Starting phenix.real_space_refine on Thu Jul 2 17:02:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x58_33011/07_2026/7x58_33011.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x58_33011/07_2026/7x58_33011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x58_33011/07_2026/7x58_33011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x58_33011/07_2026/7x58_33011.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x58_33011/07_2026/7x58_33011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x58_33011/07_2026/7x58_33011.map" } resolution = 3.93 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 5377 2.51 5 N 1846 2.21 5 O 2290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s 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: 9775 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: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 587 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} 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: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} 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: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} 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: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 587 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} 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: 1.69, per 1000 atoms: 0.17 Number of scatterers: 9775 At special positions: 0 Unit cell: (121.8, 95.55, 110.25, 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 2290 8.00 N 1846 7.00 C 5377 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: 0.91 Conformation dependent library (CDL) restraints added in 141.1 milliseconds 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1128 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 7 sheets defined 79.9% alpha, 2.3% beta 117 base pairs and 201 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.748A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.593A 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 95 removed outlier: 3.674A pdb=" N ARG B 95 " --> pdb=" O LYS B 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 79 removed outlier: 3.899A pdb=" N ASP C 77 " --> pdb=" O GLU C 73 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 114 Processing helix chain 'C' and resid 120 through 132 Processing helix chain 'D' and resid 25 through 29 removed outlier: 3.542A pdb=" N ILE D 29 " --> pdb=" O ILE D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 49 through 76 removed outlier: 3.529A pdb=" N GLU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 95 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.511A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.572A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.552A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 95 Processing helix chain 'G' and resid 63 through 79 removed outlier: 3.848A pdb=" N ASP G 77 " --> pdb=" O GLU G 73 " (cutoff:3.500A) removed outlier: 3.677A 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 Processing helix chain 'H' and resid 25 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 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.793A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 119 removed outlier: 3.637A pdb=" N ILE C 119 " --> pdb=" O ARG D 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.198A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.666A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 83 through 84 removed outlier: 6.804A pdb=" N ARG G 83 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 118 through 119 357 hydrogen bonds defined for protein. 1047 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 303 hydrogen bonds 606 hydrogen bond angles 0 basepair planarities 117 basepair parallelities 201 stacking parallelities Total time for adding SS restraints: 1.74 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1842 1.33 - 1.45: 3403 1.45 - 1.57: 4667 1.57 - 1.69: 482 1.69 - 1.81: 32 Bond restraints: 10426 Sorted by residual: bond pdb=" C3' DC I -8 " pdb=" C2' DC I -8 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DA J 45 " pdb=" C2' DA J 45 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DG I -53 " pdb=" C2' DG I -53 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DC I -18 " pdb=" C2' DC I -18 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DC I 51 " pdb=" C2' DC I 51 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 ... (remaining 10421 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 13967 1.37 - 2.73: 1078 2.73 - 4.10: 35 4.10 - 5.46: 12 5.46 - 6.83: 5 Bond angle restraints: 15097 Sorted by residual: angle pdb=" N3 DT I 33 " pdb=" C4 DT I 33 " pdb=" O4 DT I 33 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT I -37 " pdb=" C4 DT I -37 " pdb=" O4 DT I -37 " 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 31 " pdb=" C4 DT J 31 " pdb=" O4 DT J 31 " 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 J 11 " pdb=" C4 DT J 11 " pdb=" O4 DT J 11 " 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 J -18 " pdb=" C4 DT J -18 " pdb=" O4 DT J -18 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (remaining 15092 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 4570 35.47 - 70.94: 1069 70.94 - 106.41: 11 106.41 - 141.88: 1 141.88 - 177.36: 3 Dihedral angle restraints: 5654 sinusoidal: 3922 harmonic: 1732 Sorted by residual: 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 37.36 -177.36 1 3.50e+01 8.16e-04 1.57e+01 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 220.00 53.77 166.23 1 3.50e+01 8.16e-04 1.54e+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 74.13 145.87 1 3.50e+01 8.16e-04 1.43e+01 ... (remaining 5651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1409 0.062 - 0.124: 306 0.124 - 0.185: 7 0.185 - 0.247: 1 0.247 - 0.309: 1 Chirality restraints: 1724 Sorted by residual: chirality pdb=" CG LEU H 62 " pdb=" CB LEU H 62 " pdb=" CD1 LEU H 62 " pdb=" CD2 LEU H 62 " both_signs ideal model delta sigma weight residual False -2.59 -2.90 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA ARG A 131 " pdb=" N ARG A 131 " pdb=" C ARG A 131 " pdb=" CB ARG A 131 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CG LEU B 62 " pdb=" CB LEU B 62 " pdb=" CD1 LEU B 62 " pdb=" CD2 LEU B 62 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 1721 not shown) Planarity restraints: 1074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " -0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO B 32 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 31 " -0.022 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO H 32 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO H 32 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO H 32 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 65 " -0.017 5.00e-02 4.00e+02 2.64e-02 1.11e+00 pdb=" N PRO A 66 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " -0.015 5.00e-02 4.00e+02 ... (remaining 1071 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1171 2.76 - 3.29: 8687 3.29 - 3.83: 19177 3.83 - 4.36: 22265 4.36 - 4.90: 30841 Nonbonded interactions: 82141 Sorted by model distance: nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.221 3.040 nonbonded pdb=" NH2 ARG G 63 " pdb=" OP1 DA I 18 " model vdw 2.267 3.120 nonbonded pdb=" O2 DT I -24 " pdb=" N2 DG J 25 " model vdw 2.280 3.120 nonbonded pdb=" NH1 ARG B 78 " pdb=" OP2 DC I -2 " model vdw 2.293 3.120 nonbonded pdb=" NH2 ARG C 72 " pdb=" OP1 DC I -54 " model vdw 2.345 3.120 ... (remaining 82136 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 24 through 95) selection = chain 'D' selection = chain 'F' selection = (chain 'H' and resid 24 through 95) } 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: 0.590 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: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.810 Find NCS groups from input model: 0.110 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 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 10426 Z= 0.493 Angle : 0.728 6.829 15097 Z= 0.637 Chirality : 0.045 0.309 1724 Planarity : 0.003 0.033 1074 Dihedral : 27.062 177.356 4526 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % 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: 0.68 (0.29), residues: 580 helix: 1.04 (0.21), residues: 434 sheet: None (None), residues: 0 loop : -1.21 (0.37), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 129 TYR 0.004 0.001 TYR B 88 PHE 0.013 0.001 PHE H 61 HIS 0.001 0.000 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.49 (10426) covalent geometry : angle 0.72795 / 0.64 (15097) hydrogen bonds : bond 0.19993 / 13.55 ( 660) hydrogen bonds : angle 5.67620 / 4.19 ( 1653) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8253 (t0) cc_final: 0.8051 (t70) REVERT: A 87 SER cc_start: 0.9347 (m) cc_final: 0.9085 (t) REVERT: A 90 MET cc_start: 0.8114 (mmm) cc_final: 0.7792 (mmp) REVERT: B 31 LYS cc_start: 0.9128 (tttt) cc_final: 0.8903 (ttmm) REVERT: C 113 HIS cc_start: 0.9068 (t70) cc_final: 0.8687 (t-170) REVERT: C 126 LEU cc_start: 0.8913 (tp) cc_final: 0.8582 (tp) REVERT: D 53 GLU cc_start: 0.8764 (tp30) cc_final: 0.8490 (tp30) REVERT: D 84 MET cc_start: 0.8110 (tpp) cc_final: 0.7858 (tpp) REVERT: D 91 LYS cc_start: 0.8313 (tmtt) cc_final: 0.7739 (mtpt) REVERT: E 90 MET cc_start: 0.8014 (ttt) cc_final: 0.7336 (tmm) REVERT: F 32 PRO cc_start: 0.9229 (Cg_exo) cc_final: 0.8930 (Cg_endo) REVERT: F 79 LYS cc_start: 0.8776 (mttm) cc_final: 0.8375 (tptp) REVERT: F 87 VAL cc_start: 0.8283 (t) cc_final: 0.8061 (t) REVERT: F 91 LYS cc_start: 0.8504 (mttt) cc_final: 0.8160 (mtpt) REVERT: G 81 ASP cc_start: 0.8219 (t0) cc_final: 0.7963 (t70) REVERT: G 107 THR cc_start: 0.9274 (m) cc_final: 0.8713 (p) REVERT: H 31 LYS cc_start: 0.9110 (tttt) cc_final: 0.8856 (ttmm) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.1257 time to fit residues: 45.4989 Evaluate side-chains 169 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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: 8.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 30.0000 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN F 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.097206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.065821 restraints weight = 31702.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.067443 restraints weight = 18424.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.068484 restraints weight = 13524.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.069125 restraints weight = 11366.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.069475 restraints weight = 10344.349| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10426 Z= 0.213 Angle : 0.714 6.935 15097 Z= 0.421 Chirality : 0.044 0.258 1724 Planarity : 0.006 0.068 1074 Dihedral : 31.215 171.850 3290 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 5.53 % Allowed : 20.95 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.32), residues: 580 helix: 2.25 (0.23), residues: 448 sheet: None (None), residues: 0 loop : -1.34 (0.38), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 92 TYR 0.019 0.001 TYR B 88 PHE 0.010 0.002 PHE E 78 HIS 0.007 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.21 (10426) covalent geometry : angle 0.71413 / 0.42 (15097) hydrogen bonds : bond 0.07007 / 4.73 ( 660) hydrogen bonds : angle 3.48597 / 2.57 ( 1653) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9391 (m) cc_final: 0.8969 (t) REVERT: C 64 LYS cc_start: 0.9230 (tttp) cc_final: 0.8947 (tmtt) REVERT: C 90 MET cc_start: 0.7518 (tpp) cc_final: 0.6711 (tpp) REVERT: C 105 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8028 (mt-10) REVERT: C 109 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8933 (mm) REVERT: C 120 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7752 (mmt) REVERT: C 129 ARG cc_start: 0.8272 (ttm110) cc_final: 0.8059 (tpt170) REVERT: D 90 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8619 (tp) REVERT: D 91 LYS cc_start: 0.8131 (tmtt) cc_final: 0.7697 (mtmt) REVERT: E 73 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8302 (tm-30) REVERT: E 90 MET cc_start: 0.7935 (ttt) cc_final: 0.7453 (tpp) REVERT: E 105 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8099 (mt-10) REVERT: F 40 ARG cc_start: 0.8925 (tpp80) cc_final: 0.8711 (tpp80) REVERT: F 74 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8116 (tm-30) REVERT: F 79 LYS cc_start: 0.8948 (mttm) cc_final: 0.8369 (tptp) REVERT: F 84 MET cc_start: 0.8087 (mmm) cc_final: 0.7334 (tpp) REVERT: F 91 LYS cc_start: 0.8438 (mttt) cc_final: 0.8173 (mtpt) REVERT: G 61 LEU cc_start: 0.9291 (mt) cc_final: 0.9038 (mp) REVERT: G 107 THR cc_start: 0.9380 (m) cc_final: 0.8946 (p) REVERT: H 52 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7464 (tm-30) outliers start: 28 outliers final: 13 residues processed: 197 average time/residue: 0.1086 time to fit residues: 28.0378 Evaluate side-chains 176 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 96 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 30.0000 chunk 33 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 76 optimal weight: 20.0000 chunk 4 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 71 optimal weight: 30.0000 chunk 61 optimal weight: 20.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN F 64 ASN G 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.095268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.063332 restraints weight = 31608.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.064915 restraints weight = 18612.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.065942 restraints weight = 13760.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.066542 restraints weight = 11613.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.066858 restraints weight = 10603.505| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10426 Z= 0.214 Angle : 0.683 6.138 15097 Z= 0.404 Chirality : 0.043 0.311 1724 Planarity : 0.005 0.054 1074 Dihedral : 31.675 171.215 3290 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 8.10 % Allowed : 22.73 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.32), residues: 580 helix: 2.20 (0.23), residues: 450 sheet: None (None), residues: 0 loop : -1.44 (0.42), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 83 TYR 0.012 0.002 TYR D 72 PHE 0.010 0.002 PHE B 61 HIS 0.006 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.21 (10426) covalent geometry : angle 0.68268 / 0.40 (15097) hydrogen bonds : bond 0.06078 / 4.15 ( 660) hydrogen bonds : angle 3.34730 / 2.45 ( 1653) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 176 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9392 (m) cc_final: 0.8992 (t) REVERT: A 125 GLN cc_start: 0.8458 (mt0) cc_final: 0.8136 (mp10) REVERT: C 90 MET cc_start: 0.7629 (tpp) cc_final: 0.7079 (tpp) REVERT: C 105 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7910 (mt-10) REVERT: C 120 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7872 (mmt) REVERT: D 87 VAL cc_start: 0.8454 (t) cc_final: 0.8187 (p) REVERT: D 88 TYR cc_start: 0.7374 (t80) cc_final: 0.6642 (t80) REVERT: D 91 LYS cc_start: 0.8196 (tmtt) cc_final: 0.7724 (ptmm) REVERT: E 73 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8267 (tm-30) REVERT: E 90 MET cc_start: 0.7945 (ttt) cc_final: 0.7444 (tmm) REVERT: E 105 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8087 (mt-10) REVERT: F 67 ARG cc_start: 0.8238 (ttm110) cc_final: 0.7757 (ttm110) REVERT: F 79 LYS cc_start: 0.8975 (mttm) cc_final: 0.8409 (tptp) REVERT: F 84 MET cc_start: 0.8052 (mmm) cc_final: 0.7473 (tpp) REVERT: F 88 TYR cc_start: 0.8084 (m-10) cc_final: 0.7646 (m-10) REVERT: F 91 LYS cc_start: 0.8578 (mttt) cc_final: 0.8027 (mtpt) REVERT: G 97 GLU cc_start: 0.8349 (tt0) cc_final: 0.8004 (tt0) REVERT: G 120 MET cc_start: 0.8469 (mmm) cc_final: 0.7875 (mmt) REVERT: G 125 GLN cc_start: 0.8550 (mt0) cc_final: 0.8239 (mp10) REVERT: H 52 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7487 (tm-30) outliers start: 41 outliers final: 21 residues processed: 191 average time/residue: 0.1119 time to fit residues: 28.3902 Evaluate side-chains 176 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 134 ARG Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 92 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 50.0000 chunk 55 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 58 optimal weight: 30.0000 chunk 11 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN F 64 ASN G 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.096045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.065079 restraints weight = 32387.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.066725 restraints weight = 19027.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.067802 restraints weight = 13961.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.068456 restraints weight = 11699.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.068742 restraints weight = 10618.017| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10426 Z= 0.162 Angle : 0.634 6.360 15097 Z= 0.383 Chirality : 0.042 0.318 1724 Planarity : 0.004 0.037 1074 Dihedral : 31.684 171.499 3290 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 5.53 % Allowed : 24.31 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.33), residues: 580 helix: 2.42 (0.23), residues: 452 sheet: None (None), residues: 0 loop : -1.41 (0.44), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 40 TYR 0.008 0.001 TYR H 51 PHE 0.014 0.001 PHE E 78 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.16 (10426) covalent geometry : angle 0.63388 / 0.38 (15097) hydrogen bonds : bond 0.05151 / 3.46 ( 660) hydrogen bonds : angle 3.04357 / 2.24 ( 1653) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9355 (m) cc_final: 0.8963 (t) REVERT: A 125 GLN cc_start: 0.8491 (mt0) cc_final: 0.8086 (mp10) REVERT: C 61 LEU cc_start: 0.9221 (mp) cc_final: 0.8825 (mp) REVERT: C 90 MET cc_start: 0.7658 (tpp) cc_final: 0.7073 (tpp) REVERT: C 105 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7896 (mt-10) REVERT: C 120 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7814 (mmt) REVERT: D 88 TYR cc_start: 0.7407 (t80) cc_final: 0.7025 (t80) REVERT: D 91 LYS cc_start: 0.8240 (tmtt) cc_final: 0.7620 (mtmm) REVERT: E 73 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8136 (tm-30) REVERT: E 90 MET cc_start: 0.7942 (ttt) cc_final: 0.7347 (tmm) REVERT: E 97 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7776 (tt0) REVERT: E 105 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8074 (mt-10) REVERT: F 79 LYS cc_start: 0.8900 (mttm) cc_final: 0.8397 (tptp) REVERT: F 84 MET cc_start: 0.8006 (mmm) cc_final: 0.7359 (tpp) REVERT: F 91 LYS cc_start: 0.8456 (mttt) cc_final: 0.8098 (mtpt) REVERT: G 120 MET cc_start: 0.8446 (mmm) cc_final: 0.7996 (mmt) REVERT: H 52 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7346 (tm-30) outliers start: 28 outliers final: 17 residues processed: 184 average time/residue: 0.1043 time to fit residues: 25.6111 Evaluate side-chains 170 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 92 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 7 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 26 optimal weight: 20.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN F 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.096003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.064286 restraints weight = 31830.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.065864 restraints weight = 18934.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.066900 restraints weight = 14081.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.067562 restraints weight = 11880.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.067841 restraints weight = 10790.396| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10426 Z= 0.170 Angle : 0.646 7.771 15097 Z= 0.386 Chirality : 0.042 0.317 1724 Planarity : 0.004 0.037 1074 Dihedral : 31.778 171.765 3290 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 6.13 % Allowed : 25.69 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.33), residues: 580 helix: 2.54 (0.23), residues: 452 sheet: None (None), residues: 0 loop : -1.59 (0.42), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 129 TYR 0.013 0.001 TYR B 88 PHE 0.010 0.001 PHE E 67 HIS 0.003 0.001 HIS H 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.17 (10426) covalent geometry : angle 0.64587 / 0.39 (15097) hydrogen bonds : bond 0.05062 / 3.41 ( 660) hydrogen bonds : angle 3.02000 / 2.22 ( 1653) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 MET cc_start: 0.7643 (tpp) cc_final: 0.6835 (tpp) REVERT: C 105 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7977 (mt-10) REVERT: C 120 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7830 (mmt) REVERT: D 53 GLU cc_start: 0.8635 (tp30) cc_final: 0.8420 (tt0) REVERT: D 87 VAL cc_start: 0.8427 (t) cc_final: 0.7966 (p) REVERT: D 91 LYS cc_start: 0.8223 (tmtt) cc_final: 0.7742 (mtmm) REVERT: E 73 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8147 (tm-30) REVERT: E 90 MET cc_start: 0.7856 (ttt) cc_final: 0.7255 (tmm) REVERT: E 97 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7868 (tt0) REVERT: E 105 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8050 (mt-10) REVERT: F 79 LYS cc_start: 0.8874 (mttm) cc_final: 0.8339 (tptp) REVERT: F 84 MET cc_start: 0.7977 (mmm) cc_final: 0.7584 (tpp) REVERT: F 91 LYS cc_start: 0.8417 (mttt) cc_final: 0.8003 (mtpt) REVERT: G 120 MET cc_start: 0.8540 (mmm) cc_final: 0.7982 (mmt) REVERT: H 52 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7373 (tm-30) outliers start: 31 outliers final: 24 residues processed: 175 average time/residue: 0.1125 time to fit residues: 26.5116 Evaluate side-chains 175 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 92 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 73 optimal weight: 30.0000 chunk 66 optimal weight: 30.0000 chunk 54 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 60 optimal weight: 20.0000 chunk 75 optimal weight: 30.0000 chunk 39 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 HIS E 125 GLN F 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.095542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.063844 restraints weight = 31763.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.065391 restraints weight = 19265.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.066393 restraints weight = 14403.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.066983 restraints weight = 12216.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.067336 restraints weight = 11173.417| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10426 Z= 0.172 Angle : 0.654 9.233 15097 Z= 0.387 Chirality : 0.042 0.321 1724 Planarity : 0.004 0.036 1074 Dihedral : 31.872 172.315 3290 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 6.52 % Allowed : 26.68 % Favored : 66.80 % 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: 2.62 (0.34), residues: 580 helix: 2.63 (0.23), residues: 452 sheet: None (None), residues: 0 loop : -1.79 (0.42), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 92 TYR 0.007 0.001 TYR D 72 PHE 0.013 0.002 PHE E 78 HIS 0.011 0.002 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 (10426) covalent geometry : angle 0.65375 / 0.39 (15097) hydrogen bonds : bond 0.04849 / 3.26 ( 660) hydrogen bonds : angle 2.98514 / 2.19 ( 1653) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 90 MET cc_start: 0.7625 (tpp) cc_final: 0.6833 (tpp) REVERT: C 105 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8064 (mt-10) REVERT: C 120 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7697 (mmt) REVERT: D 53 GLU cc_start: 0.8619 (tp30) cc_final: 0.8409 (tt0) REVERT: D 87 VAL cc_start: 0.8415 (t) cc_final: 0.8083 (p) REVERT: D 91 LYS cc_start: 0.8264 (tmtt) cc_final: 0.7711 (mtmm) REVERT: E 73 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8130 (tm-30) REVERT: E 90 MET cc_start: 0.7911 (ttt) cc_final: 0.7446 (tpp) REVERT: E 93 GLN cc_start: 0.8845 (tp40) cc_final: 0.8608 (tp40) REVERT: E 97 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7884 (tt0) REVERT: E 105 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8073 (mt-10) REVERT: E 120 MET cc_start: 0.8323 (mtp) cc_final: 0.7871 (mtp) REVERT: F 68 ASP cc_start: 0.8008 (m-30) cc_final: 0.7047 (t0) REVERT: F 79 LYS cc_start: 0.9091 (mttm) cc_final: 0.8391 (tptp) REVERT: F 84 MET cc_start: 0.7992 (mmm) cc_final: 0.7675 (tpp) REVERT: F 91 LYS cc_start: 0.8450 (mttt) cc_final: 0.8060 (mtpt) REVERT: G 90 MET cc_start: 0.8850 (mmp) cc_final: 0.8212 (tpt) REVERT: G 120 MET cc_start: 0.8575 (mmm) cc_final: 0.8009 (mmt) REVERT: H 52 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7407 (tm-30) outliers start: 33 outliers final: 26 residues processed: 180 average time/residue: 0.1165 time to fit residues: 28.0361 Evaluate side-chains 179 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 134 ARG Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 92 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 78 optimal weight: 50.0000 chunk 59 optimal weight: 30.0000 chunk 60 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 77 optimal weight: 20.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN F 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.094178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.062455 restraints weight = 31840.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.064028 restraints weight = 18639.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.065042 restraints weight = 13730.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.065525 restraints weight = 11579.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.065940 restraints weight = 10633.143| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10426 Z= 0.205 Angle : 0.681 7.034 15097 Z= 0.398 Chirality : 0.043 0.325 1724 Planarity : 0.005 0.063 1074 Dihedral : 31.993 173.146 3290 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 6.72 % Allowed : 26.88 % Favored : 66.40 % 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: 2.51 (0.33), residues: 580 helix: 2.57 (0.23), residues: 452 sheet: None (None), residues: 0 loop : -1.90 (0.40), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 92 TYR 0.017 0.001 TYR D 88 PHE 0.011 0.002 PHE E 104 HIS 0.022 0.003 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.21 (10426) covalent geometry : angle 0.68102 / 0.40 (15097) hydrogen bonds : bond 0.05115 / 3.46 ( 660) hydrogen bonds : angle 3.07609 / 2.26 ( 1653) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8490 (mmm) cc_final: 0.7998 (mmt) REVERT: C 90 MET cc_start: 0.7655 (tpp) cc_final: 0.6872 (tpp) REVERT: C 105 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8048 (mt-10) REVERT: D 53 GLU cc_start: 0.8706 (tp30) cc_final: 0.8488 (tt0) REVERT: D 84 MET cc_start: 0.8070 (tpp) cc_final: 0.7857 (tpp) REVERT: D 91 LYS cc_start: 0.8273 (tmtt) cc_final: 0.7707 (mtmm) REVERT: E 73 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8107 (tm-30) REVERT: E 90 MET cc_start: 0.7964 (ttt) cc_final: 0.7493 (tpp) REVERT: E 93 GLN cc_start: 0.8898 (tp40) cc_final: 0.8693 (tp40) REVERT: E 105 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8086 (mt-10) REVERT: E 120 MET cc_start: 0.8376 (mtp) cc_final: 0.7955 (mtp) REVERT: F 64 ASN cc_start: 0.8885 (m-40) cc_final: 0.8674 (t0) REVERT: F 79 LYS cc_start: 0.9087 (mttm) cc_final: 0.8461 (tptp) REVERT: F 84 MET cc_start: 0.7980 (mmm) cc_final: 0.7719 (tpp) REVERT: F 88 TYR cc_start: 0.8004 (m-10) cc_final: 0.7502 (m-10) REVERT: F 91 LYS cc_start: 0.8422 (mttt) cc_final: 0.8055 (mtpt) REVERT: G 120 MET cc_start: 0.8612 (mmm) cc_final: 0.7987 (mmt) REVERT: H 52 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7387 (tm-30) outliers start: 34 outliers final: 29 residues processed: 168 average time/residue: 0.1154 time to fit residues: 25.9799 Evaluate side-chains 178 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 92 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 27 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 69 optimal weight: 30.0000 chunk 55 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 58 optimal weight: 30.0000 chunk 49 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.095248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.064459 restraints weight = 32005.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.066094 restraints weight = 18452.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.067172 restraints weight = 13435.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.067697 restraints weight = 11231.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.068122 restraints weight = 10271.388| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10426 Z= 0.157 Angle : 0.660 10.593 15097 Z= 0.388 Chirality : 0.042 0.326 1724 Planarity : 0.004 0.035 1074 Dihedral : 31.931 172.773 3290 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.94 % Allowed : 29.45 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.34), residues: 580 helix: 2.60 (0.23), residues: 454 sheet: None (None), residues: 0 loop : -1.84 (0.41), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 40 TYR 0.018 0.001 TYR D 88 PHE 0.022 0.002 PHE E 78 HIS 0.005 0.002 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.16 (10426) covalent geometry : angle 0.66004 / 0.39 (15097) hydrogen bonds : bond 0.04565 / 3.06 ( 660) hydrogen bonds : angle 2.88108 / 2.12 ( 1653) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.9176 (t0) cc_final: 0.8954 (t0) REVERT: A 120 MET cc_start: 0.8464 (mmm) cc_final: 0.7980 (mmt) REVERT: C 90 MET cc_start: 0.7650 (tpp) cc_final: 0.6863 (tpp) REVERT: C 105 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8026 (mt-10) REVERT: D 88 TYR cc_start: 0.6992 (t80) cc_final: 0.6482 (t80) REVERT: D 91 LYS cc_start: 0.8277 (tmtt) cc_final: 0.7809 (mtmt) REVERT: E 73 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8023 (tm-30) REVERT: E 90 MET cc_start: 0.7901 (ttt) cc_final: 0.7470 (tpp) REVERT: E 97 GLU cc_start: 0.8509 (mm-30) cc_final: 0.7910 (tt0) REVERT: E 105 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8019 (mt-10) REVERT: E 120 MET cc_start: 0.8402 (mtp) cc_final: 0.7988 (mtp) REVERT: F 68 ASP cc_start: 0.8555 (m-30) cc_final: 0.8085 (t70) REVERT: F 74 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8148 (mm-30) REVERT: F 79 LYS cc_start: 0.9032 (mttm) cc_final: 0.8395 (tptp) REVERT: F 84 MET cc_start: 0.7939 (mmm) cc_final: 0.7690 (tpp) REVERT: F 91 LYS cc_start: 0.8421 (mttt) cc_final: 0.8060 (mtpt) REVERT: G 83 ARG cc_start: 0.8102 (mtp85) cc_final: 0.7872 (mtp85) REVERT: G 90 MET cc_start: 0.8787 (mmp) cc_final: 0.8165 (tpt) REVERT: G 107 THR cc_start: 0.9337 (m) cc_final: 0.8984 (p) REVERT: G 120 MET cc_start: 0.8589 (mmm) cc_final: 0.7862 (mmt) REVERT: H 52 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7277 (tm-30) outliers start: 25 outliers final: 21 residues processed: 184 average time/residue: 0.1259 time to fit residues: 30.8227 Evaluate side-chains 174 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 92 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 56 optimal weight: 50.0000 chunk 41 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.094821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.064120 restraints weight = 31617.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.065574 restraints weight = 18546.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.066070 restraints weight = 13238.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.066280 restraints weight = 12307.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.066467 restraints weight = 11705.676| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10426 Z= 0.173 Angle : 0.683 10.293 15097 Z= 0.396 Chirality : 0.042 0.323 1724 Planarity : 0.004 0.030 1074 Dihedral : 31.993 173.063 3290 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.74 % Allowed : 31.23 % Favored : 64.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.34), residues: 580 helix: 2.59 (0.23), residues: 452 sheet: None (None), residues: 0 loop : -1.96 (0.39), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 128 TYR 0.017 0.001 TYR D 88 PHE 0.016 0.002 PHE E 67 HIS 0.006 0.001 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 (10426) covalent geometry : angle 0.68315 / 0.40 (15097) hydrogen bonds : bond 0.04771 / 3.22 ( 660) hydrogen bonds : angle 2.90627 / 2.13 ( 1653) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9299 (m) cc_final: 0.8976 (t) REVERT: A 90 MET cc_start: 0.8445 (tpt) cc_final: 0.8200 (tpt) REVERT: A 108 ASN cc_start: 0.9196 (t0) cc_final: 0.8943 (t0) REVERT: A 120 MET cc_start: 0.8316 (mmm) cc_final: 0.7809 (mmt) REVERT: C 90 MET cc_start: 0.7672 (tpp) cc_final: 0.6866 (tpp) REVERT: C 105 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8027 (mt-10) REVERT: D 88 TYR cc_start: 0.7028 (t80) cc_final: 0.6589 (t80) REVERT: D 91 LYS cc_start: 0.8280 (tmtt) cc_final: 0.7697 (mtmm) REVERT: E 90 MET cc_start: 0.7930 (ttt) cc_final: 0.7499 (tpp) REVERT: E 97 GLU cc_start: 0.8623 (mm-30) cc_final: 0.7985 (tt0) REVERT: E 105 GLU cc_start: 0.8261 (mt-10) cc_final: 0.8006 (mt-10) REVERT: E 120 MET cc_start: 0.8454 (mtp) cc_final: 0.8042 (mtp) REVERT: F 79 LYS cc_start: 0.9000 (mttm) cc_final: 0.8394 (tptp) REVERT: F 84 MET cc_start: 0.7940 (mmm) cc_final: 0.7713 (tpp) REVERT: F 91 LYS cc_start: 0.8484 (mttt) cc_final: 0.8136 (mtpt) REVERT: G 83 ARG cc_start: 0.8068 (mtp85) cc_final: 0.7795 (mtp85) REVERT: G 90 MET cc_start: 0.8835 (mmp) cc_final: 0.8222 (tpt) REVERT: G 120 MET cc_start: 0.8346 (mmm) cc_final: 0.7720 (mmt) REVERT: H 52 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7335 (tm-30) outliers start: 24 outliers final: 19 residues processed: 169 average time/residue: 0.1133 time to fit residues: 25.9365 Evaluate side-chains 174 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 82 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 61 optimal weight: 30.0000 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 65 optimal weight: 30.0000 chunk 14 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 66 optimal weight: 30.0000 chunk 52 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.094946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.064233 restraints weight = 31623.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.065810 restraints weight = 18524.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.066336 restraints weight = 13030.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.066534 restraints weight = 12328.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.066702 restraints weight = 11724.616| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 10426 Z= 0.174 Angle : 0.689 11.058 15097 Z= 0.399 Chirality : 0.042 0.327 1724 Planarity : 0.004 0.031 1074 Dihedral : 32.008 173.193 3290 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.35 % Allowed : 32.61 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.34), residues: 580 helix: 2.59 (0.23), residues: 452 sheet: None (None), residues: 0 loop : -1.92 (0.40), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 128 TYR 0.016 0.001 TYR D 88 PHE 0.015 0.002 PHE E 78 HIS 0.006 0.001 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (10426) covalent geometry : angle 0.68870 / 0.40 (15097) hydrogen bonds : bond 0.04636 / 3.12 ( 660) hydrogen bonds : angle 2.92087 / 2.14 ( 1653) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9300 (m) cc_final: 0.8967 (t) REVERT: A 90 MET cc_start: 0.8435 (tpt) cc_final: 0.8192 (tpt) REVERT: A 120 MET cc_start: 0.8342 (mmm) cc_final: 0.7815 (mmt) REVERT: C 90 MET cc_start: 0.7688 (tpp) cc_final: 0.6865 (tpp) REVERT: C 105 GLU cc_start: 0.8377 (mt-10) cc_final: 0.7999 (mt-10) REVERT: D 88 TYR cc_start: 0.7055 (t80) cc_final: 0.6828 (t80) REVERT: D 91 LYS cc_start: 0.8271 (tmtt) cc_final: 0.7805 (mtmt) REVERT: E 90 MET cc_start: 0.7912 (ttt) cc_final: 0.7439 (tpp) REVERT: E 97 GLU cc_start: 0.8574 (mm-30) cc_final: 0.7980 (tt0) REVERT: E 105 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7980 (mt-10) REVERT: E 120 MET cc_start: 0.8471 (mtp) cc_final: 0.8058 (mtp) REVERT: F 79 LYS cc_start: 0.8963 (mttm) cc_final: 0.8329 (tptp) REVERT: F 84 MET cc_start: 0.7904 (mmm) cc_final: 0.7668 (tpp) REVERT: F 91 LYS cc_start: 0.8493 (mttt) cc_final: 0.8170 (mtpt) REVERT: G 83 ARG cc_start: 0.8103 (mtp85) cc_final: 0.7847 (mtp85) REVERT: G 90 MET cc_start: 0.8815 (mmp) cc_final: 0.8231 (tpt) REVERT: G 120 MET cc_start: 0.8370 (mmm) cc_final: 0.7736 (mmt) REVERT: G 125 GLN cc_start: 0.8374 (mt0) cc_final: 0.8018 (mp10) REVERT: H 52 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7321 (tm-30) outliers start: 22 outliers final: 18 residues processed: 168 average time/residue: 0.1149 time to fit residues: 25.9971 Evaluate side-chains 170 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 92 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 52 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 71 optimal weight: 30.0000 chunk 6 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 0.4980 chunk 26 optimal weight: 5.9990 chunk 78 optimal weight: 50.0000 chunk 76 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.095682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.064927 restraints weight = 31979.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.066257 restraints weight = 18631.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.066639 restraints weight = 13542.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.066977 restraints weight = 12952.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.067123 restraints weight = 12186.504| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10426 Z= 0.158 Angle : 0.677 10.920 15097 Z= 0.393 Chirality : 0.042 0.325 1724 Planarity : 0.004 0.031 1074 Dihedral : 31.985 173.025 3290 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.95 % Allowed : 32.61 % Favored : 63.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.34), residues: 580 helix: 2.59 (0.23), residues: 452 sheet: None (None), residues: 0 loop : -1.84 (0.41), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 40 TYR 0.017 0.001 TYR D 88 PHE 0.011 0.001 PHE E 67 HIS 0.006 0.001 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.16 (10426) covalent geometry : angle 0.67675 / 0.39 (15097) hydrogen bonds : bond 0.04540 / 3.05 ( 660) hydrogen bonds : angle 2.88143 / 2.10 ( 1653) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1499.42 seconds wall clock time: 26 minutes 39.85 seconds (1599.85 seconds total)