t0) cc_final: 0.8762 (t0) REVERT: F 66 ILE cc_start: 0.9370 (mt) cc_final: 0.9082 (pt) REVERT: F 88 TYR cc_start: 0.9094 (m-80) cc_final: 0.8727 (m-80) REVERT: F 90 LEU cc_start: 0.8961 (tt) cc_final: 0.8716 (pp) REVERT: G 60 LEU cc_start: 0.8230 (mm) cc_final: 0.8021 (mt) REVERT: G 61 LEU cc_start: 0.9336 (tp) cc_final: 0.8875 (tp) REVERT: G 65 LEU cc_start: 0.9433 (tp) cc_final: 0.9225 (tp) REVERT: G 90 MET cc_start: 0.8802 (ttm) cc_final: 0.8276 (tmm) REVERT: G 93 GLN cc_start: 0.8628 (pt0) cc_final: 0.8290 (pt0) REVERT: G 97 GLU cc_start: 0.7806 (mt-10) cc_final: 0.6733 (mt-10) REVERT: G 107 THR cc_start: 0.9690 (p) cc_final: 0.9235 (p) REVERT: G 110 CYS cc_start: 0.9086 (p) cc_final: 0.7915 (p) REVERT: G 123 ASP cc_start: 0.8879 (m-30) cc_final: 0.8455 (t70) REVERT: G 128 ARG cc_start: 0.9071 (mtp-110) cc_final: 0.8350 (mtp-110) REVERT: H 39 ARG cc_start: 0.8673 (mmt90) cc_final: 0.8340 (mmt90) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.0964 time to fit residues: 33.9005 Evaluate side-chains 233 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 16 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 56 optimal weight: 40.0000 chunk 10 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 77 optimal weight: 30.0000 chunk 7 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.066073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.051375 restraints weight = 59727.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.052719 restraints weight = 35965.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.053651 restraints weight = 25556.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.054242 restraints weight = 20115.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.054678 restraints weight = 17204.949| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.9197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 10403 Z= 0.174 Angle : 0.742 8.727 15068 Z= 0.420 Chirality : 0.046 0.287 1723 Planarity : 0.006 0.059 1069 Dihedral : 32.831 175.428 3286 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: 0.67 (0.33), residues: 578 helix: 1.02 (0.23), residues: 459 sheet: None (None), residues: 0 loop : -1.71 (0.44), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 92 TYR 0.006 0.001 TYR B 88 PHE 0.015 0.002 PHE G 104 HIS 0.004 0.001 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (10403) covalent geometry : angle 0.74166 / 0.42 (15068) hydrogen bonds : bond 0.04717 / 3.18 ( 663) hydrogen bonds : angle 3.33728 / 2.38 ( 1649) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1329.70 seconds wall clock time: 23 minutes 34.98 seconds (1414.98 seconds total)