Starting phenix.real_space_refine on Fri Jul 3 16:28:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pf6_13369/07_2026/7pf6_13369.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pf6_13369/07_2026/7pf6_13369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pf6_13369/07_2026/7pf6_13369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pf6_13369/07_2026/7pf6_13369.map" model { file = "/net/cci-nas-00/data/ceres_data/7pf6_13369/07_2026/7pf6_13369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pf6_13369/07_2026/7pf6_13369.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic. 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 334 5.49 5 S 10 5.16 5 C 7420 2.51 5 N 2528 2.21 5 O 3178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13470 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3405 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} Chain: "J" Number of atoms: 3442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3442 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} Chain: "U" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 535 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Time building chain proxies: 3.07, per 1000 atoms: 0.23 Number of scatterers: 13470 At special positions: 0 Unit cell: (118.65, 149.1, 115.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 334 15.00 O 3178 8.00 N 2528 7.00 C 7420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 440.6 milliseconds 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 10 sheets defined 69.9% alpha, 2.8% beta 167 base pairs and 282 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.681A 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: 3.815A 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 removed outlier: 3.759A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.144A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.621A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.514A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.619A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.689A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.834A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.470A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 101 removed outlier: 3.513A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.856A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 51 removed outlier: 3.835A pdb=" N LEU U 42 " --> pdb=" O PRO U 38 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER U 50 " --> pdb=" O ALA U 46 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS U 51 " --> pdb=" O VAL U 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 57 through 69 Processing helix chain 'U' and resid 75 through 90 removed outlier: 3.884A pdb=" N GLY U 90 " --> pdb=" O LEU U 86 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.952A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.789A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.492A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.023A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.367A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'U' and resid 92 through 94 431 hydrogen bonds defined for protein. 1281 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 428 hydrogen bonds 852 hydrogen bond angles 0 basepair planarities 167 basepair parallelities 282 stacking parallelities Total time for adding SS restraints: 2.79 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2463 1.33 - 1.45: 4932 1.45 - 1.57: 6305 1.57 - 1.70: 666 1.70 - 1.82: 20 Bond restraints: 14386 Sorted by residual: bond pdb=" C3' DG J 610 " pdb=" O3' DG J 610 " ideal model delta sigma weight residual 1.435 1.524 -0.089 1.30e-02 5.92e+03 4.64e+01 bond pdb=" C5' DG J 611 " pdb=" C4' DG J 611 " ideal model delta sigma weight residual 1.512 1.542 -0.030 7.00e-03 2.04e+04 1.87e+01 bond pdb=" C3' DG J 610 " pdb=" C2' DG J 610 " ideal model delta sigma weight residual 1.516 1.549 -0.033 8.00e-03 1.56e+04 1.72e+01 bond pdb=" C3' DT I 167 " pdb=" O3' DT I 167 " ideal model delta sigma weight residual 1.435 1.488 -0.053 1.30e-02 5.92e+03 1.66e+01 bond pdb=" C3' DC I 31 " pdb=" C2' DC I 31 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.33e+01 ... (remaining 14381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.95: 20806 5.95 - 11.89: 44 11.89 - 17.84: 0 17.84 - 23.79: 2 23.79 - 29.73: 1 Bond angle restraints: 20853 Sorted by residual: angle pdb=" O3' DG J 610 " pdb=" P DG J 611 " pdb=" OP2 DG J 611 " ideal model delta sigma weight residual 108.00 78.27 29.73 3.00e+00 1.11e-01 9.82e+01 angle pdb=" O3' DG J 610 " pdb=" P DG J 611 " pdb=" OP1 DG J 611 " ideal model delta sigma weight residual 108.00 85.49 22.51 3.00e+00 1.11e-01 5.63e+01 angle pdb=" OP1 DG J 611 " pdb=" P DG J 611 " pdb=" OP2 DG J 611 " ideal model delta sigma weight residual 120.00 141.43 -21.43 3.00e+00 1.11e-01 5.10e+01 angle pdb=" O4' DG I 120 " pdb=" C4' DG I 120 " pdb=" C3' DG I 120 " ideal model delta sigma weight residual 106.00 102.23 3.77 6.00e-01 2.78e+00 3.94e+01 angle pdb=" O4' DA I 40 " pdb=" C4' DA I 40 " pdb=" C3' DA I 40 " ideal model delta sigma weight residual 106.00 102.25 3.75 6.00e-01 2.78e+00 3.92e+01 ... (remaining 20848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.71: 6024 34.71 - 69.42: 1725 69.42 - 104.13: 44 104.13 - 138.84: 3 138.84 - 173.55: 3 Dihedral angle restraints: 7799 sinusoidal: 5368 harmonic: 2431 Sorted by residual: dihedral pdb=" CA GLN G 24 " pdb=" C GLN G 24 " pdb=" N PHE G 25 " pdb=" CA PHE G 25 " ideal model delta harmonic sigma weight residual 180.00 154.35 25.65 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA ILE H 54 " pdb=" C ILE H 54 " pdb=" N SER H 55 " pdb=" CA SER H 55 " ideal model delta harmonic sigma weight residual 180.00 158.42 21.58 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ILE F 29 " pdb=" C ILE F 29 " pdb=" N THR F 30 " pdb=" CA THR F 30 " ideal model delta harmonic sigma weight residual -180.00 -158.87 -21.13 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 7796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.382: 2375 0.382 - 0.764: 0 0.764 - 1.145: 0 1.145 - 1.527: 0 1.527 - 1.909: 1 Chirality restraints: 2376 Sorted by residual: chirality pdb=" P DG J 611 " pdb=" OP1 DG J 611 " pdb=" OP2 DG J 611 " pdb=" O5' DG J 611 " both_signs ideal model delta sigma weight residual True 2.34 0.43 1.91 2.00e-01 2.50e+01 9.11e+01 chirality pdb=" CG LEU E 126 " pdb=" CB LEU E 126 " pdb=" CD1 LEU E 126 " pdb=" CD2 LEU E 126 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE G 111 " pdb=" CA ILE G 111 " pdb=" CG1 ILE G 111 " pdb=" CG2 ILE G 111 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 2373 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.046 5.00e-02 4.00e+02 6.87e-02 7.55e+00 pdb=" N PRO G 80 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 30 " 0.034 2.00e-02 2.50e+03 1.75e-02 6.88e+00 pdb=" N1 DC I 30 " -0.033 2.00e-02 2.50e+03 pdb=" C2 DC I 30 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DC I 30 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DC I 30 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC I 30 " 0.012 2.00e-02 2.50e+03 pdb=" N4 DC I 30 " 0.010 2.00e-02 2.50e+03 pdb=" C5 DC I 30 " -0.011 2.00e-02 2.50e+03 pdb=" C6 DC I 30 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO H 103 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " 0.035 5.00e-02 4.00e+02 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2943 2.79 - 3.32: 12785 3.32 - 3.85: 29386 3.85 - 4.37: 32078 4.37 - 4.90: 44329 Nonbonded interactions: 121521 Sorted by model distance: nonbonded pdb=" NZ LYS A 37 " pdb=" OP1 DC J 726 " model vdw 2.268 3.120 nonbonded pdb=" OG SER G 40 " pdb=" O ARG G 42 " model vdw 2.291 3.040 nonbonded pdb=" OG SER C 40 " pdb=" O ARG C 42 " model vdw 2.309 3.040 nonbonded pdb=" O GLU F 74 " pdb=" NH2 ARG H 92 " model vdw 2.313 3.120 nonbonded pdb=" OG SER F 47 " pdb=" OP1 DC J 662 " model vdw 2.314 3.040 ... (remaining 121516 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.720 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 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 : 0.007 0.089 14386 Z= 0.633 Angle : 1.103 29.733 20853 Z= 0.839 Chirality : 0.068 1.909 2376 Planarity : 0.008 0.084 1478 Dihedral : 29.581 173.553 6233 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.26), residues: 825 helix: -0.26 (0.20), residues: 573 sheet: None (None), residues: 0 loop : -0.72 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 99 TYR 0.034 0.004 TYR E 54 PHE 0.032 0.003 PHE E 104 HIS 0.007 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00737 / 0.63 (14386) covalent geometry : angle 1.10268 / 0.84 (20853) hydrogen bonds : bond 0.11346 / 7.63 ( 859) hydrogen bonds : angle 4.71288 / 3.46 ( 2133) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.6986 (mm) cc_final: 0.5837 (mm) REVERT: A 90 MET cc_start: 0.8665 (mmp) cc_final: 0.8320 (mmp) REVERT: A 93 GLN cc_start: 0.8953 (tt0) cc_final: 0.8694 (tp40) REVERT: A 94 GLU cc_start: 0.8981 (mp0) cc_final: 0.8595 (pm20) REVERT: B 68 ASP cc_start: 0.9022 (m-30) cc_final: 0.8784 (m-30) REVERT: C 62 ILE cc_start: 0.9108 (pt) cc_final: 0.8908 (pt) REVERT: C 73 ASN cc_start: 0.8677 (t0) cc_final: 0.8361 (p0) REVERT: D 108 LYS cc_start: 0.9237 (mppt) cc_final: 0.8997 (mtmm) REVERT: E 104 PHE cc_start: 0.8634 (m-80) cc_final: 0.8386 (m-80) REVERT: F 62 LEU cc_start: 0.9648 (mt) cc_final: 0.9444 (mt) REVERT: F 63 GLU cc_start: 0.8443 (tm-30) cc_final: 0.7914 (tm-30) REVERT: G 36 LYS cc_start: 0.9070 (mppt) cc_final: 0.8656 (mppt) REVERT: G 64 GLU cc_start: 0.8945 (tp30) cc_final: 0.8717 (tp30) REVERT: G 95 LYS cc_start: 0.8706 (mmmt) cc_final: 0.8448 (mmmt) REVERT: H 47 GLN cc_start: 0.9116 (mt0) cc_final: 0.8805 (mt0) REVERT: H 85 LYS cc_start: 0.9417 (mppt) cc_final: 0.9120 (tptp) REVERT: H 106 LEU cc_start: 0.9607 (tp) cc_final: 0.9403 (tp) REVERT: H 113 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8417 (mm-30) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1186 time to fit residues: 30.2747 Evaluate side-chains 120 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN E 108 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.055278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.045872 restraints weight = 120315.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.046984 restraints weight = 72921.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.047737 restraints weight = 52150.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.048256 restraints weight = 41242.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.048586 restraints weight = 34866.350| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14386 Z= 0.176 Angle : 0.805 24.417 20853 Z= 0.453 Chirality : 0.067 2.157 2376 Planarity : 0.006 0.061 1478 Dihedral : 33.119 179.573 4581 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.59 % Allowed : 10.39 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.27), residues: 825 helix: 0.54 (0.21), residues: 576 sheet: None (None), residues: 0 loop : -0.66 (0.34), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 31 TYR 0.024 0.003 TYR B 88 PHE 0.014 0.002 PHE H 65 HIS 0.008 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.18 (14386) covalent geometry : angle 0.80503 / 0.45 (20853) hydrogen bonds : bond 0.06035 / 4.10 ( 859) hydrogen bonds : angle 3.82972 / 2.76 ( 2133) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.6983 (mm) cc_final: 0.5748 (mm) REVERT: B 85 ASP cc_start: 0.8545 (m-30) cc_final: 0.8336 (m-30) REVERT: D 46 LYS cc_start: 0.8767 (mmtt) cc_final: 0.7951 (mmmt) REVERT: E 77 ASP cc_start: 0.9204 (m-30) cc_final: 0.8554 (t0) REVERT: E 93 GLN cc_start: 0.7868 (tp-100) cc_final: 0.7649 (tp40) REVERT: E 108 ASN cc_start: 0.8940 (m-40) cc_final: 0.8730 (m110) REVERT: F 63 GLU cc_start: 0.8411 (tm-30) cc_final: 0.7998 (tm-30) REVERT: G 95 LYS cc_start: 0.8643 (mmmt) cc_final: 0.8419 (mmmt) REVERT: H 47 GLN cc_start: 0.9108 (mt0) cc_final: 0.8712 (mt0) REVERT: H 113 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8551 (mm-30) outliers start: 11 outliers final: 5 residues processed: 150 average time/residue: 0.1092 time to fit residues: 24.4421 Evaluate side-chains 120 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 68 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 54 optimal weight: 9.9990 chunk 98 optimal weight: 30.0000 chunk 64 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 84 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 94 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.052274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.043157 restraints weight = 125467.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.044242 restraints weight = 75647.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.044934 restraints weight = 53840.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.045419 restraints weight = 42619.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.045748 restraints weight = 36166.064| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14386 Z= 0.247 Angle : 0.821 26.204 20853 Z= 0.460 Chirality : 0.066 2.098 2376 Planarity : 0.006 0.059 1478 Dihedral : 33.103 176.288 4581 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.88 % Allowed : 13.85 % Favored : 84.27 % 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: 0.11 (0.27), residues: 825 helix: 0.48 (0.20), residues: 591 sheet: None (None), residues: 0 loop : -0.75 (0.35), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 116 TYR 0.044 0.003 TYR F 88 PHE 0.029 0.003 PHE E 104 HIS 0.006 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.25 (14386) covalent geometry : angle 0.82069 / 0.46 (20853) hydrogen bonds : bond 0.09935 / 6.70 ( 859) hydrogen bonds : angle 3.93773 / 2.84 ( 2133) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.9576 (OUTLIER) cc_final: 0.9249 (mp10) REVERT: A 120 MET cc_start: 0.2999 (mtt) cc_final: 0.2555 (mtt) REVERT: B 44 LYS cc_start: 0.7763 (pttt) cc_final: 0.7377 (pttp) REVERT: B 85 ASP cc_start: 0.8596 (m-30) cc_final: 0.8300 (m-30) REVERT: C 84 GLN cc_start: 0.6357 (OUTLIER) cc_final: 0.4407 (tm-30) REVERT: E 77 ASP cc_start: 0.9174 (m-30) cc_final: 0.8654 (t70) REVERT: E 104 PHE cc_start: 0.8897 (m-80) cc_final: 0.8592 (m-80) REVERT: E 108 ASN cc_start: 0.8917 (m-40) cc_final: 0.8702 (m110) REVERT: F 63 GLU cc_start: 0.8514 (tm-30) cc_final: 0.7980 (tm-30) REVERT: G 36 LYS cc_start: 0.8884 (mppt) cc_final: 0.8588 (mmtm) REVERT: G 57 TYR cc_start: 0.8873 (t80) cc_final: 0.8567 (t80) REVERT: G 95 LYS cc_start: 0.8815 (mmmt) cc_final: 0.8491 (mmmt) REVERT: H 47 GLN cc_start: 0.9117 (mt0) cc_final: 0.8850 (mt0) REVERT: H 99 ARG cc_start: 0.9511 (mmm-85) cc_final: 0.9204 (mmm-85) outliers start: 13 outliers final: 9 residues processed: 132 average time/residue: 0.1099 time to fit residues: 21.8161 Evaluate side-chains 116 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 43 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 87 optimal weight: 30.0000 chunk 49 optimal weight: 0.9980 chunk 95 optimal weight: 20.0000 chunk 61 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 HIS ** 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 = 0.3770 r_free = 0.3770 target = 0.054263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.044923 restraints weight = 120556.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.046052 restraints weight = 71923.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.046818 restraints weight = 50758.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.047334 restraints weight = 39739.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.047676 restraints weight = 33417.733| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14386 Z= 0.163 Angle : 0.762 26.228 20853 Z= 0.425 Chirality : 0.064 2.054 2376 Planarity : 0.005 0.054 1478 Dihedral : 33.160 176.613 4581 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.73 % Allowed : 16.16 % Favored : 82.11 % 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: 0.41 (0.28), residues: 825 helix: 0.75 (0.21), residues: 593 sheet: None (None), residues: 0 loop : -0.78 (0.35), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 116 TYR 0.040 0.002 TYR F 88 PHE 0.020 0.002 PHE E 104 HIS 0.007 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.16 (14386) covalent geometry : angle 0.76179 / 0.43 (20853) hydrogen bonds : bond 0.05700 / 3.84 ( 859) hydrogen bonds : angle 3.63806 / 2.61 ( 2133) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.9544 (OUTLIER) cc_final: 0.9153 (mp10) REVERT: A 120 MET cc_start: 0.3846 (mtt) cc_final: 0.3630 (mtt) REVERT: B 85 ASP cc_start: 0.8578 (m-30) cc_final: 0.8313 (m-30) REVERT: D 46 LYS cc_start: 0.8765 (mmtt) cc_final: 0.7883 (mmmt) REVERT: D 108 LYS cc_start: 0.9188 (mppt) cc_final: 0.8641 (mmtm) REVERT: E 77 ASP cc_start: 0.9120 (m-30) cc_final: 0.8606 (t0) REVERT: E 93 GLN cc_start: 0.7652 (tp-100) cc_final: 0.7400 (tp40) REVERT: E 104 PHE cc_start: 0.8965 (m-80) cc_final: 0.8663 (m-80) REVERT: E 108 ASN cc_start: 0.8811 (m-40) cc_final: 0.8550 (m110) REVERT: F 63 GLU cc_start: 0.8512 (tm-30) cc_final: 0.7969 (tm-30) REVERT: F 74 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8536 (tm-30) REVERT: G 36 LYS cc_start: 0.8832 (mppt) cc_final: 0.8611 (mmtm) REVERT: G 57 TYR cc_start: 0.8811 (t80) cc_final: 0.8472 (t80) REVERT: G 95 LYS cc_start: 0.8820 (mmmt) cc_final: 0.8507 (mmmt) REVERT: H 47 GLN cc_start: 0.9104 (mt0) cc_final: 0.8817 (mt0) outliers start: 12 outliers final: 7 residues processed: 135 average time/residue: 0.1081 time to fit residues: 22.0370 Evaluate side-chains 118 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain F residue 43 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 47 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 107 optimal weight: 30.0000 chunk 28 optimal weight: 0.7980 chunk 80 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.054787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.045423 restraints weight = 122162.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.046570 restraints weight = 72850.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.047326 restraints weight = 51536.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.047835 restraints weight = 40411.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.048159 restraints weight = 34047.270| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14386 Z= 0.159 Angle : 0.754 26.033 20853 Z= 0.421 Chirality : 0.063 2.042 2376 Planarity : 0.005 0.056 1478 Dihedral : 33.002 175.401 4581 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.88 % Allowed : 16.74 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.28), residues: 825 helix: 0.78 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -0.66 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 67 TYR 0.052 0.002 TYR F 88 PHE 0.016 0.001 PHE E 104 HIS 0.008 0.002 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.16 (14386) covalent geometry : angle 0.75401 / 0.42 (20853) hydrogen bonds : bond 0.05398 / 3.65 ( 859) hydrogen bonds : angle 3.54444 / 2.54 ( 2133) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.9534 (OUTLIER) cc_final: 0.9126 (mp10) REVERT: A 105 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8097 (mt-10) REVERT: B 85 ASP cc_start: 0.8516 (m-30) cc_final: 0.8219 (m-30) REVERT: D 46 LYS cc_start: 0.8622 (mmtt) cc_final: 0.7839 (mmmt) REVERT: D 108 LYS cc_start: 0.9175 (mppt) cc_final: 0.8600 (mmtm) REVERT: E 77 ASP cc_start: 0.9176 (m-30) cc_final: 0.8672 (t0) REVERT: E 79 LYS cc_start: 0.7751 (tmtt) cc_final: 0.7184 (tmtt) REVERT: E 104 PHE cc_start: 0.8793 (m-80) cc_final: 0.8528 (m-80) REVERT: E 108 ASN cc_start: 0.8767 (m-40) cc_final: 0.8495 (m110) REVERT: F 63 GLU cc_start: 0.8529 (tm-30) cc_final: 0.7910 (tm-30) REVERT: F 74 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8515 (tm-30) REVERT: G 36 LYS cc_start: 0.8866 (mppt) cc_final: 0.8595 (mmtm) REVERT: G 57 TYR cc_start: 0.8827 (t80) cc_final: 0.8614 (t80) REVERT: G 95 LYS cc_start: 0.8824 (mmmt) cc_final: 0.8499 (mmmt) REVERT: H 47 GLN cc_start: 0.9083 (mt0) cc_final: 0.8797 (mt0) REVERT: H 109 HIS cc_start: 0.9613 (m170) cc_final: 0.9241 (m90) outliers start: 13 outliers final: 6 residues processed: 137 average time/residue: 0.1165 time to fit residues: 23.8634 Evaluate side-chains 119 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 43 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 39 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 95 optimal weight: 30.0000 chunk 85 optimal weight: 30.0000 chunk 41 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 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 = 0.3763 r_free = 0.3763 target = 0.054177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.044944 restraints weight = 121740.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.046033 restraints weight = 74227.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.046769 restraints weight = 53107.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.047258 restraints weight = 41923.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.047575 restraints weight = 35495.307| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14386 Z= 0.169 Angle : 0.754 26.145 20853 Z= 0.421 Chirality : 0.063 2.038 2376 Planarity : 0.005 0.057 1478 Dihedral : 32.950 174.308 4581 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.59 % Allowed : 19.48 % Favored : 78.93 % 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: 0.53 (0.28), residues: 825 helix: 0.86 (0.21), residues: 594 sheet: None (None), residues: 0 loop : -0.80 (0.36), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 99 TYR 0.050 0.002 TYR F 88 PHE 0.016 0.002 PHE B 100 HIS 0.005 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.17 (14386) covalent geometry : angle 0.75390 / 0.42 (20853) hydrogen bonds : bond 0.05977 / 4.04 ( 859) hydrogen bonds : angle 3.55320 / 2.56 ( 2133) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.9530 (OUTLIER) cc_final: 0.9156 (mp10) REVERT: A 94 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8039 (pt0) REVERT: A 105 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8131 (mt-10) REVERT: A 120 MET cc_start: 0.2917 (mtt) cc_final: 0.2597 (mtt) REVERT: B 85 ASP cc_start: 0.8542 (m-30) cc_final: 0.8217 (m-30) REVERT: B 100 PHE cc_start: 0.8782 (m-80) cc_final: 0.8258 (m-80) REVERT: D 46 LYS cc_start: 0.8703 (mmtt) cc_final: 0.7896 (mmmt) REVERT: D 108 LYS cc_start: 0.9105 (mppt) cc_final: 0.8520 (mmtm) REVERT: E 77 ASP cc_start: 0.9131 (m-30) cc_final: 0.8590 (t0) REVERT: E 79 LYS cc_start: 0.7912 (tmtt) cc_final: 0.7274 (tmtt) REVERT: E 108 ASN cc_start: 0.8685 (m-40) cc_final: 0.8413 (m110) REVERT: F 63 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7762 (tm-30) REVERT: F 74 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8428 (tm-30) REVERT: G 36 LYS cc_start: 0.8899 (mppt) cc_final: 0.8631 (mmtm) REVERT: G 95 LYS cc_start: 0.8879 (mmmt) cc_final: 0.8603 (mmmt) REVERT: H 47 GLN cc_start: 0.9109 (mt0) cc_final: 0.8808 (mt0) REVERT: H 99 ARG cc_start: 0.9453 (mtp85) cc_final: 0.8678 (ttm110) REVERT: H 109 HIS cc_start: 0.9617 (m170) cc_final: 0.9214 (m170) outliers start: 11 outliers final: 8 residues processed: 134 average time/residue: 0.1135 time to fit residues: 22.8367 Evaluate side-chains 127 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 43 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 98 optimal weight: 30.0000 chunk 22 optimal weight: 8.9990 chunk 103 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 chunk 73 optimal weight: 30.0000 chunk 57 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 90 optimal weight: 30.0000 chunk 106 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 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 = 0.3650 r_free = 0.3650 target = 0.049423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.040541 restraints weight = 128438.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.041545 restraints weight = 77947.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.042224 restraints weight = 55534.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.042699 restraints weight = 43852.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.043008 restraints weight = 36955.735| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 14386 Z= 0.324 Angle : 0.910 27.647 20853 Z= 0.501 Chirality : 0.068 2.046 2376 Planarity : 0.007 0.069 1478 Dihedral : 33.170 173.925 4581 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 31.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.89 % Allowed : 19.77 % Favored : 77.34 % 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: -0.44 (0.27), residues: 825 helix: 0.10 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -1.03 (0.35), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 52 TYR 0.049 0.004 TYR F 88 PHE 0.027 0.003 PHE E 104 HIS 0.011 0.003 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.32 (14386) covalent geometry : angle 0.91043 / 0.50 (20853) hydrogen bonds : bond 0.13631 / 9.12 ( 859) hydrogen bonds : angle 4.28884 / 3.09 ( 2133) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLN cc_start: 0.9574 (OUTLIER) cc_final: 0.9363 (mp10) REVERT: A 94 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8669 (mt-10) REVERT: B 44 LYS cc_start: 0.7890 (pttt) cc_final: 0.7423 (pttp) REVERT: B 85 ASP cc_start: 0.8578 (m-30) cc_final: 0.8197 (m-30) REVERT: B 100 PHE cc_start: 0.8828 (m-80) cc_final: 0.8506 (m-80) REVERT: D 42 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.7898 (t80) REVERT: E 77 ASP cc_start: 0.9226 (m-30) cc_final: 0.8696 (t0) REVERT: E 104 PHE cc_start: 0.8987 (m-80) cc_final: 0.8714 (m-80) REVERT: E 108 ASN cc_start: 0.8984 (m-40) cc_final: 0.8675 (m110) REVERT: F 63 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8005 (tm-30) REVERT: F 74 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8617 (tm-30) REVERT: G 95 LYS cc_start: 0.8900 (mmmt) cc_final: 0.8665 (mmmt) REVERT: H 47 GLN cc_start: 0.9154 (mt0) cc_final: 0.8733 (mt0) REVERT: H 109 HIS cc_start: 0.9645 (m170) cc_final: 0.9202 (m90) outliers start: 20 outliers final: 16 residues processed: 123 average time/residue: 0.1112 time to fit residues: 20.7360 Evaluate side-chains 123 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 80 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 5.9990 chunk 98 optimal weight: 30.0000 chunk 96 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 78 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 24 optimal weight: 0.0470 chunk 39 optimal weight: 1.9990 chunk 92 optimal weight: 20.0000 chunk 107 optimal weight: 30.0000 chunk 45 optimal weight: 0.7980 overall best weight: 1.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 112 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.051976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.042937 restraints weight = 120597.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.044004 restraints weight = 72793.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.044722 restraints weight = 51508.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.045171 restraints weight = 40402.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.045516 restraints weight = 34302.430| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14386 Z= 0.183 Angle : 0.799 27.248 20853 Z= 0.442 Chirality : 0.065 2.012 2376 Planarity : 0.005 0.063 1478 Dihedral : 33.255 174.557 4581 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.59 % Allowed : 22.08 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.27), residues: 825 helix: 0.50 (0.20), residues: 592 sheet: None (None), residues: 0 loop : -1.03 (0.34), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 116 TYR 0.051 0.003 TYR F 88 PHE 0.027 0.002 PHE E 104 HIS 0.008 0.002 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.18 (14386) covalent geometry : angle 0.79859 / 0.44 (20853) hydrogen bonds : bond 0.06414 / 4.30 ( 859) hydrogen bonds : angle 3.85414 / 2.77 ( 2133) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8622 (mt-10) REVERT: A 105 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8330 (mt-10) REVERT: C 91 GLU cc_start: 0.7141 (tp30) cc_final: 0.6884 (tp30) REVERT: D 42 TYR cc_start: 0.8099 (OUTLIER) cc_final: 0.7602 (t80) REVERT: D 108 LYS cc_start: 0.9190 (mppt) cc_final: 0.8606 (mmtm) REVERT: E 77 ASP cc_start: 0.9231 (m-30) cc_final: 0.8739 (t70) REVERT: E 79 LYS cc_start: 0.8007 (tmtt) cc_final: 0.7440 (tmtt) REVERT: E 97 GLU cc_start: 0.7883 (pt0) cc_final: 0.7430 (mt-10) REVERT: E 104 PHE cc_start: 0.9004 (m-80) cc_final: 0.8767 (m-80) REVERT: E 108 ASN cc_start: 0.8813 (m-40) cc_final: 0.8540 (m-40) REVERT: F 63 GLU cc_start: 0.8499 (tm-30) cc_final: 0.7900 (tm-30) REVERT: F 74 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8439 (tm-30) REVERT: G 36 LYS cc_start: 0.8700 (mppt) cc_final: 0.8489 (mmtm) REVERT: G 95 LYS cc_start: 0.8868 (mmmt) cc_final: 0.8625 (mmmt) REVERT: H 47 GLN cc_start: 0.9161 (mt0) cc_final: 0.8841 (mt0) REVERT: H 99 ARG cc_start: 0.9507 (mtp85) cc_final: 0.8765 (ttm110) REVERT: H 109 HIS cc_start: 0.9627 (m170) cc_final: 0.9298 (m170) REVERT: H 113 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8570 (mm-30) outliers start: 11 outliers final: 10 residues processed: 134 average time/residue: 0.1121 time to fit residues: 22.7785 Evaluate side-chains 127 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 43 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 74 optimal weight: 30.0000 chunk 75 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 84 optimal weight: 20.0000 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** 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 = 0.3702 r_free = 0.3702 target = 0.051645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.042574 restraints weight = 124125.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.043648 restraints weight = 74942.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.044345 restraints weight = 52974.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.044834 restraints weight = 41789.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.045160 restraints weight = 35207.181| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14386 Z= 0.195 Angle : 0.804 26.905 20853 Z= 0.445 Chirality : 0.064 2.018 2376 Planarity : 0.005 0.063 1478 Dihedral : 33.086 174.359 4581 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.44 % Allowed : 22.51 % Favored : 76.05 % 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: 0.05 (0.27), residues: 825 helix: 0.52 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -1.02 (0.34), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 79 TYR 0.048 0.003 TYR F 88 PHE 0.018 0.002 PHE E 104 HIS 0.007 0.002 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.20 (14386) covalent geometry : angle 0.80434 / 0.44 (20853) hydrogen bonds : bond 0.07232 / 4.84 ( 859) hydrogen bonds : angle 3.82633 / 2.75 ( 2133) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.3467 (mtt) cc_final: 0.3230 (ptp) REVERT: B 44 LYS cc_start: 0.7822 (pttt) cc_final: 0.6911 (pptt) REVERT: C 91 GLU cc_start: 0.7281 (tp30) cc_final: 0.6972 (tp30) REVERT: D 42 TYR cc_start: 0.8045 (OUTLIER) cc_final: 0.7507 (t80) REVERT: D 108 LYS cc_start: 0.9174 (mppt) cc_final: 0.8618 (mmtm) REVERT: E 77 ASP cc_start: 0.9224 (m-30) cc_final: 0.8709 (t70) REVERT: E 108 ASN cc_start: 0.8786 (m-40) cc_final: 0.8521 (m-40) REVERT: F 63 GLU cc_start: 0.8474 (tm-30) cc_final: 0.7865 (tm-30) REVERT: F 74 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8605 (tm-30) REVERT: G 36 LYS cc_start: 0.8739 (mppt) cc_final: 0.8508 (mmtm) REVERT: G 95 LYS cc_start: 0.8904 (mmmt) cc_final: 0.8675 (mmmt) REVERT: H 47 GLN cc_start: 0.9174 (mt0) cc_final: 0.8845 (mt0) REVERT: H 71 GLU cc_start: 0.7926 (tt0) cc_final: 0.7556 (tm-30) REVERT: H 99 ARG cc_start: 0.9518 (mtp85) cc_final: 0.8782 (ttm110) REVERT: H 109 HIS cc_start: 0.9612 (m170) cc_final: 0.9271 (m170) REVERT: H 113 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8572 (mm-30) outliers start: 10 outliers final: 9 residues processed: 123 average time/residue: 0.1156 time to fit residues: 21.2143 Evaluate side-chains 119 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 43 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 88 optimal weight: 30.0000 chunk 93 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 chunk 108 optimal weight: 0.0040 chunk 29 optimal weight: 6.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 94 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.052825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.043704 restraints weight = 121656.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.044797 restraints weight = 72800.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.045527 restraints weight = 51440.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.046000 restraints weight = 40377.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.046337 restraints weight = 34215.834| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14386 Z= 0.169 Angle : 0.795 26.674 20853 Z= 0.440 Chirality : 0.064 2.012 2376 Planarity : 0.005 0.060 1478 Dihedral : 32.961 173.136 4581 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.73 % Allowed : 22.66 % Favored : 75.61 % 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: 0.06 (0.27), residues: 825 helix: 0.53 (0.21), residues: 594 sheet: None (None), residues: 0 loop : -1.04 (0.34), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 29 TYR 0.062 0.003 TYR F 88 PHE 0.064 0.002 PHE E 104 HIS 0.006 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.17 (14386) covalent geometry : angle 0.79482 / 0.44 (20853) hydrogen bonds : bond 0.05382 / 3.63 ( 859) hydrogen bonds : angle 3.72364 / 2.68 ( 2133) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8704 (pt0) REVERT: A 105 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8299 (mt-10) REVERT: D 42 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.7280 (t80) REVERT: D 46 LYS cc_start: 0.8727 (mmtt) cc_final: 0.7636 (mmmt) REVERT: D 84 ASN cc_start: 0.8508 (m-40) cc_final: 0.8305 (t0) REVERT: D 108 LYS cc_start: 0.9183 (mppt) cc_final: 0.8650 (mmtm) REVERT: E 77 ASP cc_start: 0.9215 (m-30) cc_final: 0.8663 (t0) REVERT: E 79 LYS cc_start: 0.8100 (tmtt) cc_final: 0.7540 (tmtt) REVERT: E 97 GLU cc_start: 0.7794 (pt0) cc_final: 0.7384 (mt-10) REVERT: E 108 ASN cc_start: 0.8719 (m-40) cc_final: 0.8475 (m-40) REVERT: F 63 GLU cc_start: 0.8467 (tm-30) cc_final: 0.7881 (tm-30) REVERT: F 74 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8477 (tm-30) REVERT: F 86 VAL cc_start: 0.8452 (t) cc_final: 0.8218 (t) REVERT: G 36 LYS cc_start: 0.8731 (mppt) cc_final: 0.8509 (mmtm) REVERT: G 95 LYS cc_start: 0.8918 (mmmt) cc_final: 0.8684 (mmmt) REVERT: H 47 GLN cc_start: 0.9153 (mt0) cc_final: 0.8818 (mt0) REVERT: H 71 GLU cc_start: 0.7858 (tt0) cc_final: 0.7508 (tm-30) REVERT: H 109 HIS cc_start: 0.9607 (m170) cc_final: 0.9265 (m170) REVERT: H 113 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8598 (mm-30) outliers start: 12 outliers final: 10 residues processed: 130 average time/residue: 0.1135 time to fit residues: 22.1800 Evaluate side-chains 129 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 88 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 98 optimal weight: 30.0000 chunk 57 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 74 optimal weight: 30.0000 chunk 27 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** 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 = 0.3720 r_free = 0.3720 target = 0.052475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.043538 restraints weight = 121805.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.044604 restraints weight = 73835.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.045297 restraints weight = 52451.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.045779 restraints weight = 41402.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.046091 restraints weight = 34980.870| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14386 Z= 0.178 Angle : 0.786 26.477 20853 Z= 0.435 Chirality : 0.063 2.030 2376 Planarity : 0.005 0.060 1478 Dihedral : 32.857 172.325 4581 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.59 % Allowed : 22.94 % Favored : 75.47 % 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: 0.06 (0.27), residues: 825 helix: 0.53 (0.21), residues: 594 sheet: None (None), residues: 0 loop : -1.05 (0.34), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.054 0.003 TYR F 88 PHE 0.056 0.003 PHE E 104 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.18 (14386) covalent geometry : angle 0.78573 / 0.44 (20853) hydrogen bonds : bond 0.06102 / 4.10 ( 859) hydrogen bonds : angle 3.71813 / 2.68 ( 2133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2252.70 seconds wall clock time: 39 minutes 51.36 seconds (2391.36 seconds total)